Inducing Cellular Immune Responses to Plasmodium Falciparum Using Peptide and Nucleic Acid Compositions

Description

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 09/390,061, filed Sep. 3, 1999, wherein U.S. application Ser. No. 09/390,061 is a continuation-in-part of U.S. application Ser. No. 09/017,743, filed Feb. 3, 1998 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/821,739, filed Mar. 20, 1997 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/452,843, filed May 30, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/454,033, filed May 26, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); said Ser. No. 09/017,743 (abandoned) is a continuation-in-part of U.S. application Ser. No. 08/753,615, filed Nov. 23, 1996 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/590,298, filed Jan. 23, 1996 (abandoned); which is a continuation-in-part of said Ser. No. 08/452,843, filed May 30, 1995 (abandoned); which is a continuation-in-part of said Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/278,634, filed Jul. 21, 1994 (abandoned); said Ser. No. 08/821,739 (abandoned) claims the benefit of U.S. Provisional Application No. 60/013,833, filed Mar. 21, 1996 (now inactive); and is a continuation-in-part of U.S. application Ser. No. 08/451,913, filed May 26, 1995 (abandoned).

This application is related to U.S. Ser. No. 09/189,702 filed Nov. 10, 1998, now U.S. Pat. No. 7,252,829, which is a CIP of U.S. Ser. No. 08/205,713 filed Mar. 4, 1994 (abandoned), which is a CIP of Ser. No. 08/159,184 filed Nov. 29, 1993 and now abandoned, which is a CIP of Ser. No. 08/073,205 filed Jun. 4, 1993 and now abandoned, which is a CIP of Ser. No. 08/027,146 filed Mar. 5, 1993 and now abandoned. The present application is also related to U.S. Ser. No. 09/226,775 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/815,396, which claims benefit of abandoned U.S. Ser. No. 60/013,113 filed Mar. 21, 1996. Furthermore, the present application is related to U.S. Ser. No. 09/017,735 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/589,108; U.S. Ser. No. 08/454,033 (abandoned); and U.S. Ser. No. 08/349,177 (abandoned). The present application is also related to U.S. Ser. No. 09/017,524 (abandoned), U.S. Ser. No. 08/821,739 (abandoned), which claims benefit of abandoned U.S. Ser. No. 60/013,833 filed Mar. 21, 1996; and U.S. Ser. No. 08/347,610 (abandoned), which is a CIP of U.S. Ser. No. 08/159,339, now U.S. Pat. No. 6,037,135, which is a CIP of abandoned U.S. Ser. No. 08/103,396, which is a CIP of abandoned U.S. Ser. No. 08/027,746, which is a CIP of abandoned U.S. Ser. No. 07/926,666. The present application is also related to U.S. Ser. No. 09/017,743 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/590,298; and U.S. Ser. No. 08/452,843 (abandoned), which is a CIP of U.S. Ser. No. 08/344,824 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/278,634. The present application is also related to PCT application PCT/US99/12066 filed May 28, 1999 which claims benefit of provisional U.S. Ser. No. 60/087,192, filed May 29, 1998 (now inactive), and U.S. Ser. No. 09/009,953 (abandoned), which is a CIP of abandoned U.S. Ser. No. 60/036,713 and abandoned U.S. Ser. No. 60/037,432. In addition, the present application is related to U.S. Ser. No. 09/098,584 (abandoned), U.S. Ser. No. 09/239,043 now U.S. Pat. No. 6,689,363, and to Provisional U.S. Patent Application 60/117,486 filed Jan. 27, 1999 (now inactive). The present application is also related to Ser. No. 09/350,401 filed Jul. 8, 1999, and U.S. Ser. No. 09/357,737 filed Jul. 19, 1999. All of the above applications are incorporated herein by reference.

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was funded, in part, by the United States government under grants with the National Institutes of Health. The U.S. government has certain rights in this invention.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing (Name: 2473 0510005_SeqListing_ST25.txt, Size: 962,033 bytes; and Date of Creation: Dec. 21, 2015) filed herewith was originally filed with U.S. application Ser. No. 09/390,061 and is incorporated herein by reference in its entirety.

INDEX

I. Background of the Invention

II. Summary of the Invention

III. Brief Description of the Figures

IV. Detailed Description of the Invention

• • A. Definitions
  • B. Stimulation of CTL and HTL responses
  • C. Binding Affinity of Peptide Epitopes for HLA Molecules
  • D. Peptide Epitope Binding Motifs and Supermotifs
    • 1. HLA-A1 supermotif
    • 2. HLA-A2 supermotif
    • 3. HLA-A3 supermotif
    • 4. HLA-A24 supermotif
    • 5. HLA-B7 supermotif
    • 6. HLA-B27 supermotif
    • 7. HLA-B44 supermotif
    • 8. HLA-B58 supermotif
    • 9. HLA-B62 supermotif
    • 10. HLA-A1 motif
    • 11. HLA-A2.1 motif
    • 12. HLA-A3 motif
    • 13. HLA-A11 motif
    • 14. HLA-A24 motif
    • 15. HLA-DR-1-4-7 supermotif
    • 16. HLA-DR3 motifs
  • E. Enhancing Population Coverage of the Vaccine
  • F. Immune Response-Stimulating Peptide Epitope Analogs
  • G. Computer Screening of Protein Sequences from Disease-Related Antigens for Supermotif- or Motif-Containing Epitopes
  • H. Preparation of Peptide Epitopes
  • I. Assays to Detect T-Cell Responses
  • J. Use of Peptide Epitopes for Evaluating Immune Responses
  • K. Vaccine Compositions
    • 1. Minigene Vaccines
    • 2. Combinations of CTL Peptides with Helper Peptides
  • L. Administration of Vaccines for Therapeutic or Prophylactic Purposes
  • M. Kits

V. Examples

VI. Claims

VII. Abstract

I. BACKGROUND OF THE INVENTION

Malaria, which is caused by infection with the parasite Plasmodium falciparum (PF), represents a major world health problem. Approximately 500 million people in the world are at risk from the disease, with approximately 200 million people actually harboring the parasites. An estimated 1 to 2 million deaths occur each year due to malaria. (Miller et al., Science 234:1349, 1986).

Fatal outcomes are not confined to first infections, and constant exposure is apparently a prerequisite for maintaining immunity. Naturally acquired sterile immunity is rare, if it exists at all. Accordingly, major efforts to develop an efficacious malaria vaccine have been undertaken.

Human volunteers injected with irradiated PF sporozoites are resistant to subsequent sporozoite challenges, which demonstrates that development of a malaria vaccine is indeed immunologically feasible. Furthermore, these immune individuals developed a vigorous response, including antibodies, and cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) components, directed against multiple antigens. Reproducing the breadth and multiplicity of this response in a vaccine, however, is a task of large proportions. The epitope approach, as described herein, may represent a solution to this challenge, in that it allows the incorporation of various antibody, CTL and HTL epitopes, from various proteins, in a single vaccine composition.

Anti-sporozoite antibodies are by themselves, in general, not completely efficacious in clearing the infection (Egan et al., Science 236:453, 1987). However, high concentrations of antibodies directed against the repeated region of the major B cell antigen of the sporozoite/circumsporozoite protein (CSP) have been shown to prevent liver cell infection in certain experimental models (Egan et al., Science 236:453, 1987; Potocnjak, P. et al., Science 207:71, 1980). The present inventors have shown that constructs encompassing CSP-repeat B cell epitopes and the optimized helper epitope PADRE™ (San Diego, Calif.) are highly immunogenic, and can protect in vitro against sporozoite invasion in both mouse and human liver cells, and protect mice in vivo against live sporozoite challenge (Franke et al., Vaccine 17:1201-1205, 1999)

PF-specific CD4⁺ T cells also have a role in malarial immunity beyond providing help for B cell and CTL responses. Experiments by Renia et al. (Renia, et al., Proc. Natl. Acad. Sci. USA 88:7963, 1991) demonstrated that HTLs directed against the Plasmodium yoelli CS protein could in fact adoptivley transfer protection against malaria.

Considerable data implicate CTLs in protection against pre-erythrocytic-stage malaria. CD8⁺ CTLs can eliminate Plasmodium berghei- or Plasmodium yoelii-infected mouse hepatocytes from in vitro culture in a major histocompatibility complex (MHC)-restricted and antigen-restricted manner (Hoffman et al., Science 244:1078-1081, 1989; Weiss et al., J. Exp. Med. 171:763-773, 1990). Further, it has also been shown that the immunity that developed in mice vaccinated with irradiated sporozoites is also dependent upon the present of CD8+ T cells. These T cells accumulate in inflammatory liver infiltrates subsequent to challenge. Passive transfer of circumsporozoite (CSP)-specific CTL clones as long as three hours after inoculation of sporozoites (i.e., after the parasites have left the bloodstream and infected liver cells) were capable of protecting animals against infection (Romero et al., Nature 341:323, 1989).

It is notable that CTL-restricted responses directed against a single antigen are insufficient to protect mice with different MHC alleles, and a combination of multiple antigens was required even to protect mice from the most common laboratory strains of Plasmodium. These data indicate that a combination of epitopes form several antigens is necessary to elicit a protective CTL response.

Indirect evidence that CTLs are important in protective immunity against Pf in humans has also accumulated. It has been reported that cytotoxic CD8⁺ T cells can be identified in humans immunized with PF sporozoites (Moreno, et al., Int. Immunol. 3:997, 1991). Further, humans immunized with irradiated sporozoites or naturally exposed to malaria can generate a CTL response to the pre-erythrocytic-stage antigens, CSP, sporozoite surface protein 2 (SSP2), liver-stage antigen-1 (LSA-1), and exported protein-1 (Exp-1) (see, e.g. Malik et al., Proc. Natl. Acad. Sci. USA 88, 3300-3304, 1991; Doolan et al., Int. Immunol. 3:511-516, 1991; Hill et al., Nature 360:434-439, 1992). Additionally, there is evidence that the polymorphism within the CSP may be the result of selection by CTLs of parasites that express variant forms (MCutchan and Water, Immunol. Lett. 25:23-26, 1990). This is based on the observation that the variation is nonsynonymous at the nucleotide level, thereby indicating selective pressure at the protein level. The polymorphism primarily maps to identified CTL and T helper epitopes (Doolan et al., Int. Immunol. 5:27-46, 1993); and CTL responses to some of the parasite variants do not cross-react (Hill et al., supra). Finally, the MHC class I human leukocyte antigen (HLA)-Bw53 has been associated with resistance to severe malaria in The Gambia, and CTLs to a conserved epitope restricted by the HLA-Bw53 allele have been identified on P. falciparum LSA-1 (Hill et al., Nature 352:595-600, 1991; Hill et al., Nature 340:434-439, 1992). Since HLA-Bw53 is found in 15%-40% of the population of sub-Saharan Africa but in less than 1% of Caucasians and Asians, these data suggest evolutionary selection on the basis of protection against severe malaria.

Thus, antibody, and both HLA class I and class II restricted responses directed against multiple sporozoite antigens appear to be involved in generating protective immunity to malaria. Furthermore, several important antigenic epitopes against which humoral and cellular immunity is focused have already been exactly delineated.

HLA class I molecules are expressed on the surface of almost all nucleated cells. Following intracellular processing of antigens, epitopes from the antigens are presented as a complex with the HLA class I molecules on the surface of such cells. CTL recognize the peptide-HLA class I complex, which then results in the destruction of the cell bearing the HLA-peptide complex directly by the CTL and/or via the activation of non-destructive mechanisms e.g., the production of interferon.

In view of the heterogeneous immune response observed with PF infection, induction of a multi-specific cellular immune response directed simultaneously against multiple PF epitopes appears to be important for the development of an efficacious vaccine against PF. There is a need, however, to establish vaccine embodiments that elicit immune responses that correspond to responses seen in patients that clear PF infection.

The information provided in this section is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, information in this section is not intended, in any way, to delineate the priority date for the invention.

II. SUMMARY OF THE INVENTION

This invention applies our knowledge of the mechanisms by which antigen is recognized by T cells, for example, to develop epitope-based vaccines directed towards PF. More specifically, this application communicates our discovery of specific epitope pharmaceutical compositions and methods of use in the prevention and treatment of PF infection.

Upon development of appropriate technology, the use of epitope-based vaccines has several advantages over current vaccines, particularly when compared to the use of whole antigens in vaccine compositions. There is evidence that the immune response to whole antigens is directed largely toward variable regions of the antigen, allowing for immune escape due to mutations. The epitopes for inclusion in an epitope-based vaccine are selected from conserved regions of antigens of pathogenic organisms or tumor-associated antigens, which thereby reduces the likelihood of escape mutants. Furthermore, immunosuppressive epitopes that may be present in whole antigens can be avoided with the use of epitope-based vaccines.

An additional advantage of an epitope-based vaccine approach is the ability to combine selected epitopes (CTL and HTL), and further, to modify the composition of the epitopes, achieving, for example, enhanced immunogenicity. Accordingly, the immune response can be modulated, as appropriate, for the target disease. Similar engineering of the response is not possible with traditional approaches.

Another major benefit of epitope-based immune-stimulating vaccines is their safety. The possible pathological side effects caused by infectious agents or whole protein antigens, which might have their own intrinsic biological activity, is eliminated.

An epitope-based vaccine also provides the ability to direct and focus an immune response to multiple selected antigens from the same pathogen. Thus, patient-by-patient variability in the immune response to a particular pathogen may be alleviated by inclusion of epitopes from multiple antigens from that pathogen in a vaccine composition. A “pathogen” may be an infectious agent or a tumor associated molecule.

One of the most formidable obstacles to the development of broadly efficacious epitope-based immunotherapeutics, however, has been the extreme polymorphism of HLA molecules. To date, effective non-genetically biased coverage of a population has been a task of considerable complexity; such coverage has required that epitopes be used that are specific for HLA molecules corresponding to each individual HLA allele; impractically large numbers of epitopes would therefore have to be used in order to cover ethnically diverse populations. Thus, there has existed a need for peptide epitopes that are bound by multiple HLA antigen molecules for use in epitope-based vaccines. The greater the number of HLA antigen molecules bound, the greater the breadth of population coverage by the vaccine.

Furthermore, as described herein in greater detail, a need has existed to modulate peptide binding properties, e.g., so that peptides that are able to bind to multiple HLA antigens do so with an affinity that will stimulate an immune response. Identification of epitopes restricted by more than one HLA allele at an affinity that correlates with immunogenicity is important to provide thorough population coverage, and to allow the elicitation of responses of sufficient vigor to prevent or clear an infection in a diverse segment of the population. Such a response can also target a broad array of epitopes. The technology disclosed herein provides for such favored immune responses.

In a preferred embodiment, epitopes for inclusion in vaccine compositions of the invention are selected by a process whereby protein sequences of known antigens are evaluated for the presence of motif or supermotif-bearing epitopes. Peptides corresponding to a motif- or supermotif-bearing epitope are then synthesized and tested for the ability to bind to the HLA molecule that recognizes the selected motif. Those peptides that bind at an intermediate or high affinity i.e., an IC₅₀ (or a K_D value) of 500 nM or less for HLA class I molecules or an IC₅₀ of 1000 nM or less for HLA class II molecules, are further evaluated for their ability to induce a CTL or HTL response. Immunogenic peptide epitopes are selected for inclusion in vaccine compositions.

Supermotif-bearing peptides may additionally be tested for the ability to bind to multiple alleles within the HLA supertype family. Moreover, peptide epitopes may be analogued to modify binding affinity and/or the ability to bind to multiple alleles within an HLA supertype.

The invention also includes embodiments comprising methods for monitoring or evaluating an immune response to PF in patient having a known HLA-type. Such methods comprise incubating a T cell sample from the patient with a peptide composition comprising an PF epitope consisting essentially of an amino acid sequence described in Tables VII to Table XX or Table XXII which binds the product of at least one HLA allele present in the patient, and detecting for the presence of a T cell that binds to the peptide. A CTL peptide epitope may, for example, be used as a component of a tetrameric complex for such an analysis.

An alternative modality for defining the peptide epitopes in accordance with the invention is to recite the physical properties, such as length; primary structure; or charge, which are correlated with binding to a particular allele-specific HLA molecule or group of allele-specific HLA molecules. A further modality for defining peptide epitopes is to recite the physical properties of an HLA binding pocket, or properties shared by several allele-specific HLA binding pockets (e.g. pocket configuration and charge distribution) and reciting that the peptide epitope fits and binds to said pocket or pockets.

As will be apparent from the discussion below, other methods and embodiments are also contemplated. Further, novel synthetic peptides produced by any of the methods described herein are also part of the invention.

III. BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 provides a graph of total frequency of genotypes as a function of the number of PF candidate epitopes bound by HLA-A and B molecules, in an average population.

IV. DETAILED DESCRIPTION OF THE INVENTION

The peptide epitopes and corresponding nucleic acid compositions of the present invention are useful for stimulating an immune response to PF by stimulating the production of CTL or HTL responses. The peptide epitopes, which are derived directly or indirectly from native PF protein amino acid sequences, are able to bind to HLA molecules and stimulate an immune response to PF. The complete sequence of the PF proteins to be analyzed can be obtained from Genbank. Peptide epitopes and analogs thereof can also be readily determined from sequence information that may subsequently be discovered for heretofore unknown variants of PF, as will be clear from the disclosure provided below.

The peptide epitopes of the invention have been identified in a number of ways, as will be discussed below. Also discussed in greater detail is that analog peptides have been derived and the binding activity for HLA molecules modulated by modifying specific amino acid residues to create peptide analogs exhibiting altered immunogenicity. Further, the present invention provides compositions and combinations of compositions that enable epitope-based vaccines that are capable of interacting with HLA molecules encoded by various genetic alleles to provide broader population coverage than prior vaccines.

IV.A. DEFINITIONS

The invention can be better understood with reference to the following definitions, which are listed alphabetically:

A “computer” or “computer system” generally includes: a processor; at least one information storage/retrieval apparatus such as, for example, a hard drive, a disk drive or a tape drive; at least one input apparatus such as, for example, a keyboard, a mouse, a touch screen, or a microphone; and display structure. Additionally, the computer may include a communication channel in communication with a network. Such a computer may include more or less than what is listed above.

“Cross-reactive binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is degenerate binding.

A “cryptic epitope” elicits a response by immunization with an isolated peptide, but the response is not cross-reactive in vitro when intact whole protein which comprises the epitope is used as an antigen.

A “dominant epitope” is an epitope that induces an immune response upon immunization with a whole native antigen (see, e.g., Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993). Such a response is cross-reactive in vitro with an isolated peptide epitope.

With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues which is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor (TCR) proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vivo or in vitro, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, TCR or HLA molecule. Throughout this disclosure epitope and peptide are often used interchangeably. It is to be appreciated, however, that isolated or purified protein or peptide molecules larger than and comprising an epitope of the invention are still within the bounds of the invention.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II MHC protein (see, e.g., Stites, et al., IMMUNOLOGY, 8^TH ED., Lange Publishing, Los Altos, Calif. (1994).

An “HLA supertype or family”, as used herein, describes sets of HLA molecules grouped on the basis of shared peptide-binding specificities. HLA class I molecules that share somewhat similar binding affinity for peptides bearing certain amino acid motifs are grouped into HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecules (where xx denotes a particular HLA type), are synonyms.

Throughout this disclosure, results are expressed in terms of “IC₅₀'s.” IC₅₀ is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (i.e., limiting HLA proteins and labeled peptide concentrations), these values approximate K_D values. Assays for determining binding are described in detail, e.g., in PCT publications WO 94/20127 and WO 94/03205. It should be noted that IC₅₀ values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC₅₀ of a given ligand.

Alternatively, binding is expressed relative to a reference peptide. Although as a particular assay becomes more, or less, sensitive, the IC₅₀'s of the peptides tested may change somewhat, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC₅₀ of the reference peptide increases 10-fold, the IC₅₀ values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC₅₀, relative to the IC₅₀ of a standard peptide.

Binding may also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392, 1989; Christnick et al., Nature 352:67, 1991; Busch et al., Immunol. 2:443, 1990; Hill et al., J. Immunol. 147:189, 1991; del Guercio et al., J. Immunol. 154:685, 1995), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069, 1991), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et al., J. Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al., EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476, 1990; Schumacher et al., Cell 62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J. Immunol. 149:1896, 1992).

As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC₅₀, or K_D value, of 50 nM or less; “intermediate affinity” is binding with an IC₅₀ or K_D value of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an IC₅₀ or K_D value of 100 nM or less; “intermediate affinity” is binding with an IC₅₀ or K_D value of between about 100 and about 1000 nM.

The terms “identical” or percent “identity,” in the context of two or more peptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.

An “immunogenic peptide” or “peptide epitope” is a peptide that comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL and/or HTL response. Thus, immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and thereafter inducing a cytotoxic T cell response, or a helper T cell response, to the antigen from which the immunogenic peptide is derived.

The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.

“Major Histocompatibility Complex” or “MHC” is a cluster of genes that plays a role in control of the cellular interactions responsible for physiologic immune responses. In humans, the MHC complex is also known as the HLA complex. For a detailed description of the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3^RD ED., Raven Press, New York, 1993.

The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

A “negative binding residue” or “deleterious residue” is an amino acid which, if present at certain positions (typically not primary anchor positions) in a peptide epitope, results in decreased binding affinity of the peptide for the peptide's corresponding HLA molecule.

The term “peptide” is used interchangeably with “oligopeptide” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the alpha-amino and carboxyl groups of adjacent amino acids. The preferred CTL-inducing peptides of the invention are 13 residues or less in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. The preferred HTL-inducing peptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between about 12 and 25, and often between about 15 and 20 residues.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and physiologically compatible composition.

A “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding grooves of an HLA molecule, with their side chains buried in specific pockets of the binding grooves themselves. In one embodiment, for example, the primary anchor residues are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 9-residue peptide epitope in accordance with the invention. The primary anchor positions for each motif and supermotif are set forth in Table 1. For example, analog peptides can be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to modulate the binding affinity of a peptide comprising a particular motif or supermotif.

“Promiscuous recognition” is where a distinct peptide is recognized by the same T cell clone in the context of various HLA molecules. Promiscuous recognition or binding is synonymous with cross-reactive binding.

A “protective immune response” or “therapeutic immune response” refers to a CTL and/or an HTL response to an antigen derived from an infectious agent or a tumor antigen, which prevents or at least partially arrests disease symptoms or progression. The immune response may also include an antibody response which has been facilitated by the stimulation of helper T cells.

The term “residue” refers to an amino acid or amino acid mimetic incorporated into an oligopeptide by an amide bond or amide bond mimetic.

A “secondary anchor residue” is an amino acid at a position other than a primary anchor position in a peptide which may influence peptide binding. A secondary anchor residue occurs at a significantly higher frequency amongst bound peptides than would be expected by random distribution of amino acids at one position. The secondary anchor residues are said to occur at “secondary anchor positions.” A secondary anchor residue can be identified as a residue which is present at a higher frequency among high or intermediate affinity binding peptides, or a residue otherwise associated with high or intermediate affinity binding. For example, analog peptides can be created by altering the presence or absence of particular residues in these secondary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.

A “subdominant epitope” is an epitope which evokes little or no response upon immunization with whole antigens which comprise the epitope, but for which a response can be obtained by immunization with an isolated peptide, and this response (unlike the case of cryptic epitopes) is detected when whole protein is used to recall the response in vitro or in vivo.

A “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Preferably, a supermotif-bearing peptide is recognized with high or intermediate affinity (as defined herein) by two or more HLA antigens.

“Synthetic peptide” refers to a peptide that is not naturally occurring, but is man-made using such methods as chemical synthesis or recombinant DNA technology.

The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in a peptide epitope they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal end of the epitope, or the peptide or protein of which it may be a part. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. Symbols for the amino acids are shown below.

Single Letter	Three Letter	Amino
Symbol	Symbol	Acids
A	Ala	Alanine
C	Cys	Cysteine
D	Asp	Aspartic Acid
E	Glu	Glutamic Acid
F	Phe	Phenylalanine
G	Gly	Glycine
H	His	Histidine
I	Ile	Isoleucine
K	Lys	Lysine
L	Leu	Leucine
M	Met	Methionine
N	Asn	Asparagine
P	Pro	Proline
Q	Gln	Glutamine
R	Arg	Arginine
S	Ser	Serine
T	Thr	Threonine
V	Val	Valine
W	Trp	Tryptophan
Y	Tyr	Tyrosine

IV.B. STIMULATION OF CTL AND HTL RESPONSES

The mechanism by which T cells recognize antigens has been delineated during the past ten years. Based on our understanding of the immune system we have developed efficacious peptide epitope vaccine compositions that can induce a therapeutic or prophylactic immune response to PF in a broad population. For an understanding of the value and efficacy of the claimed compositions, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are described herein and are set forth in Tables I, II, and III (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via web at: http://134.2.96.221/scripts.hlaserver.d11/home.htm; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics, in press, 1999).

Furthermore, x-ray crystallographic analysis of HLA-peptide complexes has revealed pockets within the peptide binding cleft of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that have the potential of binding particular HLA antigen(s).

The present inventors have found that the correlation of binding affinity with immunogenicity, which is disclosed herein, is an important factor to be considered when evaluating candidate peptides. Thus, by a combination of motif searches and HLA-peptide binding assays, candidates for epitope-based vaccines have been identified. After determining their binding affinity, additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, antigenicity, and immunogenicity.

Various strategies can be utilized to evaluate immunogenicity, including:

1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998); This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a ⁵¹Cr-release assay involving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997); In this method, peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals who have effectively been vaccinated, recovered from infection, and/or from chronically infected patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). In applying this strategy, recall responses are detected by culturing PBL from subjects that have been naturally exposed to the antigen, for instance through infection, and thus have generated an immune response “naturally”, or from patients who were vaccinated against the infection. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays for T cell activity including ⁵¹Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

The following describes the peptide epitopes and corresponding nucleic acids of the invention.

IV.C. BINDING AFFINITY OF PEPTIDE EPITOPES FOR HLA MOLECULES

As indicated herein, the large degree of HLA polymorphism is an important factor to be taken into account with the epitope-based approach to vaccine development. To address this factor, epitope selection encompassing identification of peptides capable of binding at high or intermediate affinity to multiple HLA molecules is preferably utilized, most preferably these epitopes bind at high or intermediate affinity to two or more allele-specific HLA molecules.

CTL-inducing peptides of interest for vaccine compositions preferably include those that have an IC₅₀ or binding affinity value for class I HLA molecules of 500 nM or better (i.e., the value is ≦500 nM). HTL-inducing peptides preferably include those that have an IC₅₀ or binding affinity value for class II HLA molecules of 1000 nM or better, (i.e., the value is ≦1,000 nM). For example, peptide binding is assessed by testing the capacity of a candidate peptide to bind to a purified HLA molecule in vitro. Peptides exhibiting high or intermediate affinity are then considered for further analysis. Selected peptides are tested on other members of the supertype family. In preferred embodiments, peptides that exhibit cross-reactive binding are then used in cellular screening analyses or vaccines.

As disclosed herein, higher HLA binding affinity is correlated with greater immunogenicity. Greater immunogenicity can be manifested in several different ways. Immunogenicity corresponds to whether an immune response is elicited at all, and to the vigor of any particular response, as well as to the extent of a population in which a response is elicited. For example, a peptide might elicit an immune response in a diverse array of the population, yet in no instance produce a vigorous response. In accordance with these principles, close to 90% of high binding peptides have been found to be immunogenic, as contrasted with about 50% of the peptides which bind with intermediate affinity. Moreover, higher binding affinity peptides leads to more vigorous immunogenic responses. As a result, less peptide is required to elicit a similar biological effect if a high affinity binding peptide is used. Thus, in preferred embodiments of the invention, high affinity binding epitopes are particularly useful.

The relationship between binding affinity for HLA class I molecules and immunogenicity of discrete peptide epitopes on bound antigens has been determined for the first time in the art by the present inventors. The correlation between binding affinity and immunogenicity was analyzed in two different experimental approaches (see, e.g., Sette, et al., J. Immunol. 153:5586-5592, 1994). In the first approach, the immunogenicity of potential epitopes ranging in HLA binding affinity over a 10,000-fold range was analyzed in HLA-A*0201 transgenic mice. In the second approach, the antigenicity of approximately 100 different hepatitis B virus (HBV)-derived potential epitopes, all carrying A*0201 binding motifs, was assessed by using PBL from acute hepatitis patients. Pursuant to these approaches, it was determined that an affinity threshold value of approximately 500 nM (preferably 50 nM or less) determines the capacity of a peptide epitope to elicit a CTL response. These data are true for class I binding affinity measurements for naturally processed peptides and for synthesized T cell epitopes. These data also indicate the important role of determinant selection in the shaping of T cell responses (see, e.g., Schaeffer et al. Proc. Natl. Acad. Sci. USA 86:4649-4653, 1989).

An affinity threshold associated with immunogenicity in the context of HLA class II DR molecules has also been delineated (see, e.g., Southwood et al. J. Immunology 160:3363-3373,1998, and U.S. Ser. No. 09/009,953 filed Jan. 21, 1998, now U.S. Pat. No. 6,413,517). In order to define a biologically significant threshold of DR binding affinity, a database of the binding affinities of 32 DR-restricted epitopes for their restricting element (i.e., the HLA molecule that binds the motif) was compiled. In approximately half of the cases (15 of 32 epitopes), DR restriction was associated with high binding affinities, i.e. binding affinity values of 100 nM or less. In the other half of the cases (16 of 32), DR restriction was associated with intermediate affinity (binding affinity values in the 100-1000 nM range). In only one of 32 cases was DR restriction associated with an IC₅₀ of 1000 nM or greater. Thus, 1000 nM can be defined as an affinity threshold associated with immunogenicity in the context of DR molecules.

The binding affinity of peptides for HLA molecules can be determined as described in Example 1, below.

IV.D. PEPTIDE EPITOPE BINDING MOTIFS AND SUPERMOTIFS

Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues required for allele-specific binding to HLA molecules have been identified. The presence of these residues correlates with binding affinity for HLA molecules. The identification of motifs and/or supermotifs that correlate with high and intermediate affinity binding is an important issue with respect to the identification of immunogenic peptide epitopes for the inclusion in a vaccine. Kast et al. (J. Immunol. 152:3904-3912, 1994) have shown that motif-bearing peptides account for 90% of the epitopes that bind to allele-specific HLA class I molecules. In this study all possible peptides of 9 amino acids in length and overlapping by eight amino acids (240 peptides), which cover the entire sequence of the E6 and E7 proteins of human papillomavirus type 16, were evaluated for binding to five allele-specific HLA molecules that are expressed at high frequency among different ethnic groups. This unbiased set of peptides allowed an evaluation of the predictive value of HLA class I motifs. From the set of 240 peptides, 22 peptides were identified that bound to an allele-specific HLA molecule with high or intermediate affinity. Of these 22 peptides, 20 (i.e. 91%) were motif-bearing. Thus, this study demonstrates the value of motifs for the identification of peptide epitopes for inclusion in a vaccine: application of motif-based identification techniques will identify about 90% of the potential epitopes in a target antigen protein sequence.

Such peptide epitopes are identified in the Tables described below.

Peptides of the present invention may also comprise epitopes that bind to MEW class II DR molecules. A greater degree of heterogeneity in both size and binding frame position of the motif, relative to the N and C termini of the peptide, exists for class II peptide ligands. This increased heterogeneity of HLA class II peptide ligands is due to the structure of the binding groove of the HLA class II molecule which, unlike its class I counterpart, is open at both ends. Crystallographic analysis of HLA class II DRB*0101-peptide complexes showed that the major energy of binding is contributed by peptide residues complexed with complementary pockets on the DRB*0101 molecules. An important anchor residue engages the deepest hydrophobic pocket (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587, 1995) and is referred to as position 1 (P1). P1 may represent the N-terminal residue of a class II binding peptide epitope, but more typically is flanked towards the N-terminus by one or more residues. Other studies have also pointed to an important role for the peptide residue in the 6^th position towards the C-terminus, relative to P1, for binding to various DR molecules.

In the past few years evidence has accumulated to demonstrate that a large fraction of HLA class I and class II molecules can be classified into a relatively few supertypes, each characterized by largely overlapping peptide binding repertoires, and consensus structures of the main peptide binding pockets. Thus, peptides of the present invention are identified by any one of several HLA-specific amino acid motifs (see, e.g., Tables or if the presence of the motif corresponds to the ability to bind several allele-specific HLA antigens, a supermotif. The HLA molecules that bind to peptides that possess a particular amino acid supermotif are collectively referred to as an HLA “supertype.”

The peptide motifs and supermotifs described below, and summarized in Tables I-III, provide guidance for the identification and use of peptide epitopes in accordance with the invention.

Examples of peptide epitopes bearing a respective supermotif or motif are included in Tables as designated in the description of each motif or supermotif below. The Tables include a binding affinity ratio listing for some of the peptide epitopes. The ratio may be converted to IC₅₀ by using the following formula: IC₅₀ of the standard peptide/ratio=IC₅₀ of the test peptide (i.e., the peptide epitope). The IC₅₀ values of standard peptides used to determine binding affinities for Class I peptides are shown in Table IV. The IC₅₀ values of standard peptides used to determine binding affinities for Class II peptides are shown in Table V. The peptides used as standards for the binding assays described herein are examples of standards; alternative standard peptides can also be used when performing binding analyses.

To obtain the peptide epitope sequences listed in each Table, protein sequence data for four P. falciparum antigens were evaluated for the presence of the designated supermotif or motif. These antigens are: EXP-1, LSA-1, SSP2, and CSP. Nineteen sequences were available for CSP, 10 sequences were available for SSP, and one sequence each was available for EXP-1 and LSA-1. Peptide epitopes were additionally evaluated on the basis of their conservancy among the protein sequences for the PF antigens for which multiple sequences were available. A criterion for conservancy requires that the entire sequence of an HLA class I binding peptide be totally (i.e., 100%) conserved in 79% of the sequences available for a specific protein. Similarly, a criterion for conservancy requires that the entire 9-mer core region of an HLA class II binding peptide be totally conserved in 79% of the sequences available for a specific protein. The percent conservancy of the selected peptide epitopes is indicated on the Tables. The frequency, i.e. the number of sequences of the PF protein antigen in which the totally conserved peptide sequence was identified, is also shown. The “pos” (position) column in the Tables designates the amino acid position in the PF protein that corresponds to the first amino acid residue of the epitope. The “number of amino acids” indicates the number of residues in the epitope sequence.

HLA Class I Motifs Indicative of CTL Inducing Peptide Epitopes:

The primary anchor residues of the HLA class I peptide epitope supermotifs and motifs delineated below are summarized in Table I. The HLA class I motifs set out in Table I(a) are those most particularly relevant to the invention claimed here. Primary and secondary anchor positions are summarized in Table II. Allele-specific HLA molecules that comprise HLA class I supertype families are listed in Table VI. In some cases, peptide epitopes may be listed in both a motif and a supermotif Table. The relationship of a particular motif and respective supermotif is indicated in the description of the individual motifs.

IV.D.1. HLA-A1 SUPERMOTIF

The HLA-A1 supermotif is characterized by the presence in peptide ligands of a small (T or S) or hydrophobic (L, I, V, or M) primary anchor residue in position 2, and an aromatic (Y, F, or W) primary anchor residue at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A1 supermotif (i.e., the HLA-A1 supertype) is comprised of at least A*0101, A*2601, A*2602, A*2501, and A*3201 (see, e.g., DiBrino, M. et al., J. Immunol. 151:5930, 1993; DiBrino, M. et al., J. Immunol. 152:620, 1994; Kondo, A. et al., Immunogenetics 45:249, 1997). Other allele-specific HLA molecules predicted to be members of the A1 supertype are shown in Table VI. Peptides binding to each of the individual HLA proteins can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A1 supermotif are set forth on the attached Table VII.

IV.D.2. HLA-A2 Supermotif

Primary anchor specificities for allele-specific HLA-A2.1 molecules (see, e.g., Falk et al., Nature 351:290-296, 1991; Hunt et al., Science 255:1261-1263, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992; Ruppert et al., Cell 74:929-937, 1993) and cross-reactive binding among HLA-A2 and -A28 molecules have been described. (See, e.g., Fruci et al., Human Immunol. 38:187-192, 1993; Tanigaki et al., Human Immunol. 39:155-162, 1994; Del Guercio et al., J. Immunol. 154:685-693, 1995; Kast et al., J. Immunol. 152:3904-3912, 1994 for reviews of relevant data.) These primary anchor residues define the HLA-A2 supermotif; which presence in peptide ligands corresponds to the ability to bind several different HLA-A2 and -A28 molecules. The HLA-A2 supermotif comprises peptide ligands with L, I, V, M, A, T, or Q as a primary anchor residue at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope.

The corresponding family of HLA molecules (i.e., the HLA-A2 supertype that binds these peptides) is comprised of at least: A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*0209, A*0214, A*6802, and A*6901. Other allele-specific HLA molecules predicted to be members of the A2 supertype are shown in Table VI. As explained in detail below, binding to each of the individual allele-specific HLA molecules can be modulated by substitutions at the primary anchor and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise an A2 supermotif are set forth on the attached Table VIII. The motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein.

IV.D.3. HLA-A3 Supermotif

The HLA-A3 supermotif is characterized by the presence in peptide ligands of A, L, I, V, M, S, or, T as a primary anchor at position 2, and a positively charged residue, R or K, at the C-terminal position of the epitope, e.g., in position 9 of 9-mers (see, e.g., Sidney et al., Hum. Immunol. 45:79, 1996). Exemplary members of the corresponding family of HLA molecules (the HLA-A3 supertype) that bind the A3 supermotif include at least A*0301, A*1101, A*3101, A*3301, and A*6801. Other allele-specific HLA molecules predicted to be members of the A3 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions of amino acids at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A3 supermotif are set forth on the attached Table IX.

IV.D.4. HLA-A24 Supermotif

The HLA-A24 supermotif is characterized by the presence in peptide ligands of an aromatic (F, W, or Y) or hydrophobic aliphatic (L, I, V, M, or T) residue as a primary anchor in position 2, and Y, F, W, L, I, or M as primary anchor at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A24 supermotif (i.e., the A24 supertype) includes at least A*2402, A*3001, and A*2301. Other allele-specific HLA molecules predicted to be members of the A24 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A24 supermotif are set forth on the attached Table X.

IV.D.5. HLA-B7 Supermotif

The HLA-B7 supermotif is characterized by peptides bearing proline in position 2 as a primary anchor, and a hydrophobic or aliphatic amino acid (L, I, V, M, A, F, W, or Y) as the primary anchor at the C-terminal position of the epitope. The corresponding family of HLA molecules that bind the B7 supermotif (i.e., the HLA-B7 supertype) is comprised of at least twenty six HLA-B proteins including: B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601, B*5602, B*6701, and B*7801 (see, e.g., Sidney, et al., J. Immunol. 154:247, 1995; Barber, et al., Curr. Biol. 5:179, 1995; Hill, et al., Nature 360:434, 1992; Rammensee, et al., Immunogenetics 41:178, 1995 for reviews of relevant data). Other allele-specific HLA molecules predicted to be members of the B7 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B7 supermotif are set forth on the attached Table XI.

IV.D.6. HLA-B27 Supermotif

The HLA-B27 supermotif is characterized by the presence in peptide ligands of a positively charged (R, H, or K) residue as a primary anchor at position 2, and a hydrophobic (F, Y, L, W, M, I, A, or V) residue as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B27 supermotif (i.e., the B27 supertype) include at least B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2706, B*3801, B*3901, B*3902, and B*7301. Other allele-specific HLA molecules predicted to be members of the B27 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B27 supermotif are set forth on the attached Table XII.

IV.D.7. HLA-B44 Supermotif

The HLA-B44 supermotif is characterized by the presence in peptide ligands of negatively charged (D or E) residues as a primary anchor in position 2, and hydrophobic residues (F, W, Y, L, I, M, V, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney et al., Immunol. Today 17:261, 1996). Exemplary members of the corresponding family of HLA molecules that bind to the B44 supermotif (i.e., the B44 supertype) include at least: B*1801, B*1802, B*3701, B*4001, B*4002, B*4006, B*4402, B*4403, and B*4006. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the supermotif.

IV.D.8. HLA-B58 Supermotif

The HLA-B58 supermotif is characterized by the presence in peptide ligands of a small aliphatic residue (A, S, or T) as a primary anchor residue at position 2, and an aromatic or hydrophobic residue (F, W, Y, L, I, V, M, or A) as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999 for reviews of relevant data). Exemplary members of the corresponding family of HLA molecules that bind to the B58 supermotif (i.e., the B58 supertype) include at least: B*1516, B*1517, B*5701, B*5702, and B*5801. Other allele-specific HLA molecules predicted to be members of the B58 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B58 supermotif are set forth on the attached Table XIII.

IV.D.9. HLA-B62 Supermotif

The HLA-B62 supermotif is characterized by the presence in peptide ligands of the polar aliphatic residue Q or a hydrophobic aliphatic residue (L, V, M, I, or P) as a primary anchor in position 2, and a hydrophobic residue (F, W, Y, M, I, V, L, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B62 supermotif (i.e., the B62 supertype) include at least: B*1501, B*1502, B*1513, and B5201. Other allele-specific HLA molecules predicted to be members of the B62 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B62 supermotif are set forth on the attached Table XIV.

IV.D.10. HLA-A1 Motif

The HLA-A1 motif is characterized by the presence in peptide ligands of T, S, or M as a primary anchor residue at position 2 and the presence of Y as a primary anchor residue at the C-terminal position of the epitope. An alternative allele-specific A1 motif is characterized by a primary anchor residue at position 3 rather than position 2. This motif is characterized by the presence of D, E, A, or S as a primary anchor residue in position 3, and a Y as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., J. Immunol., 152:620, 1994; Kondo et al., Immunogenetics 45:249, 1997; and Kubo et al., J. Immunol. 152:3913, 1994 for reviews of relevant data). Peptide binding to HLA A1 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise either A1 motif are set forth on the attached Table XV. Those epitopes comprising T, S, or M at position 2 and Y at the C-terminal position are also included in the listing of HLA-A1 supermotif-bearing peptide epitopes listed in Table VII, as these residues are a subset of the A1 supermotif primary anchors.

IV.D.11. HLA-A*0201 Motif

An HLA-A2*0201 motif was determined to be characterized by the presence in peptide ligands of L or M as a primary anchor residue in position 2, and L or V as a primary anchor residue at the C-terminal position of a 9-residue peptide (see, e.g., Falk et al., Nature 351:290-296, 1991) and was further found to comprise an I at position 2 and I or A at the C-terminal position of a nine amino acid peptide (see, e.g., Hunt et al., Science 255:1261-1263, Mar. 6, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992). The A*0201 allele-specific motif has also been defined by the present inventors to additionally comprise V, A, T, or Q as a primary anchor residue at position 2, and M or T as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kast et al., J. Immunol. 152:3904-3912, 1994). Thus, the HLA-A*0201 motif comprises peptide ligands with L, I, V, M, A, T, or Q as primary anchor residues at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope. The preferred and tolerated residues that characterize the primary anchor positions of the HLA-A*0201 motif are identical to the residues describing the A2 supermotif. (For reviews of relevant data, see, e.g., Del Guercio et al., J. Immunol. 154:685-693, 1995; Ruppert et al., Cell 74:929-937, 1993; Sidney et al., Immunol. Today 17:261-266, 1996; Sette and Sidney, Curr. Opin. in Immunol. 10:478-482, 1998). Secondary anchor residues that characterize the A*0201 motif have additionally been defined (see, e.g., Ruppert et al., Cell 74:929-937, 1993). These are shown in Table II. Peptide binding to HLA-A*0201 molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise an A*0201 motif are set forth on the attached Table VIII. The A*0201 motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein

IV.D.12. HLA-A3 Motif

The HLA-A3 motif is characterized by the presence in peptide ligands of L, M, V, I, S, A, T, F, C, G, or D as a primary anchor residue at position 2, and the presence of K, Y, R, H, F, or A as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., Proc. Natl. Acad. Sci USA 90:1508, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A3 motif are set forth on the attached Table XVI. Those peptide epitopes that also comprise the A3 supermotif are also listed in Table IX. The A3 supermotif primary anchor residues comprise a subset of the A3- and A11-allele specific motif primary anchor residues.

IV.D.13. HLA-A11 Motif

The HLA-A11 motif is characterized by the presence in peptide ligands of V, T, M, L, I, S, A, G, N, C, D, or F as a primary anchor residue in position 2, and K, R, Y, or H as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Zhang et al., Proc. Natl. Acad. Sci USA 90:2217-2221, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A11 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A11 motif are set forth on the attached Table XVII; peptide epitopes comprising the A3 allele-specific motif are also present in this Table because of the extensive overlap between the A3 and A11 motif primary anchor specificities. Further, those peptide epitopes that comprise the A3 supermotif are also listed in Table IX.

IV.D.14. HLA-A24 Motif

The HLA-A24 motif is characterized by the presence in peptide ligands of Y, F, W, or M as a primary anchor residue in position 2, and F, L, I, or W as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kondo et al., J. Immunol. 155:4307-4312, 1995; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A24 molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A24 motif are set forth on the attached Table XVIII. These epitopes are also listed in Table X, which sets forth HLA-A24-supermotif-bearing peptide epitopes, as the primary anchor residues characterizing the A24 allele-specific motif comprise a subset of the A24 supermotif primary anchor residues.

Motifs Indicative of Class II HTL Inducing Peptide Epitopes

The primary and secondary anchor residues of the HLA class II peptide epitope supermotifs and motifs delineated below are summarized in Table III.

IV.D.15. HLA DR-1-4-7 Supermotif

Motifs have also been identified for peptides that bind to three common HLA class II allele-specific HLA molecules: HLA DRB1*0401, DRB1*0101, and DRB1*0701 (see, e.g., the review by Southwood et al. J. Immunology 160:3363-3373,1998). Collectively, the common residues from these motifs delineate the HLA DR-1-4-7 supermotif. Peptides that bind to these DR molecules carry a supermotif characterized by a large aromatic or hydrophobic residue (Y, F, W, L, I, V, or M) as a primary anchor residue in position 1, and a small, non-charged residue (S, T, C, A, P, V, I, L, or M) as a primary anchor residue in position 6 of a 9-mer core region. Allele-specific secondary effects and secondary anchors for each of these HLA types have also been identified (Southwood et al., supra). These are set forth in Table III. Peptide binding to HLA-DRB1*0401, DRB1*0101, and/or DRB1*0701 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Conserved 9-mer core regions (i.e., sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis), comprising the DR-1-4-7 supermotif, wherein position 1 of the supermotif is at position 1 of the nine-residue core, are set forth in Table XIXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in section “a” of the Table. Cross-reactive binding data for exemplary 15-residue supermotif-bearing peptides are shown in Table XIXb.

IV.D.16. HLA DR3 Motifs

Two alternative motifs (i.e., submotifs) characterize peptide epitopes that bind to HLA-DR3 molecules (see, e.g., Geluk et al., J. Immunol. 152:5742, 1994). In the first motif (submotif DR3A) a large, hydrophobic residue (L, I, V, M, F, or Y) is present in anchor position 1 of a 9-mer core, and D is present as an anchor at position 4, towards the carboxyl terminus of the epitope. As in other class II motifs, core position 1 may or may not occupy the peptide N-terminal position.

The alternative DR3 submotif provides for lack of the large, hydrophobic residue at anchor position 1, and/or lack of the negatively charged or amide-like anchor residue at position 4, by the presence of a positive charge at position 6 towards the carboxyl terminus of the epitope. Thus, for the alternative allele-specific DR3 motif (submotif DR3B): L, I, V, M, F, Y, A, or Y is present at anchor position 1; D, N, Q, E, S, or T is present at anchor position 4; and K, R, or H is present at anchor position 6. Peptide binding to HLA-DR3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Conserved 9-mer core regions (i.e., those sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis) corresponding to a nine residue sequence comprising the DR3A submotif (wherein position 1 of the motif is at position 1 of the nine residue core) are set forth in Table XXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in Table XXa. Table XXb shows binding data of exemplary DR3 submotif A-bearing peptides.

Conserved 9-mer core regions (i.e., those that are 100% conserved in at least 79% conserved in the PF antigen protein sequences used for the analysis) comprising the DR3B submotif and respective exemplary 15-mer peptides comprising the DR3 submotif-B epitope are set forth in Table XXc. Table XXd shows binding data of exemplary DR3 submotif B-bearing peptides.

Each of the HLA class I or class II peptide epitopes set out in the Tables herein are deemed singly to be an inventive aspect of this application. Further, it is also an inventive aspect of this application that each peptide epitope may be used in combination with any other peptide epitope.

IV.E. ENHANCING POPULATION COVERAGE OF THE VACCINE

Vaccines that have broad population coverage are preferred because they are more commercially viable and generally applicable to the most people. Broad population coverage can be obtained using the peptides of the invention (and nucleic acid compositions that encode such peptides) through selecting peptide epitopes that bind to HLA alleles which, when considered in total, are present in most of the population. Table XXI lists the overall frequencies of the HLA class I supertypes in various ethnicities (Table XXIa) and the combined population coverage achieved by the A2-, A3-, and B7-supertypes (Table XXIb). The A2-, A3-, and B7 supertypes are each present on the average of over 40% in each of these five major ethnic groups. Coverage in excess of 80% is achieved with a combination of these supermotifs. These results suggest that effective and non-ethnically biased population coverage is achieved upon use of a limited number of cross-reactive peptides. Although the population coverage reached with these three main peptide specificities is high, coverage can be expanded to reach 95% population coverage and above, and more easily achieve truly multispecific responses upon use of additional supermotif or allele-specific motif bearing peptides.

The B44-, A1-, and A24-supertypes are present, on average, in a range from 25% to 40% in these major ethnic populations (Table XXIa). While less prevalent overall, the B27-, B58-, and B62 supertypes are each present with a frequency >25% in at least one major ethnic group (Table XXIa). Table XXIb summarizes the estimated prevalence of combinations of HLA supertypes that have been identified in five major ethnic groups. The incremental coverage obtained by the inclusion of A1-, A24-, and B44-supertypes with the A2, A3, and B7 coverage and coverage obtained with all of the supertypes described herein, is shown.

The data presented herein, together with the previous definition of the A2-, A3-, and B7-supertypes, indicates that all antigens, with the possible exception of A29, B8, and B46, can be classified into a total of nine HLA supertypes. By including epitopes from the six most frequent supertypes, an average population coverage of 99% is obtained for five major ethnic groups.

IV.F. IMMUNE RESPONSE-STIMULATING PEPTIDE ANALOGS

In general, CTL and HTL responses are not directed against all possible epitopes. Rather, they are restricted to a few “immunodominant” determinants (Zinkernagel, et al., Adv. Immunol. 27:5159, 1979; Bennink, et al., J. Exp. Med. 168:19351939, 1988; Rawle, et al., J. Immunol. 146:3977-3984, 1991). It has been recognized that immunodominance (Benacerraf, et al., Science 175:273-279, 1972) could be explained by either the ability of a given epitope to selectively bind a particular HLA protein (determinant selection theory) (Vitiello, et al., J. Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977), or to be selectively recognized by the existing TCR (T cell receptor) specificities (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OF SELFNONSELF DISCRIMINATION, John Wiley & Sons, New York, pp. 270-310, 1982). It has been demonstrated that additional factors, mostly linked to processing events, can also play a key role in dictating, beyond strict immunogenicity, which of the many potential determinants will be presented as immunodominant (Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993).

The concept of dominance and subdominance is relevant to immunotherapy of both infectious diseases and cancer. For example, in the course of chronic infectious disease, recruitment of subdominant epitopes can be important for successful clearance of the infection, especially if dominant CTL or HTL specificities have been inactivated by functional tolerance, suppression, mutation of viruses and other mechanisms (Franco, et al., Curr. Opin. Immunol. 7:524-531, 1995). In the case of cancer and tumor antigens, CTLs recognizing at least some of the highest binding affinity peptides might be functionally inactivated. Lower binding affinity peptides are preferentially recognized at these times, and may therefore be preferred in therapeutic or prophylactic anti-cancer vaccines.

In particular, it has been noted that a significant number of epitopes derived from known non-viral tumor associated antigens (TAA) bind HLA class I with intermediate affinity (IC₅₀ in the 50-500 nM range). For example, it has been found that 8 of 15 known TAA peptides recognized by tumor infiltrating lymphocytes (TIL) or CTL bound in the 50-500 nM range. (These data are in contrast with estimates that 90% of known viral antigens were bound by HLA class I molecules with IC₅₀ of 50 nM or less, while only approximately 10% bound in the 50-500 nM range (Sette, et al., J. Immunol., 153:558-5592, 1994). In the cancer setting this phenomenon is probably due to elimination or functional inhibition of the CTL recognizing several of the highest binding peptides, presumably because of T cell tolerization events.

Without intending to be bound by theory, it is believed that because T cells to dominant epitopes may have been clonally deleted, selecting subdominant epitopes may allow existing T cells to be recruited, which will then lead to a therapeutic or prophylactic response. However, the binding of HLA molecules to subdominant epitopes is often less vigorous than to dominant ones. Accordingly, there is a need to be able to modulate the binding affinity of particular immunogenic epitopes for one or more HLA molecules, and thereby to modulate the immune response elicited by the peptide, for example to prepare analog peptides which elicit a more vigorous response. This ability would greatly enhance the usefulness of peptide epitope-based vaccines and therapeutic agents.

Although peptides with suitable cross-reactivity among all alleles of a superfamily are identified by the screening procedures described above, cross-reactivity is not always as complete as possible, and in certain cases procedures to increase cross-reactivity of peptides can be useful; moreover, such procedures can also be used to modify other properties of the peptides such as binding affinity or peptide stability. Having established the general rules that govern cross-reactivity of peptides for HLA alleles within a given motif or supermotif, modification (i.e., analoging) of the structure of peptides of particular interest in order to achieve broader (or otherwise modified) HLA binding capacity can be performed. More specifically, peptides which exhibit the broadest cross-reactivity patterns, can be produced in accordance with the teachings herein. The present concepts related to analog generation are set forth in greater detail in U.S. Ser. No. 09/226,775 filed Jan. 6, 1999, now abandoned.

In brief, the strategy employed utilizes the motifs or supermotifs which correlate with binding to certain HLA molecules. The motifs or supermotifs are defined by having primary anchors, and in many cases secondary anchors. Analog peptides can be created by substituting amino acid residues at primary anchor, secondary anchor, or at primary and secondary anchor positions. Generally, analogs are made for peptides that already bear a motif or supermotif. Preferred secondary anchor residues of supermotifs and motifs that have been defined for HLA class I and class II binding peptides are shown in Tables II and III, respectively.

For a number of the motifs or supermotifs in accordance with the invention, residues are defined which are deleterious to binding to allele-specific HLA molecules or members of HLA supertypes that bind the respective motif or supermotif (Tables II and III). Accordingly, removal of such residues that are detrimental to binding can be performed in accordance with the present invention. For example, in the case of the A3 supertype, when all peptides that have such deleterious residues are removed from the population of peptides used for the analysis, the incidence of cross-reactivity increased from 22% to 37% (see, e.g., Sidney, J. et al., Hu. Immunol. 45:79, 1996). Thus, one strategy to improve the cross-reactivity of peptides within a given supermotif is simply to delete one or more of the deleterious residues present within a peptide and substitute a small “neutral” residue such as Ala (that may not influence T cell recognition of the peptide). An enhanced likelihood of cross-reactivity is expected if, together with elimination of detrimental residues within a peptide, “preferred” residues associated with high affinity binding to an allele-specific HLA molecule or to multiple HLA molecules within a superfamily are inserted.

To ensure that an analog peptide, when used as a vaccine, actually elicits a CTL response to the native epitope in vivo (or, in the case of class II epitopes, elicits helper T cells that cross-react with the wild type peptides), the analog peptide may be used to immunize T cells in vitro from individuals of the appropriate HLA allele. Thereafter, the immunized cells' capacity to induce lysis of wild type peptide sensitized target cells is evaluated. It will be desirable to use as antigen presenting cells, cells that have been either infected, or transfected with the appropriate genes, or, in the case of class II epitopes only, cells that have been pulsed with whole protein antigens, to establish whether endogenously produced antigen is also recognized by the relevant T cells.

Another embodiment of the invention is to create analogs of weak binding peptides. Class I binding peptides exhibiting binding affinities of 500-5000 nM, and carrying an acceptable but suboptimal primary anchor residue at one or both positions can be “fixed” by substituting preferred anchor residues in accordance with the respective supertype. The analog peptides can then be tested for crossbinding activity.

Another embodiment for generating effective peptide analogs involves the substitution of residues that have an adverse impact on peptide stability or solubility in, e.g., a liquid environment. This substitution may occur at any position of the peptide epitope. For example, a cysteine (C) can be substituted out in favor of α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substituting α-amino butyric acid for C not only alleviates this problem, but actually improves binding and crossbinding capability in certain instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999). Substitution of cysteine with α-amino butyric acid may occur at any residue of a peptide epitope, i.e. at either anchor or non-anchor positions.

Representative analog peptides are set forth in Table XXII. The Table indicates the length and sequence of the analog peptide as well as the motif or supermotif, if appropriate. The information in the “Fixed Nomenclature” column indicates the residues substituted at the indicated position numbers for the respective analog.

IV.G. COMPUTER SCREENING OF PROTEIN SEQUENCES FROM DISEASE-RELATED ANTIGENS FOR SUPERMOTIF- OR MOTIF-BEARING PEPTIDES

In order to identify supermotif- or motif-bearing epitopes in a target antigen, a native protein sequence, e.g., a tumor-associated antigen, or sequences from an infectious organism, or a donor tissue for transplantation, is screened using a means for computing, such as an intellectual calculation or a computer, to determine the presence of a supermotif or motif within the sequence. The information obtained from the analysis of native peptide can be used directly to evaluate the status of the native peptide or may be utilized subsequently to generate the peptide epitope.

Computer programs that allow the rapid screening of protein sequences for the occurrence of the subject supermotifs or motifs are encompassed by the present invention; as are programs that permit the generation of analog peptides. These programs are implemented to analyze any identified amino acid sequence or operate on an unknown sequence and simultaneously determine the sequence and identify motif-bearing epitopes thereof; analogs can be simultaneously determined as well. Generally, the identified sequences will be from a pathogenic organism or a tumor-associated peptide. For example, the target molecules considered herein include, without limitation, the EXP1, LSA1, SSP2, and CSP1 proteins of PF.

In cases where the sequence of multiple variants of the same target protein are available, peptides may also be selected on the basis of their conservancy. A presently preferred criterion for conservancy defines that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide, be totally (i.e., 100%) conserved in at least 79% of the sequences evaluated for a specific protein. This definition of conservancy has been employed herein; although, as appreciated by those in the art, lower or higher degrees of conservancy can be employed as appropriate for a given antigenic target.

It is important that the selection criteria utilized for prediction of peptide binding are as accurate as possible, to correlate most efficiently with actual binding. Prediction of peptides that bind, for example, to HLA-A*0201, on the basis of the presence of the appropriate primary anchors, is positive at about a 30% rate (see, e.g., Ruppert, J. et al. Cell 74:929, 1993). However, by extensively analyzing peptide-HLA binding data disclosed herein, data in related patent applications, and data in the art, the present inventors have developed a number of allele-specific polynomial algorithms that dramatically increase the predictive value over identification on the basis of the presence of primary anchor residues alone. These algorithms take into account not only the presence or absence of primary anchors, but also consider the positive or deleterious presence of secondary anchor residues (to account for the impact of different amino acids at different positions). The algorithms are essentially based on the premise that the overall affinity (or AG) of peptide-HLA interactions can be approximated as a linear polynomial function of the type:

ΔG=a_1i×a_2i×a_3i . . . ×a_ni

where a_ji is a coefficient that represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. An important assumption of this method is that the effects at each position are essentially independent of each other. This assumption is justified by studies that demonstrated that peptides are bound to HLA molecules and recognized by T cells in essentially an extended conformation. Derivation of specific algorithm coefficients has been described, for example, in Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997.

Additional methods to identify preferred peptide sequences, which also make use of specific motifs, include the use of neural networks and molecular modeling programs (see, e.g., Milik et al., Nature Biotechnology 16:753, 1998; Altuvia et al., Hum. Immunol. 58:1, 1997; Altuvia et al, J. Mol. Biol. 249:244, 1995; Buus, S. Curr. Opin. Immunol. 11:209-213, 1999; Brusic, V. et al., Bioinformatics 14:121-130, 1998; Parker et al., J. Immunol. 152:163, 1993; Meister et al., Vaccine 13:581, 1995; Hammer et al., J. Exp. Med. 180:2353, 1994; Sturniolo et al., Nature Biotechnol. 17:555 1999).

For example, it has been shown that in sets of A*0201 motif-bearing peptides containing at least one preferred secondary anchor residue while avoiding the presence of any deleterious secondary anchor residues, 69% of the peptides will bind A*0201 with an IC₅₀ less than 500 nM (Ruppert, J. et al. Cell 74:929, 1993). These algorithms are also flexible in that cut-off scores may be adjusted to select sets of peptides with greater or lower predicted binding properties, as desired.

In utilizing computer screening to identify peptide epitopes, a protein sequence or translated sequence may be analyzed using software developed to search for motifs, for example the “FINDPATTERNS’ program (Devereux, et al. Nucl. Acids Res. 12:387-395, 1984) or MotifSearch 1.4 software program (D. Brown, San Diego, Calif.) to identify potential peptide sequences containing appropriate HLA binding motifs. The identified peptides can be scored using customized polynomial algorithms to predict their capacity to bind specific HLA class I or class II alleles. As appreciated by one of ordinary skill in the art, a large array of computer programming software and hardware options are available in the relevant art which can be employed to implement the motifs of the invention in order to evaluate (e.g., without limitation, to identify epitopes, identify epitope concentration per peptide length, or to generate analogs) known or unknown peptide sequences.

In accordance with the procedures described above, PF peptide epitopes and analogs thereof that are able to bind HLA supertype groups or allele-specific HLA molecules have been identified (Tables VII-XX; Table XXII).

IV.H. PREPARATION OF PEPTIDE EPITOPES

Peptides in accordance with the invention can be prepared synthetically, by recombinant DNA technology or chemical synthesis, or from natural sources such as native tumors or pathogenic organisms. Peptide epitopes may be synthesized individually or as polyepitopic peptides. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides may be synthetically conjugated to native fragments or particles.

The peptides in accordance with the invention can be a variety of lengths, and either in their neutral (uncharged) forms or in forms which are salts. The peptides in accordance with the invention are either free of modifications such as glycosylation, side chain oxidation, or phosphorylation; or they contain these modifications, subject to the condition that modifications do not destroy the biological activity of the peptides as described herein.

Desirably, the peptide epitope will be as small as possible while still maintaining substantially all of the immunologic activity of the native protein. When possible, it may be desirable to optimize HLA class I binding peptide epitopes of the invention to a length of about 8 to about 13 amino acid residues, preferably 9 to 10. HLA class II binding peptide epitopes may be optimized to a length of about 6 to about 30 amino acids in length, preferably to between about 13 and about 20 residues. Preferably, the peptide epitopes are commensurate in size with endogenously processed pathogen-derived peptides or tumor cell peptides that are bound to the relevant HLA molecules.

The identification and preparation of peptides of other lengths can also be carried out using the techniques described herein. Moreover, it is preferred to identify native peptide regions that contain a high concentration of class I and/or class II epitopes. Such a sequence is generally selected on the basis that it contains the greatest number of epitopes per amino acid length. It is to be appreciated that epitopes can be present in a frame-shifted manner, e.g. a 10 amino acid long peptide could contain two 9 amino acid long epitopes and one 10 amino acid long epitope; upon intracellular processing, each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. This larger, preferably multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source.

The peptides of the invention can be prepared in a wide variety of ways. For the preferred relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. (See, for example, Stewart & Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co., 1984). Further, individual peptide epitopes can be joined using chemical ligation to produce larger peptides that are still within the bounds of the invention.

Alternatively, recombinant DNA technology can be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant polypeptides which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope.

The nucleotide coding sequence for peptide epitopes of the preferred lengths contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981). Peptide analogs can be made simply by substituting the appropriate and desired nucleic acid base(s) for those that encode the native peptide sequence; exemplary nucleic acid substitutions are those that encode an amino acid defined by the motifs/supermotifs herein. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast, insect or mammalian cell hosts may also be used, employing suitable vectors and control sequences.

IV.I. ASSAYS TO DETECT T-CELL RESPONSES

Once HLA binding peptides are identified, they can be tested for the ability to elicit a T-cell response. The preparation and evaluation of motif-bearing peptides are described in PCT publications WO 94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from a particular antigen are synthesized and tested for their ability to bind to the appropriate HLA proteins. These assays may involve evaluating the binding of a peptide of the invention to purified HLA class I molecules in relation to the binding of a radioiodinated reference peptide. Alternatively, cells expressing empty class I molecules (i.e. lacking peptide therein) may be evaluated for peptide binding by immunofluorescent staining and flow microfluorimetry. Other assays that may be used to evaluate peptide binding include peptide-dependent class I assembly assays and/or the inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule, typically with an affinity of 500 nM or less, are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with selected target cells associated with a disease. Corresponding assays are used for evaluation of HLA class II binding peptides. HLA class II motif-bearing peptides that are shown to bind, typically at an affinity of 1000 nM or less, are further evaluated for the ability to stimulate HTL responses.

Conventional assays utilized to detect T cell responses include proliferation assays, lymphokine secretion assays, direct cytotoxicity assays, and limiting dilution assays. For example, antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells. Alternatively, mutant non-human mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides and that have been transfected with the appropriate human class I gene, may be used to test for the capacity of the peptide to induce in vitro primary CTL responses.

Peripheral blood mononuclear cells (PBMCs) may be used as the responder cell source of CTL precursors. The appropriate antigen-presenting cells are incubated with peptide, after which the peptide-loaded antigen-presenting cells are then incubated with the responder cell population under optimized culture conditions. Positive CTL activation can be determined by assaying the culture for the presence of CTLs that kill radio-labeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed forms of the antigen from which the peptide sequence was derived.

More recently, a method has been devised which allows direct quantification of antigen-specific CTLs by staining with Fluorescein-labelled HLA tetrameric complexes (Altman, J. D. et al., Proc. Natl. Acad. Sci. USA 90:10330, 1993; Altman, J. D. et al., Science 274:94, 1996). Other relatively recent technical developments include staining for intracellular lymphokines, and interferon release assays or ELISPOT assays. Tetramer staining, intracellular lymphokine staining and ELISPOT assays all appear to be at least 10-fold more sensitive than more conventional assays (Lalvani, A. et al., J. Exp. Med. 186:859, 1997; Dunbar, P. R. et al., Curr. Biol. 8:413, 1998; Murali-Krishna, K. et al., Immunity 8:177, 1998).

HTL activation may also be assessed using such techniques known to those in the art such as T cell proliferation and secretion of lymphokines, e.g. IL-2 (see, e.g. Alexander et al., Immunity 1:751-761, 1994).

Alternatively, immunization of HLA transgenic mice can be used to determine immunogenicity of peptide epitopes. Several transgenic mouse models including mice with human A2.1, A11 (which can additionally be used to analyze HLA-A3 epitopes), and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed. Additional transgenic mouse models with other HLA alleles may be generated as necessary. Mice may be immunized with peptides emulsified in Incomplete Freund's Adjuvant and the resulting T cells tested for their capacity to recognize peptide-pulsed target cells and target cells transfected with appropriate genes. CTL responses may be analyzed using cytotoxicity assays described above. Similarly, HTL responses may be analyzed using such assays as T cell proliferation or secretion of lymphokines. Exemplary immunogenic peptide epitopes are set out in Table XXIII

IV.J. USE OF PEPTIDE EPITOPES AS DIAGNOSTIC AGENTS AND FOR EVALUATING IMMUNE RESPONSES

HLA class I and class II binding peptides as described herein can be used, in one embodiment of the invention, as reagents to evaluate an immune response. The immune response to be evaluated may be induced by using as an immunogen any agent that may result in the production of antigen-specific CTLs or HTLs that recognize and bind to the peptide epitope(s) to be employed as the reagent. The peptide reagent need not be used as the immunogen. Assay systems that may be used for such an analysis include relatively recent technical developments such as tetramers, staining for intracellular lymphokines and interferon release assays, or ELISPOT assays.

For example, a peptide of the invention may be used in a tetramer staining assay to assess peripheral blood mononuclear cells for the presence of antigen-specific CTLs following exposure to a pathogen or immunogen. The HLA-tetrameric complex is used to directly visualize antigen-specific CTLs (see, e.g., Ogg et al., Science 279:2103-2106, 1998; and Altman et al., Science 174:94-96, 1996) and determine the frequency of the antigen-specific CTL population in a sample of peripheral blood mononuclear cells. A tetramer reagent using a peptide of the invention may be generated as follows: A peptide that binds to an HLA molecule is refolded in the presence of the corresponding HLA heavy chain and β₂-microglobulin to generate a trimolecular complex. The complex is biotinylated at the carboxyl terminal end of the heavy chain at a site that was previously engineered into the protein. Tetramer formation is then induced by the addition of streptavidin. By means of fluorescently labeled streptavidin, the tetramer can be used to stain antigen-specific cells. The cells may then be identified, for example, by flow cytometry. Such an analysis may be used for diagnostic or prognostic purposes.

Peptides of the invention may also be used as reagents to evaluate immune recall responses. (see, e.g., Bertoni et al., J. Clin. Invest. 100:503-513, 1997 and Penna et al., J. Exp. Med. 174:1565-1570, 1991.) For example, patient PBMC samples from individuals infected with PF may be analyzed for the presence of antigen-specific CTLs or HTLs using specific peptides. A blood sample containing mononuclear cells may be evaluated by cultivating the PBMCs and stimulating the cells with a peptide of the invention. After an appropriate cultivation period, the expanded cell population may be analyzed, for example, for CTL or for HTL activity.

The peptides may also be used as reagents to evaluate the efficacy of a vaccine. PBMCs obtained from a patient vaccinated with an immunogen may be analyzed using, for example, either of the methods described above. The patient is HLA typed, and peptide epitope reagents that recognize the allele-specific molecules present in that patient are selected for the analysis. The immunogenicity of the vaccine is indicated by the presence of PF epitope-specific CTLs and/or HTLs in the PBMC sample.

The peptides of the invention may also be used to make antibodies, using techniques well known in the art (see, e.g. CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY; and Antibodies A Laboratory Manual Harlow, Harlow and Lane, Cold Spring Harbor Laboratory Press, 1989), which may be useful as reagents to diagnose PF infection. Such antibodies include those that recognize a peptide in the context of an HLA molecule, i.e., antibodies that bind to a peptide-WIC complex.

IV.K. VACCINE COMPOSITIONS

Vaccines that contain an immunogenically effective amount of one or more peptides as described herein are a further embodiment of the invention. Once appropriately immunogenic epitopes have been defined, they can be sorted and delivered by various means, herein referred to as “vaccine” compositions. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptide(s). The peptide(s) can be individually linked to its own carrier; alternatively, the peptide(s) can exist as a homopolymer or heteropolymer of active peptide units. Such a polymer has the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition may be a naturally occurring region of an antigen or may be prepared, e.g., recombinantly or by chemical synthesis.

Furthermore, useful carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS).

As disclosed in greater detail herein, upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later infection, or at least partially resistant to developing an ongoing chronic infection, or derives at least some therapeutic benefit when the antigen was tumor-associated.

In some instances it may be desirable to combine the class I peptide vaccines of the invention with vaccines which induce or facilitate neutralizing antibody responses to the target antigen of interest, particularly to surface antigens. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a PADRE™ (Epimmune, San Diego, Calif.) molecule (described, for example, in U.S. Pat. No. 5,736,142). Furthermore, any of these embodiments can be administered as a nucleic acid mediated modality.

The vaccine compositions of the invention may also be used in combination with antiviral drugs such as interferon-α.

For therapeutic or prophylactic immunization purposes, the peptides of the invention can also be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a non-infected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL and/or HTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

Antigenic peptides are used to elicit a CTL and/or HTL response ex vivo, as well. Ex vivo administration is described, for example, in application U.S. Ser. No. 09/016,361 filed Jan. 30, 1998, now abandoned. The resulting CTL or HTL cells, can be used to treat chronic infections, or tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (an infected cell or a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells. Alternatively, dendritic cells are transfected, e.g., with a minigene construct in accordance with the invention, in order to elicit immune responses. Minigenes will be discussed in greater detail in a following section.

Vaccine compositions may also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

DNA or RNA encoding one or more of the peptides of the invention can also be administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. Exemplary epitopes that may be utilized in a vaccine to treat or prevent PF infection are set out in Tables XXXIII and XXXIV. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

It is preferred that each of the following principles are balanced in order to make the selection.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen (see e.g., Rosenberg et al., Science 278:1447-1450).

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC₅₀ of 500 nM or less, or for Class II an IC₅₀ of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

4.) When selecting epitopes from cancer-related antigens it is often preferred to select analogs because the patient may have developed tolerance to the native epitope. When selecting epitopes for infectious disease-related antigens it is preferable to select either native or analoged epitopes. Of particular relevance for infectious disease vaccines (but for cancer-related vaccines as well), are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.

When providing nested epitopes, it is preferable to provide a sequence that has the greatest number of epitopes per provided sequence. Preferably, one avoids providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, it is important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

5.) When creating a minigene, as disclosed in greater detail in the following section, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Furthermore, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis, that only exists because two discrete peptide sequences are encoded directly next to each other. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

IV.K.1. Minigene Vaccines

A growing body of experimental evidence demonstrates that a number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention. The use of multi-epitope minigenes is described below and in, e.g., application U.S. Ser. No. 09/311,784, now U.S. Pat. No. 6,534,482; Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding nine dominant HLA-A*0201- and A11-restricted epitopes derived from the polymerase, envelope, and core proteins of HBV and human immunodeficiency virus (HIV), the PADRE™ universal HTL epitope, and an endoplasmic reticulum-translocating signal sequence was engineered. Immunization of HLA transgenic mice with this plasmid construct resulted in strong CTL induction responses against the nine epitopes tested, similar to those observed with a lipopeptide of known immunogenicity in humans, and significantly greater than immunization in oil-based adjuvants. Moreover, the immunogenicity of DNA-encoded epitopes in vivo correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these data show that the minigene served to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes. A similar approach may be used to develop minigenes encoding PF epitopes.

For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). HTL epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids can also be used in the formulation; in addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) can also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987).

Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by ⁵¹Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (IP) for lipid-complexed DNA).

Twenty-one days after immunization, splenocytes are harvested and restimulated for 1 week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, ⁵¹Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is evaluated in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

IV.K.2. Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising the peptides of the present invention, or analogs thereof, which have immunostimulatory activity may be modified to provide desired attributes, such as improved serum half life, or to enhance immunogenicity.

For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. The use of T helper epitopes in conjunction with CTL epitopes to enhance immunogenicity is illustrated, for example, in applications U.S. Ser. No. 08/197,484, now U.S. Pat. No. 6,419,931, and U.S. Ser. No. 08/464,234, now abandoned.

Particularly preferred CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the CTL peptide may be linked to the T helper peptide without a spacer.

The CTL peptide epitope may be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated. The HTL peptide epitopes used in the invention can be modified in the same manner as CTL peptides. For instance, they may be modified to include D-amino acids or be conjugated to other molecules such as lipids, proteins, sugars and the like.

In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in the majority of the population. This can be accomplished by selecting amino acid sequences that bind to many, most, or all of the HLA class II molecules. These are known as “loosely HLA-restricted” or “promiscuous” T helper sequences. Examples of amino acid sequences that are promiscuous include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 3799), Plasmodium falciparum CS protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 3800), and Streptococcus 18 kD protein at positions 116 (GAVDSILGGVATYGAA; SEQ ID NO: 3801). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed to most preferrably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVWANTLKAAa (SEQ ID NO: 3802), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biological properties. For example, peptides comprising HTL epitopes can contain D-amino acids to increase their resistance to proteases and thus extend their serum half-life. Also, the epitope peptides of the invention can be conjugated to other molecules such as lipids, proteins or sugars, or any other synthetic compounds, to increase their biological activity. Specifically, the T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes cytotoxic T cells. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide. (See, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P₃CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P₃CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses to infection.

As noted herein, additional amino acids can be added to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide, particularly class I peptides. However, it is to be noted that modification at the carboxyl terminus of a CTL epitope may, in some cases, alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH₂ acylation, e.g., by alkanoyl (C₁-C₂₀) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.

IV.L. ADMINISTRATION OF VACCINES FOR THERAPEUTIC OR PROPHYLACTIC PURPOSES

The peptides of the present invention and pharmaceutical and vaccine compositions of the invention are useful for administration to mammals, particularly humans, to treat and/or prevent malaria. Vaccine compositions containing the peptides of the invention are administered to an individual susceptible to, or otherwise at risk for, malaria or to a patient infected with PF to elicit an immune response against PF antigens and thus enhance the patient's own immune response capabilities. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective CTL and/or HTL response to the PF antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

The vaccine compositions of the invention may also be used purely as prophylactic agents. The level of expected exposure (e.g., a traveler versus a resident of an area where malaria is endemic) determines the magnitude of response that is desired to be achieved by the vaccination. Therefore, some vaccination regimens may employ higher doses of the vaccine compositions, or more doses may be administered.

Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine may be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

As noted above, peptides comprising CTL and/or HTL epitopes of the invention induce immune responses when presented by HLA molecules and contacted with a CTL or HTL specific for an epitope comprised by the peptide. The manner in which the peptide is contacted with the CTL or HTL is not critical to the invention. For instance, the peptide can be contacted with the CTL or HTL either in vivo or in vitro. If the contacting occurs in vivo, the peptide itself can be administered to the patient, or other vehicles, e.g., DNA vectors encoding one or more peptides, viral vectors encoding the peptide(s), liposomes and the like, can be used, as described herein.

For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual who has not been infected with PF. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences.

The pharmaceutical compositions may also be used to treat individuals already infected with PF. Patients can be treated with the immunogenic peptide epitopes separately or in conjunction with other treatments, as appropriate.

For therapeutic use, administration should generally begin at the first diagnosis of PF infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. Loading doses followed by boosting doses may be required.

The peptide or other compositions used for prophylaxis or the treatment of PF infection can be used, e.g., in persons who are not manifesting symptoms of disease but who act as a disease vector. In this context, it is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. The peptides and compositions of the present invention may be employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

Thus, for treatment of a chronically infected individual, a representative dose is in the range disclosed above. Initial doses followed by boosting doses at established intervals, e.g., from four weeks to six months, may be required, possibly for a prolonged period of time to effectively immunize an individual. Administration should continue until at least clinical symptoms or laboratory tests indicate that the PF infection has been eliminated or substantially abated and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, intrathecal, or local administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

A human unit dose form of the peptide composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, preferably an aqueous carrier, and is administered in a volume of fluid that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17^th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985).

The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or to target selectively to infected cells, as well as to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.

For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

IV.M. KITS

The peptide and nucleic acid compositions of this invention can be provided in kit form together with instructions for vaccine administration. Typically the kit would include desired peptide compositions in a container, preferably in unit dosage form and instructions for administration. An alternative kit would include a minigene construct with desired nucleic acids of the invention in a container, preferably in unit dosage form together with instructions for administration. Lymphokines such as IL-2 or IL-12 may also be included in the kit. Other kit components that may also be desirable include, for example, a sterile syringe, booster dosages, and other desired excipients.

The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non-critical parameters that can be changed or modified to yield alternative embodiments in accordance with the invention.

V. EXAMPLES

The following examples illustrate identification, selection, and use of immunogenic Class I and Class II peptide epitopes for inclusion in vaccine compositions.

Example 1

HLA Class I and Class II Binding Assays

The following example of peptide binding to HLA molecules demonstrates quantification of binding affinities of HLA class I and class II peptides. Binding assays can be performed with peptides that are either motif-bearing or not motif-bearing.

Epstein-Barr virus (EBV)-transformed homozygous cell lines, fibroblasts, CIR, or 721.22 transfectants were used as sources of HLA class I molecules. These cells were maintained in vitro by culture in RPMI 1640 medium supplemented with 2 mM L-glutamine (GIBCO, Grand Island, N.Y.), 50 μM 2-ME, 100 μg/ml of streptomycin, 100 U/ml of penicillin (Irvine Scientific) and 10% heat-inactivated FCS (Irvine Scientific, Santa Ana, Calif.). Cells were grown in 225-cm² tissue culture flasks or, for large-scale cultures, in roller bottle apparatuses. The specific cell lines routinely used for purification of MHC class I and class II molecules are listed in Table XXIV.

Cell lysates were prepared and HLA molecules purified in accordance with disclosed protocols (Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, cells were lysed at a concentration of 10⁸ cells/ml in 50 mM Tris-HCl, pH 8.5, containing 1% Nonidet P-40 (Fluka Biochemika, Buchs, Switzerland), 150 mM NaCl, 5 mM EDTA, and 2 mM PMSF. Lysates were cleared of debris and nuclei by centrifugation at 15,000×g for 30 min.

HLA molecules were purified from lysates by affinity chromatography. Lysates prepared as above were passed twice through two pre-columns of inactivated Sepharose CL4-B and protein A-Sepharose. Next, the lysate was passed over a column of Sepharose CL-4B beads coupled to an appropriate antibody. The antibodies used for the extraction of HLA from cell lysates are listed in Table XXV. The anti-HLA column was then washed with 10-column volumes of 10 mM Tris-HCL, pH 8.0, in 1% NP-40, PBS, 2-column volumes of PBS, and 2-column volumes of PBS containing 0.4% n-octylglucoside. Finally, MHC molecules were eluted with 50 mM diethylamine in 0.15M NaCl containing 0.4% n-octylglucoside, pH 11.5. A 1/25 volume of 2.0M Tris, pH 6.8, was added to the eluate to reduce the pH to ˜8.0. Eluates were then be concentrated by centrifugation in Centriprep 30 concentrators at 2000 rpm (Amicon, Beverly, Mass.). Protein content was evaluated by a BCA protein assay (Pierce Chemical Co., Rockford, Ill.) and confirmed by SDS-PAGE.

A detailed description of the protocol utilized to measure the binding of peptides to Class I and Class II MEW has been published (Sette et al., Mol. Immunol. 31:813, 1994; Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998). Briefly, purified MHC molecules (5 to 500 nM) were incubated with various unlabeled peptide inhibitors and 1-10 nM ¹²⁵I-radiolabeled probe peptides for 48 h in PBS containing 0.05% Nonidet P-40 (NP40) (or 20% w/v digitonin for H-2 IA assays) in the presence of a protease inhibitor cocktail. The final concentrations of protease inhibitors (each from CalBioChem, La Jolla, Calif.) were 1 mM PMSF, 1.3 nM 1.10 phenanthroline, 73 μM pepstatin A, 8 mM EDTA, 6 mM N-ethylmaleimide (for Class II assays), and 200 μM N alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK). All assays were performed at pH 7.0 with the exception of DRB1*0301, which was performed at pH 4.5, and DRB1*1601 (DR2w21β₁) and DRB4*0101 (DRw53), which were performed at pH 5.0. pH was adjusted as described elsewhere (see Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998).

Following incubation, MHC-peptide complexes were separated from free peptide by gel filtration on 7.8 mm×15 cm TSK200 columns (TosoHaas 16215, Montgomeryville, Pa.), eluted at 1.2 mls/min with PBS pH 6.5 containing 0.5% NP40 and 0.1% NaN₃. Because the large size of the radiolabeled peptide used for the DRB1*1501 (DR2w2β₁) assay makes separation of bound from unbound peaks more difficult under these conditions, all DRB1*1501 (DR2w2β₁) assays were performed using a 7.8 mm×30 cm TSK2000 column eluted at 0.6 mls/min. The eluate from the TSK columns was passed through a Beckman 170 radioisotope detector, and radioactivity was plotted and integrated using a Hewlett-Packard 3396A integrator, and the fraction of peptide bound was determined.

Radiolabeled peptides were iodinated using the chloramine-T method. Representative radiolabeled probe peptides utilized in each assay, and its assay specific IC₅₀ nM, are summarized in Tables IV and V. Typically, in preliminary experiments, each MHC preparation was titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays were performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC50≧[HLA], the measured IC₅₀ values are reasonable approximations of the true K_D values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC₅₀ of a positive control for inhibition by the IC₅₀ for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC₅₀ nM values by dividing the IC₅₀ nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation has proven to be the most accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

Because the antibody used for HLA-DR purification (LB3.1) is α-chain specific, β₁ molecules are not separated from β₃ (and/or β₄ and β₅) molecules. The β₁ specificity of the binding assay is obvious in the cases of DRB1*0101 (DR1), DRB1*0802 (DR8w2), and DRB1*0803 (DR8w3), where no β₃ is expressed. It has also been demonstrated for DRB1*0301 (DR3) and DRB3*0101 (DR52a), DRB1*0401 (DR4w4), DRB1*0404 (DR4w14), DRB1*0405 (DR4w15), DRB1*1101 (DR5), DRB1*1201 (DR5w12), DRB1*1302 (DR6w19) and DRB1*0701 (DR7). The problem of β chain specificity for DRB1*1501 (DR2w2β₁), DRB5*0101 (DR2w2β₂), DRB1*1601 (DR2w21β₁), DRB5*0201 (DR51Dw21), and DRB4*0101 (DRw53) assays is circumvented by the use of fibroblasts. Development and validation of assays with regard to DRβ molecule specificity have been described previously (see, e.g., Southwood et al., J. Immunol. 160:3363-3373, 1998).

Binding assays as outlined above may be used to analyze supermotif and/or motif-bearing epitopes as, for example, described in Example 2.

Example 2

Identification of Conserved HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

Vaccine compositions of the invention may include multiple epitopes that comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Additional experimental details that may be relevant to this example are found in Doolan, D. L. et al., Immunity 7:97, 1997. Calculation of population coverage was performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes

Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs were performed as follows. All translated PF protein sequences were analyzed using a text string search software program, e.g., MotifSearch 1.4 (D. Brown, San Diego) to identify potential peptide sequences containing appropriate HLA binding motifs;

alternative programs are readily produced in accordance with information in the art in view of the motif/supermotif disclosure herein. Furthermore, such calculations can be made mentally. Identified A2-, A3-, and DR-supermotif sequences were scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms take into account both extended and refined motifs (that is, to account for the impact of different amino acids at different positions), and are essentially based on the premise that the overall affinity (or AG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:

“ΔG”=a_1i×a_2i×a_3i×a_ni

where a_ji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount j_i to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide. This assumption is justified by studies from our laboratories that demonstrated that peptides are bound to MHC and recognized by T cells in essentially an extended conformation (data omitted herein).

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of j_i. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

Selection of HLA-A2 Supertype Cross-Reactive Peptides

Complete protein sequences from PF antigens were aligned, then scanned, utilizing motif identification software, to identify conserved 9- and 10-mer sequences containing the HLA-A*0201-motif main anchor specificity. Following conservancy determination and algorithm analysis to take into account the influence of secondary anchors, 53 peptides containing the HLA-A*0201 of potential interest were identified and tested for their capacity to bind to purified HLA-A*0201 molecules in vitro. Fifteen peptides bound A*0201 with IC₅₀ values ≦500 nM.

Fourteen of these peptides were subsequently tested for immunogenicity as described below. Of these, 5 scored positive both in primary in vitro CTL responses and in HLA transgenic mice.

The five immunogenic peptides were then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). The peptide SSP2_14-23, which was immunogenic in primary human CTL cultures and contains the SSP2_14-22 epitope (rather than SSP2_14-22 itself), was included in the analysis. In addition, the peptide Exp-1₈₃, which was positive in the murine CTL assays and the peptide CSP₄₂₅ and SSP2₂₃₀, were also analyzed for cross-reactive binding. As shown in Table XXVI, all eight of these peptides were found to be A2-supertype cross-reactive binders with six of these binding to three or more A2 supertype alleles.

Selection of HLA-A3 Supermotif-Bearing Epitopes

The PF protein sequences scanned above were also examined for the presence of conserved peptides with the HLA-A3 supermotif primary anchors. Further analysis using the A03 and A11 algorithms (see, e.g., Gulukota et al, J. Mol. Biol. 267:1258-1267, 1997 and Sidney et al, Human Immunol. 45:79-93, 1996) identified 203 conserved 9- or 10-mer motif-containing peptide sequences that scored high in either or both algorithms. Of these candidates, twenty five peptides were identified that bound A3 and/or A11 with binding affinities of ≦500 nM. These peptides were then tested for binding cross-reactivity to the other common A3-supertype alleles (A*3101, A*3301, and A*6801). Seven of them bound at least three of the five HLA-A3-supertype molecules tested. An eighth peptide, LSA-1₁₁ was also considered for further study because it bound strongly to two of the A3 supertype alleles and weakly to the other two A3 supertype alleles. (Table XXVII)

In summary, eight HLA-A3 supertype cross-reactive binding peptides derived from conserved regions of PF proteins were identified.

Selection of HLA-B7 Supermotif Bearing Epitopes

When the same PF target antigen protein sequences were also analyzed for the presence of conserved 9- or 10-mer peptides with the HLA-B7-supermotif, 26 sequences were identified. Of these 26, 24 corresponding peptides were synthesized and tested for binding to HLA-B*0702, the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Four of the peptides bound B*0702 with IC₅₀ of ≦500 nM. These four peptides were then tested for binding to other common B7-supertype molecules (B*3501, B*51, B*5301, and B*5401). As shown in Table XXVIII, one peptide was capable of to four of the five B7 supertype alleles; another was found to bind three of the five alles.

Selection of A1 and A24 Motif-Bearing Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into potential vaccine constructs.

An analysis of the protein sequence data from the PF target antigens utilized above identified 40 A1- and 81 A24-motif-containing conserved sequences. Testing for binding to the appropriate HLA molecule (i.e., A1 or A24) was performed on a subset of those peptides. Four A1-motif peptides and four A24-motif peptides, shown in Table Table XXIX, were found to have binding capacities of 500 nM or less for the appropriate allele-specific HLA molecule.

Example 3

Confirmation of Immunogenicity

Evaluation of A*0201 Immunogenicity

It has been shown that CTL induced in A*0201/K^b transgenic mice exhibit specificity similar to CTL induced in the human system (see, e.g., Vitiello et al., J Exp. Med. 173:1007-1015, 1991; Wentworth et al., Eur. J. Immunol. 26:97-101, 1996). Accordingly, these mice were used to evaluate the immunogenicity of the fourteen conserved A*0201 motif-bearing high affinity binding peptides identified in Example 2 above.

CTL induction in transgenic mice following peptide immunization has been described (Vitiello et al., J. Exp. Med. 173:1007-1015, 1991; Alexander et al.; J. Immunol. 159:4753-4761, 1997). In these studies, mice were injected subcutaneously at the base of the tail with each peptide (50 μg/mouse) emulsified in IFA in the presence of an excess of an IA^b-restricted helper peptide (140 μg/mouse) (HBV core 128-140, Sette et al., J Immunol. 153:5586-5592, 1994). Eleven days after injection, splenocytes were incubated in the presence of peptide-loaded syngenic LPS blasts. After six days, cultures were assayed for cytotoxic activity using peptide-pulsed targets. The data indicated that 5 of the 14 peptides were capable of inducing primary CTL responses in A*0201/K^b transgenic mice. (For these studies, a peptide was considered positive if it induced CTL (L.U. 30/10⁶ cells in at least two transgenic animals (Wentworth et al., Eur. Immunol. 26:97-101, 1996).

The fourteen peptides that bound to HLA-A*0201 with good affinity were also tested for immunogenicity with PBMCs from at least four malaria-naive human donors. The induction of primary CTL responses in vitro with PBMCs from normal naive humans requires a brief treatment of the antigen-presenting cells with acidic buffer and subsequent neutralization in the presence of excess B₂-microglobulin and exogenous peptide (Wentworth et al., supra). By ensuring that the majority of the HLA class I molecules are occupied by exogenous peptide, these steps are essential for the induction of primary CTL responses. Such responses cannot be induced using methods developed for the induction of recall CTL responses. A peptide was considered positive if yielding more than 2 LU₃₀/10⁶ cells (lytic units 20% per 10⁴ cells, where one lytic unit corresponds to the number of effector cells required to induce 30% ⁵¹Cr release from 10,000 target cells during a 6 hr assay.) or 15% peptide-specific lysis, respectively, in at least two different primary CTL cultures. The five peptides that were positive in HLA transgenic mice were also shown to induce primary CTL responses.

The HLA-A2 cross-reactive binding peptides were tested for their ability to elicit in vitro recall responses from PBMCs of six volunteers, each of whom had an HLA-A*0201 allele, immunized with irradiated sporozoites. The results demonstrated that all of the A2-binding peptides were recognized in association with HLA-A*0201.

In addition to investigating whether the peptides could be recognized as CTL epitopes, the ability of the peptides to induce specific cytokine responses was also measured. In particular, induction of interferon-γ and TNF-α were measured, both of which have been implicated in protective immunity against malaria. PBMC from irradiated sporozoite-immunized volunteers and PBMC from naturally exposed individuals were tested. The results indicate that significant peptide-induced cytokine responses were observed for all of the A2 supermotif-bearing peptides. (See Doolan et al., Immunity 7:97-112, 1997.)

Evaluation of A*03/A11 Immunogenicity

The immunogenicity of the eight supermotif-bearing peptides was also evaluated in recall responses using PBMC from volunteers bearing HLA-A3 supertype alleles who had previously been immunized with irradiated sporozoites. All the peptides were recognized in association with both A3 and A33. The fraction of individuals responding to each peptide varied for the supertype overall from 50% for one of the peptides to 100% for three of the peptides.

Immunogenicity was also evaluated using PBMCs of semi-immune or nonimmune individuals naturally exposed to malaria. In this population, recall CTL responses (percentage specific lysis greater than 10%) were detected for five of the eight A3-binding peptides.

Immunogenicity of A3 supermotif-bearing peptides can also be evaluated in transgenic mice that bear a human HLA-A11 allele using methodology analagous to that for immunogenicity studies using HLA-A2.1 transgenic mice.

Evaluation of B7 Immunogenicity

Immunogenicity of two B7 supermotif-bearing peptides, SSP2₅₃₉ and the HLA-B-restricted peptide Pfs16₇₇ was also examined in individuals who had been exposed to PF, either through immunization or natural exposure, as described for the evaluation of A2- and A3-supermotif-bearing peptides.

Both peptides were found to be capable of inducing CTL responses. The two peptides were recognized as CTL epitopes in the context of three of the five B7 supertype alleles.

Example 4

Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analogued, or “fixed” to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analog peptides that exhibit modulated binding affinity are set forth in this example.

Analoging at Primary Anchor Residues

The primary anchor residues are analogued to modulate binding activity. For example, peptide engineering strategies are implemented to further increase the cross-reactivity of the A3-supertype candidate epitopes identified above. On the basis of the data disclosed, e.g., in related and U.S. Ser. No. 09/226,775, now abandoned, the main anchors of A3-supermotif-bearing peptides are altered, for example, to introduce a preferred V, S, or M at position 2.

To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A3 supertype alleles A3 and A11; then, if binding capacity is maintained, for additional A3-supertype cross-reactivity.

Similarly, analogs of HLA-A2 supermotif-bearing epitopes may also be generated. For example, peptides binding to A2-supertype molecules may be engineered at primary anchor residues to possess a preferred residue (L, I, V, or M) at position 2 and/or a preferred I or V as a position 9 primary anchor residue.

The analog peptides are then tested for the ability to bind the A2 supermotif prototype allele, A*0201. Those peptides that demonstrate 500 nM binding capacity are then tested for A2-supertype cross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptide binding to B7-supertype alleles may be improved, where possible, to achieve increased cross-reactive binding. B7 supermotif-bearing peptides may, for example, be engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of an analog of the B7 supermotif-bearing peptide Pf SSP2₁₂₆, representing a discreet single amino acid substitution at position one, is analyzed. The peptide may be substituted with an F at position 1, rather than and L. The peptide, which binds to 3 of 5 B7 supertype alles, is then analyzed for the ability to bind all five B7-supertype molecules with a good affinity.

Because so few B7-supertype cross-reactive epitopes were identified in the initial binding screen, results from previous binding evaluations may be analyzed to identify conserved (8-, 9-, 10-, or 11-mer) peptides which bind, minimally, 3/5 B7 supertype molecules with weak affinity (IC₅₀ of 500 nM-5 μM). This analysis identifies additional candidate peptides that can be analogued. These peptides are tested for enhanced binding affinity and B7-supertype cross-reactivity.

Engineered analogs with sufficiently improved binding capacity or cross-reactivity are tested as described in Example 2 for the ability of the peptide to induce CTL responses using PBMC from individuals who had previously been exposed to Pf antigens. Immunogenicity may also be studied in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization.

In conclusion, these data demonstrate that by the use of even single amino acid substitutions, it is possible to increase the binding affinity and/or cross-reactivity of peptide ligands for HLA supertype molecules.

Example 5

Identification of Conserved PF-Derived Sequences with HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif may also be identified as outlined below using methodology similar to that described in Examples 1-3.

Selection of HLA-DR-Supermotif-Bearing Epitopes

To identify PF-derived, HLA class II HTL epitopes, the protein sequences from the same four PF antigens used for the identification of HLA Class I supermotif/motif sequences were analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences were selected comprising a DR-supermotif, further comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total). It was also required that the 9-mer core sequence be 100% conserved in at least 79% of the sequences analyzed.

The conserved, PF-derived peptides identified above were tested for their binding capacity for various common HLA-DR molecules. All peptides were initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least 2 of these 3 DR molecules were then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least 2 of the 4 secondary panel DR molecules, and thus cumulatively at least 4 of 7 different DR molecules, were screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least 7 of the 10 DR molecules comprising the primary, secondary, and tertiary screening assays were considered cross-reactive DR binders. The composition of these screening panels, and the phenotypic frequency of associated antigens, are shown in Table XXX.

In conclusion, 8 cross-reactive DR-binding peptides derived from 6 independent regions were identified that bind 7 or more HLA DR alleles. Five other peptides were also identified that bound between 4 and 6 DR alleles (Table XXXI).

Selection of Conserved DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is an important criterion in the selection of HTL epitopes. However, data generated previously indicated that DR3 only rarely cross-reacts with other DR alleles (Sidney et al., J. Immunol. 149:2634-2640, 1992; Geluk et al., J. Immunol. 152:5742-5748, 1994; Southwood et al., J. Immunol. 160:3363-3373, 1998). This is not entirely surprising in that the DR3 peptide-binding motif appears to be distinct from the specificity of most other DR alleles.

To efficiently identify peptides that bind DR3, target proteins were analyzed for conserved sequences carrying one of the two DR3 specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). Peptides containing a DR3 motif were then synthesized and tested for their DR3 binding capacity. Three peptides were found to bind DR3 with an affinity of 1 μM or less (Table XXXI), and thereby qualify as HLA class II high affinity binders. On of these peptides was also identified above as a cross-reactive DR binding peptide.

DR3 binding epitopes identified in this manner that are found to induce immunological responses as in Example 6 below may then be included in vaccine compositions with DR supermotif-bearing peptide epitopes.

Example 6

Immunogenicity of PF-Derived HTL Epitopes

The immunogenicity of the HLA class II binding epitopes identified in Example 5 was evaluated in a study testing PBMC from either healthy volunteers previously immunized with an irradiated sporozoite vaccine, and thereby immune to malaria, or PBMC from naturally exposed individuals from the Irian Java (Indonesia) region where malaria is highly endemic. Vigorous responses were seen in volunteers vaccinated with whole irradiate sporozoites. All peptides were recognized in at least one immune individual, but not in either of the two individuals for which pre-immunization sample were available. All individuals recognized at least two, and up to nine different epitopes.

In the case of Irian Java population, PBMC from over 100 different individuals were screened for reactivity. Proliferation and secretion of various lymphokines has been measured. The results demonstrate that also in this semi-immune chronically exposed population, all peptides are recognized, with the percentage of individuals yielding positive responses ranging from 7% to 29% for IFN-γ, 36% to 51% for TNF-α and 12% to 2% for proliferative responses (Table XXII.

In conclusion, the immunogenicity of class II epitopes derived from conserved regions of the PF genome has been demonstrated.

Example 7

Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA alleles were determined. Gene frequencies for each HLA allele were calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies were calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)²].

Where frequency data was not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies was assumed. To obtain total potential supertype population coverage no linkage disequilibrium was assumed, and only alleles confirmed to belong to each of the supertypes were included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations were made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups (see Table XXI). Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analagous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Summary of Candidate HLA Class I and Class II Epitopes

In summary, on the basis of the data presented in the above examples, candidate peptide epitopes derived from conserved regions of PF have been identified (Table XXXIII) These include eight HLA-A2 supermotif-bearing epitopes, eight HLA-A3 supermotif-bearing epitopes, and two HLA-B7 supermotif-bearing epitope, each capable of binding to multiple A2-, A3-, or B7-supertype molecules, and immunogenic in HLA transgenic mice or antigenic for human PBL. In addition four A1 motif-bearing and four A24 motif-bearing epitopes are also include candidate CTL epitopes for inclusion in a vaccine composition.

With these 26 CTL epitopes (as disclosed herein and from the art), average population coverage, (i.e., recognition of at least one PF epitope), is predicted to be, on average, greater than 95% (range of 90.6%-99.1%), in five major ethnic populations. The potential redundancy of coverage afforded by these epitopes can be estimated using the game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994). As shown in FIG. 1, it is estimated that 90% of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize 8 or more of the candidate epitopes described herein.

A list of PF-derived HTL epitopes that would be preferred for use in the design of minigene constructs or other vaccine formulations is summarized in Table XXXIV. As shown, 13 different peptide-binding regions have been identified which bind multiple HLA-DR molecules or bind HLA-DR3.

It is estimated that each of 10 common DR molecules recognizing the DR supermotif, and DR3, are covered by a minimum of 2 epitopes. Correspondingly, the total estimated population coverage represented by this panel of epitopes is, on average, in excess of 94% in each of the 5 major ethnic populations (Table XXXV).

Example 8

Recognition of Generation of Endogenous Processed Antigens after Priming

This example determines that CTL induced by native or analogued peptide epitopes identified and selected as described in Examples 1-6 recognize endogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized with peptide epitopes as in Example 3, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on ⁵¹Cr labeled Jurkat-A2.1/K^b target cells in the absence or presence of peptide, and also tested on ⁵¹Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with PF expression vectors.

The result will demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized PF antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that is being evaluated. In addition to HLA-A*0201/K^b transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 9

Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenic mice by use of a PF CTL/HTL peptide conjugate whereby the vaccine composition comprises peptides administered to a PF-infected patient or an individual at risk for malaria. The peptide composition can comprise multiple CTL and/or HTL epitopes. This analysis demonstrates enhanced immunogenicity that can be achieved by inclusion of one or more HTL epitopes in a vaccine composition. Such a peptide composition can comprise a lipidated HTL epitope conjugated to a preferred CTL epitope containing, for example, at least one CTL epitope selected from Tables VII-XVIII, or an analog of that epitope. The HTL epitope is, for example, selected from Table XIX or XX.

Lipopeptide preparation: Lipopeptides are prepared by coupling the appropriate fatty acid to the amino terminus of the resin bound peptide. A typical procedure is as follows: A dichloromethane solution of a four-fold excess of a pre-formed symmetrical anhydride of the appropriate fatty acid is added to the resin and the mixture is allowed to react for two hours. The resin is washed with dichloromethane and dried. The resin is then treated with trifluoroacetic acid in the presence of appropriate scavengers [e.g. 5% (v/v) water] for 60 minutes at 20° C. After evaporation of excess trifluoroacetic acid, the crude peptide is washed with diethyl ether, dissolved in methanol and precipitated by the addition of water. The peptide is collected by filtration and dried.

Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/K^b mice, which are transgenic for the human HLA A2.1 allele and are useful for the assessment of the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, are primed subcutaneously (base of the tail) with 0.1 ml of peptide conjugate formulated in saline, or DMSO/saline. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/K^b chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×10⁶ cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) are incubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 10^{4 51}Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a 6 hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a 6 hour ⁵¹Cr release assay. To obtain specific lytic units/10⁶, the lytic units/10⁶ obtained in the absence of peptide is subtracted from the lytic units/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×10⁵ effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1/50,000)−(1/500,000)]×10⁶=18 LU.

The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using the CTL epitope as outlined in Example 3. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures it is found that a CTL response is induced, and concomitantly that an HTL response is induced, upon administration of such compositions.

Example 10

Selection of CTL and HTL Epitopes for Inclusion in a PF-Specific Vaccine

This example illustrates the procedure for the selection of peptide epitopes for vaccine compositions of the invention. The peptides in the composition may be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or may be single and/or polyepitopic peptides.

The following principles are utilized when selecting an array of epitopes for inclusion in a vaccine composition. Each of the following principles are balanced in order to make the selection.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. In other words, it has been observed that patients who spontaneously clear PF generate an immune response to at least 3 epitopes on at least one PF antigen. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen.

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC₅₀ of 500 nM or less, or for Class II an IC₅₀ of 1000 nM or less.

3.) Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art and discussed herein, can be employed to assess breadth, or redundancy, of population coverage.

4.) When selecting epitopes for PF antigens it may be preferable to select native epitopes. Therefore, of particular relevance for infectious disease vaccines, are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.

When providing nested epitopes, a sequence that has the greatest number of epitopes per provided sequence is provided. A limitation on this principle is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, the sequence is screened in order to insure that it does not have pathological or other deleterious biological properties.

5.) When creating a minigene, as disclosed in greater detail in Example 11, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Additionally, however, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that epitope, which is not present in a native PF protein sequence. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

Peptide epitopes for inclusion in vaccine compositions are, for example, selected from those listed in Tables XXXIII and XXXIV. A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude of an immune response that clears an acute PF infection.

Example 11

Construction of Minigene Multi-Epitope DNA Plasmids

This example describes the design and construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of CTL and/or HTL epitopes or epitope analogs as described herein. Expression plasmids have been constructed and evaluated as described, for example, in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and in Ishioka et al., J. Immunol. 162:3915-3925, 1999.

A minigene expression plasmid may include multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. Preferred epitopes are identified, for example, in Tables XXXIII and XXXIV. HLA class I supermotif or motif-bearing peptide epitopes derived from multiple PF antigens, e.g., EXP-1, SSP2, CSP and LSA-1, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from multiple PF antigens to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

This example illustrates the methods to be used for construction of such a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

The minigene DNA plasmid contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

Overlapping oligonucleotides, for example eight oligonucleotides, averaging approximately 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

For the first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: Oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH₄)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product for 25 additional cycles. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 12

The Plasmid Construct and the Degree to which it Induces Immunogenicity

The degree to which the plasmid construct prepared using the methodology outlined in Example 11 is able to induce immunogenicity is evaluated through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analysed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and Alexander et al., Immunity 1:751-761, 1994. To assess the capacity of the pMin minigene construct to induce CTLs in vivo, HLA-A11/K^b transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a ⁵¹Cr release assay. The results indicate the magnitude of the CTL response directed against the A3-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine. It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A3 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A2 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A2 and HLA-B7 motif or supermotif epitopes.

To assess the capacity of a class II epitope encoding minigene to induce HTLs in vivo, I-A^b restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant.

CD4⁺ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a ³H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al., Immunity 1:751-761, 1994). the results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

DNA minigenes, constructed as described in Example 11, may also be evaluated as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent may consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Reotroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).

For example, the efficacy of the DNA minigene may be evaluated in transgenic mice. In this example, A2.1/K^b transgenic mice are immunized IM with 100 μg of the DNA minigene encoding the immunogenic peptides. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an IFN-y ELISA. It is found that the minigene utilized in a prime-boost mode elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis is also performed using other HLA-A11 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes.

Example 13

Peptide Composition for Prophylactic Uses

Vaccine compositions of the present invention are used to prevent PF infection in persons who are at risk for such infection. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in Examples 9 and/or 10, which are also selected to target greater than 80% of the population, is administered to individuals at risk for PF infection. The composition is provided as a single lipidated polypeptide that encompasses multiple epitopes. The vaccine is administered in an aqueous carrier comprised of Freunds Incomplete Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against PF infection.

Alternatively, the polyepitopic peptide composition can be administered as a nucleic acid in accordance with methodologies known in the art and disclosed herein.

Example 14

Polyepitopic Vaccine Compositions Derived from Native PF Sequences

A native PF polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes and is preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct, even overlapping, epitopes is selected and used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with frame shifted overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

The vaccine composition will preferably include, for example, three CTL epitopes and at least one HTL epitope from PF. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent analogs) directs the immune response to multiple peptide sequences that are actually present in native PF antigens thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions.

Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

Example 15

Polyepitopic Vaccine Compositions Directed to Multiple Diseases

The PF peptide epitopes of the present invention are used in conjunction with peptide epitopes from target antigens related to one or more other diseases, to create a vaccine composition that is useful for the prevention or treatment of PF as well as the one or more other disease(s). Examples of the other diseases include, but are not limited to, HIV, HCV, and HBV.

For example, a polyepitopic peptide composition comprising multiple CTL and HTL epitopes that target greater than 98% of the population may be created for administration to individuals at risk for both PF and HIV infection. The composition can be provided as a single polypeptide that incorporates the multiple epitopes from the various disease-associated sources, or can be administered as a composition comprising one or more discrete epitopes.

Example 16

Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response for the presence of specific CTL or HTL populations directed to PF. Such an analysis may be performed in a manner as that described by Ogg et al., Science 279:2103-2106, 1998. In the following example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, PF HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of infection or following immunization using an PF peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive uninfected donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the PF epitope, and thus the stage of infection with PF, the status of exposure to PF, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 17

Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from infection, who are chronically infected with PF, or who have been vaccinated with a PF vaccine.

For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any PF vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that are preferably highly conserved and, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

In the microculture format, 4×10⁵ PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 ml of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific ⁵¹Cr release, based on comparison with uninfected control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

Cytolytic activity is determined in a standard 4-h, split well ⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release−spontaneous release)/maximum release−spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to PF or a PF vaccine.

The class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×10⁵ cells/well and are stimulated with 10 μg/ml synthetic peptide, whole antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 ³H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for ³H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of ³H-thymidine incorporation in the presence of antigen divided by the ³H-thymidine incorporation in the absence of antigen.

Example 18

Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that used to evaluated the efficacy of a DNA vaccine in transgenic mice, which was described in Example 12, may also be used for the administration of the vaccine to humans. Such a vaccine regimen is includes an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptides mixture administered in an adjuvant.

For example, the initial immunization may be performed using an expression vector, such as that constructed in Example 11, in the form of naked DNA administered IM (or SC or ID) in the amounts of 0.5-5, typically 100 g, at multiple sites. The DNA (0.1 to 1000 mg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu. Alternative recombinant virus, such as MVA, canarypox, adenovirus, and adeno-associated viruses can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples will be obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results will indicate that a magnitude of sufficient response to achieve protective immunity against Pf is generated.

Example 19

Induction of Specific CTL Response in Humans

A human clinical trial to evaluate an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial in patients are not infected with Pf. Such a trial is designed, for example, as follows:

A total of about 27 subjects are enrolled and divided into 3 groups:

Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

A prophylactic field trial can also be conducted to evaluate a vaccine composition of the invention. In such a trial, issues of patient compliance are also considered in the determination of vaccine efficacy.

Example 20

Administration of Vaccine Compositions Using Dendritic Cells

Vaccines comprising peptide epitopes of the invention may be administered using dendritic cells. In this example, the immunogenic peptide epitopes are used to elicit a CTL and/or HTL response ex vivo.

Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptides. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., PF-infected cells.

Example 21

Alternative Method of Identifying Motif-Bearing Peptides

Another way of identifying motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing, have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can then be infected with a pathogenic organism, e.g., PF, HIV, etc. or transfected with nucleic acids that express the antigen of interest. Thereafter, peptides produced by endogenous antigen processing of peptides produced consequent to infection (or as a result of transfection) will bind to HLA molecules within the cell and be transported and displayed on the cell surface.

The peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because, as disclosed herein, the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express any endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells may then be used as described, i.e., they may be infected with a pathogenic organism or transfected with nucleic acid encoding an antigen of interest to isolate peptides corresponding to the pathogen or antigen of interest that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than infection or transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

The above examples are provided to illustrate the invention but not to limit its scope. For example, the human terminology for the Major Histocompatibility Complex, namely HLA, is used throughout this document. It is to be appreciated that these principles can be extended to other species as well. Thus, other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent application cited herein are hereby incorporated by reference for all purposes.

TABLE I
SUPERMOTIFS	POSITION	POSITION	POSITION
	2	3	C Terminus
	(Primary Anchor)	(Primary Anchor)	(Primary Anchor)
A1	TILVMS		FWY
A2	LIVMATQ		IVMATL
A3	VSMATLI		RK
A24	YFWIVLMT		FIYWLM
B7	P		VILFMWYA
B27	RHK		FYLWMIVA
B44	ED		FWYLIMVA
B58	ATS		FWYLIVMA
B62	QLIVMP		FWYMIVLA
MOTIFS
A1	TSM		Y
A1		DEAS	Y
A2.1	LMVQIAT		VLIMAT
A3	LMVISATFCGD		KYRHFA
A11	VTMLISAGNCDF		KRYH
A24	YFWM		FLIW
A*3101	MVTALIS		RK
A*3301	MVALFIST		RK
A*6801	AVTMSLI		RK
B*0702	P		LMFWYAIV
B*3501	P		LMFWYIVA
B51	P		LIVFWYAM
B*5301	P		IMFWYALV
B*5401	P		ATIVLMFWY
Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearingif it has primary anchors at each primary anchor position for a motif or superrnotifas specified in the above table.

TABLE Ia
SUPERMOTIFS	POSITION	POSITION	POSITION
	2	3	C Terminus
	(Primary Anchor)	(Primary Anchor)	(Primary Anchor)
A1	TILVMS		FWY
A2	VQAT		VLIMAT
A3	VSMATLI		RK
A24	YFWIVLMT		FIYWLM
B7	P		VILFMWYA
B27	RHK		FYLWMIVA
B58	ATS		FWYLIVMA
B62	QLIVMP		FWYMIVLA
MOTIFS
A1	TSM		Y
A1		DEAS	Y
A2.1	VQAT*		VLIMAT
A3.2	LMVISATFCGD		KYRHFA
A11	VTMLISAGNCDF		KRHY
A24	YFW		FLIW
*If 2 is V, or Q, the C-term is not L
Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearingif it has primary anchors at each primary anchor position for a motif or supermotifas specified in the above table.

TABLE 11
	Position

SUPERMOTIFS	1	2	3	4	5

A1			1° Anchor
			TILVMS
A2			1° Anchor
			LIVMATQ
A3	preferred		1° Anchor	YFW (4/5)
			VSMATLI			RK
	deleterious	DE (3/5);		DE (4/5)
		P (5/5)
A24			1° Anchor
			YFWIVLMT
B7	preferred	FWY (5/5)	1° Anchor	FWY (4/5)
		LIVM (3/5)	P
	deleterious	DE (3/5);
		P(5/5);

	G(4/5);
	A(3/5);
	QN (3/5)

B27			1° Anchor
			RHK
B44			1° Anchor
			ED
B58			1° Anchor
			ATS
B62			1° Anchor
			QLIVMP

Position

SUPERMOTIFS	6	7	8	C-terminus

A1				1° Anchor
				FWY
A2				1° Anchor
				LIVMAT
A3	YFW (3/5)	YFW (4/5)	P (4/5)	1° Anchor
				RK
A24				1° Anchor
				FIYWLM
B7			FWY (3/5)	1° Anchor
				VILFMWYA
	/5)	QN (4/5)	DE (4/5)
B27				1° Anchor
				FYLWMIVA
B44				1° Anchor
				FWYLIMVA
B58				1° Anchor
				FWYLIVMA
B62				1° Anchor
				FWYMIVLA

Position

MOTIFS	1	2	3	4	5

A1	preferred	GFYW	1° Anchor	DEA	YFW
9-mer			STM
	deleterious	DE	RHKLIVM		A	G
			P
A1	preferred	GRHK	ASTCLIV	1° Anchor	GSTC
9-mer			M	DEAS
	deleterious	A	RHKDEPY		DE	PQN
			FW

Position

MOTIFS	6	7	8	C-terminus

A1	P	DEQN	YFW	1° Anchor
9-mer				Y
	A
A1	ASTC	LIVM	DE	1° Anchor
9-mer				Y
	RHK	PG	GP

Position

		1	2	3	4
A1	peferred	YFW	1° Anchor	DEAQN	A
10-			STM
mer	deleterious	GP		RHKGLIV	DE
				M
A1	preferred	YFW	STCLIVM	1° Anchor	A
l0-				DEAS
mer	deleterious	RHK	RHKDEPY
			FW
A2.1	preferred	YFW	1° Anchor	YFW	STC
9-mer			LMIVQAT
	deleterious	DEP		DERKH
A2.1	preferred	AYFW	1° Anchor	LVIM	G
l0-			LMIVQAT
mer	deleterious	DEP		DE	RKHA
A3	preferred	RHK	1° Anchor	YFW	PRHKYFW
			LMVISAT
			FCGD
	deleterious	DEP		DE
A11	preferred	A	1° Anchor	YFW	YFW
			VTLMISA
			GNCDF
	deleterious	DEP
A24	preferred	YFWRHK	1° Anchor		STC
9-mer			YFWM
	deleterious	DEG		DE	G
A24	preferred		1° Anchor		P
10-			YFWM
mer	deleterious			GDE	QN
A3101	preferred	RHK	1° Anchor	YFW	P
			MVTALIS
	deleterious	DEP		DE
A3301	preferred		1° Anchor	YFW
			MVALFIS
			T
	deleterious	GP		DE
A6801	preferred	YFWSTC	1° Anchor
			AVTMSLI
	deleterious	GP		DEG
B0702	preferred	RHKFWY	1° Anchor	RHK
			P
	deleterious	DEQNP		DEP	DE
B3501	preferred	FWYLIVM	1° Anchor	FWY
			P
	deleterious	AGP
B51	preferred	LIVMFWY	1° Anchor	FWY	STC
			P
	deleterious	AGPDERHKSTC
B5301	preferred	LIVMFWY	1° Anchor	FWY	STC
			P
	deleterious	AGPQN
B5401	preferred	FWY	1° Anchor	FWYLIVM
			P
	deleterious	GPQNDE		GDESTC

Position

					9
					or C-
		6	7	8	terminus
A1	peferred		PASTC	GDE	P
10-
mer	deleterious	QNA	RHKYFW	RHK	A
A1	preferred		PG	G	YFW
l0-
mer	deleterious	G		PRHK	QN
A2.1	preferred		A	P	1° Anchor
9-mer					VLIMAT
	deleterious	RKH	DERKH
A2.1	preferred	G		FYWL
l0-				VIM
mer	deleterious		RKH	DERK	RKH
A3	preferred	A	YFW	P	1° Anchor
					KYRHFA
	deleterious
A11	preferred	YFW	YFW	P	1° Anchor
					KRYH
	deleterious		A	G
A24	preferred		YFW	YFW	1° Anchor
9-mer					FLIW
	deleterious	DERHK	G	AQN
A24	preferred		P
10-
mer	deleterious	DE	A	QN	DEA
A3101	preferred	YFW	YFW	AP	1° Anchor
					RK
	deleterious	DE	DE	DE
A3301	preferred		AYFW		1° Anchor
					RK
	deleterious
A6801	preferred		YFW	P	1° Anchor
					RK
	deleterious			A
B0702	preferred	RHK	RHK	PA	1° Anchor
					LMFWYAIV
	deleterious	GDE	QN	DE
B3501	preferred		FWY		1° Anchor
					LMFWYIVA
	deleterious	G
B51	preferred		G	FWY	1° Anchor
					LIVFWYAM
	deleterious	G	DEQN	GDE
B5301	preferred		LIVMFWY	FWY	1° Anchor
					IMFWYALV
	deleterious	G	RHKQN	DE
B5401	preferred		ALIVM	FWYAP	1° Anchor
					ATIVLMFW
					Y
	deleterious	DE	QNDGE	DE
Italicized residues indicate less preferred or ″tolerated″ residues. The information in Table II is specific for 9-meRs unless otherwise specified.

TABLE III
	POSITION

SEQ ID		1°					1°
NO:	MOTIFS	anchor 1	2	3	4	5	anchor 6	7	8	9

	DR4	preferred	FMYLIYW	M	T		I	VSTCPALIM	MH		MEI
		deleterious				W			R		WDE
	DR1	preferred	MFLIVWY			PAMQ		VMATSPLIC	M		AVM
		deleterious		C	CH	FD	CWD		GDE	D
3841	DR7	preferred	MFLIVWY	M	W	A		IVMSACTPL	M		IV
3842		deleterious		C		G			GRD	N	G

	DR Supermotif	MFLIVWY					VMSTACPLI

	DR3 MOTIFS	1° anchor 1	2	3	1° anchor 4	5	1° anchor 6
	motif a	LIVMFY			D
	preferred
	motif b	LIVMFAY			DNQEST		KRH
	preferred
Italicized residues indicate less preferred or ″tolerated″ residues.

TABLE IV
HLA Class I Standard Peptide Binding Affinity.

			SEQ	STANDARD
	STANDARD		ID	BINDING
ALLELE	PEPTIDE	SEQUENCE	NO:	AFFINITY (nM)
A*0101	944.02	YLEPAIAKY	3575	25
A*0201	941.01	FLPSDYFPSV	3576	5.0
A*0202	941.01	FLPSDYFPSV	3577	4.3
A*0203	941.01	FLPSDYFPSV	3578	10
A*0205	941.01	FLPSDYFPSV	3579	4.3
A*0206	941.01	FLPSDYFPSV	3580	3.7
A*0207	941.01	FLPSDYFPSV	3581	23
A*6802	1072.34	YVIKVSARV	3582	8.0
A*0301	941.12	KVFPYALINK	3583	11
A*1101	940.06	AVDLYHFLK	3584	6.0
A*3101	941.12	KVFPYALINK	3585	18
A*3301	1083.02	STLPETYVVRR	3586	29
A*6801	941.12	KVFPYALINK	3587	8.0
A*2402	979.02	AYIDNYNKF	3588	12
B*0702	1075.23	APRTLVYLL	3589	5.5
B*3501	1021.05	FPFKYAAAF	3590	7.2
B51	1021.05	FPFKYAAAF	3591	5.5
B*5301	1021.05	FPFKYAAAF	3592	9.3
B*5401	1021.05	FPFKYAAAF	3593	10

TABLE V
HLA Class II Standard Peptide Binding Affinity.

					Binding
		Standard			Affinity
Allele	Nomenclature	Peptide	SEQ ID	Sequence	(nM)
DRB1*0101	DR1	515.01	3594	PKYVKQNTLKLAT	5.0
DRB1*0301	DR3	829.02	3595	YKTIAFDEEARR	300
DRB1*0401	DR4w4	515.01	3596	PKYVKQNTLKLAT	45
DRB1*0404	DR4w14	717.01	3597	YARFQSQTTLKQKT	50
DRB1*0405	DR4w15	717.01	3598	YARFQSQTTLKQKT	38
DRB1*0701	DR7	553.01	3599	QYIKANSKFIGITE	25
DRB1*0802	DR8w2	553.01	3600	QYIKANSKFIGITE	49
DRB1*0803	DR8w3	553.01	3601	QYIKANSKFIGITE	1600
DRB1*0901	DR9	553.01	3602	QYIKANSKFIGITE	75
DRB1*1101	DR5w11	553.01	3603	QYIKANSKFIGITE	20
DRB1*1201	DR5w12	1200.05	3604	EALIHQLKINPYVLS	298
DRB1*1302	DR6w19	650.22	3605	QYIKANAKFIGITE	3.5
DRB1*1501	DR2w2β1	507.02	3606	GRTQDENPVVHFFK	9.1
				NIVTPRTPPP
DRB3*0101	DR52a	511	3607	NGQIGNDPNRDIL	470
DRB4*0101	DRw53	717.01	3608	YARFQSQTTLKQKT	58
DRB5*0101	DR2w2β2	553.01	3609	QYIKANSKFIGITE	20

The “Nomenclature” column lists the allelic designations used in Tables XIX and XX.

Table VI
HLA-	Allelle-specific HLA-supertype members

supertype	Verifieda	Predictedb
A1	A*0101, A*2501, A*2601, A*2602, A*3201	A*0102, A*2604, A*3601, A*4301, A*8001
A2	A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207,	A*0208, A*0210, A*0211, A*0212, A*0213
	A*0209, A*0214, A*6802, A*6901
A3	A*0301, A*1101, A*3101, A*3301, A*6801	A*0302, A*1102, A*2603, A*3302, A*3303, A*3401,
		A*3402, A*6601, A*6602, A*7401
A24	A*2301, A*2402, A*3001	A*2403, A*2404, A*3002, A*3003
B7	B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503,	B*1511, B*4201, B*5901
	B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102,
	B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601,
	B*5602, B*6701, B*7801
B27	B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705,	B*2701, B*2707, B*2708, B*3802, B*3903, B*3904,
	B*2706, B*3801, B*3901, B*3902, B*7301	B*3905, B*4801, B*4802, B*1510, B*1518, B*1503
B44	B*1801, B*1802, B*3701, B*4402, B*4403, B*4404, B*4001,	B*4101, B*4501, B*4701, B*4901, B*5001
	B*4002, B*4006
B58	B*5701, B*5702, B*5801, B*5802, B*1516, B*1517
B62	B*1501, B*1502, B*1513, B*5201	B*1301, B*1302, B*1504, B*1505, B*1506, B*1507,
		B*1515, B*1520, B*1521, B*1512, B*1514, B*1510
aVerified alleles include alleles whose specificity has been determined by pool sequencing analysis, peptide binding assays, or by analysis of the sequences of CTL epitopes.
bPredicted alleles are alleles whose specificity is predicted on the basis of B and F pocket structure to overlap with the supertype specificity.

TABLE VII
Malaria A01 Super Motif Peptides With Binding Data

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*010I	Seq. Id.

CSP	AILSVSSF	6	8	19	100		1
CSP	AILSVSSFLF	6	10	19	100		2
CSP	ALFQEYQCY	18	9	19	100		3
CSP	EMNYYGKQENW	52	11	19	100		4
CSP	FLFVEALF	13	8	19	100		5
CSP	FLFVEALFQEY	13	11	19	100		6
CSP	FVEALFQEY	15	9	19	100	3.4000	7
CSP	GLIMVLSF	421	8	19	100		8
CSP	GLIMVLSFLF	421	10	19	100		9
CSP	ILSVSSFLF	7	9	19	100		10
CSP	IMVLSFLF	423	8	19	100		11
CSP	KIQNSLSTEW	357	10	19	79		12
CSP	KLAILSVSSF	4	10	19	100		13
CSP	KMEKCSSVF	405	9	19	100		14
CSP	LIMVLSFLF	422	9	19	100		15
CSP	LSVSSFLF	8	8	19	100		16
CSP	NLYNELEMNY	46	10	19	100		17
CSP	NLYNELEMNYY	46	11	19	100		18
CSP	NTRVLNELNY	31	10	19	100	0.0096	19
CSP	PSDKHIEQY	346	9	19	79		20
CSP	RVLELNY	33	8	19	100		21
CSP	SIGLIMVLSF	419	10	19	100		22
CSP	SSFLFVEALF	11	10	19	100		23
CSP	SSIGLIMVLSF	418	11	19	100		24
CSP	VSSFLFVEALF	10	11	19	100		25
CSP	EVNKRKSKY	66	9	1	100		26
EXP	FLALFFIIF	8	9	1	100		27
EXP	ILSVFFLALF	3	10	1	100		28
EXP	ILSVFFLALFF	3	11	1	100		29
EXP	KILSVFFLALF	2	11	1	100		30
EXP	LLGGVGLVLY	92	10	1	100		31
EXP	LSVFFLALF	4	9	1	100		32
EXP	LSVFFLALFF	4	10	1	100		33
EXP	LVEVNKRKSKY	64	11	1	100		34
EXP	NTEKGRHPF	102	9	1	100		35
EXP	SVFFLALF	5	8	1	100		36
EXP	SVFFLALFF	5	9	1	100		37
EXP	VLLGGVGLVLY	91	11	1	100		38
LSA	DLDEFKPIVQY	1781	11	1	100		39
LSA	DVLQEDLY	1646	8	1	100		40
LSA	DVNDFQISKY	1751	10	1	100		41
LSA	ELPSENERGY	1662	10	1	100		42
LSA	ELPSENERGYY	1662	11	1	100		43
LSA	ELSEDITTKY	1897	9	1	100		44
LSA	ELSEDITKYF	1897	10	1	100		45
LSA	ETVNISDVNDF	1745	11	1	100		46
LSA	FIKSLFHIF	1877	9	1	100		47
LSA	FILVNLLIF	11	9	1	100		48
LSA	HILYISFY	3	8	1	100		49
LSA	HILYISFYF	3	9	1	100		50
LSA	HVLSHNSY	59	8	1	100		51
LSA	IINDDDDKKKY	127	11	1	100		52
LSA	ILVNLLIF	12	8	1	100		53
LSA	ILYISFYF	4	8	1	100		54
LSA	KIKKGKKY	1834	8	1	100		55
LSA	KSLYDEHIKKY	1854	11	1	100		56
LSA	KTKNNENNKF	68	10	1	100		57
ISA	KTKNNENNKFF	68	11	1	100		58
LSA	LSEDITKY	1898	8	1	100		59
LSA	LSEDITKYF	1898	9	1	100		60
LSA	NISDVNDF	1748	8	1	100		61
LSA	NLGVSENIF	103	9	1	100		62
ISA	NVKNVSQTNF	88	10	1	100		63
ISA	PIVQYDNF	1787	8	1	100		64
LSA	PSENERGY	1664	8	1	100		65
LSA	PSENERGYY	1664	9	1	100	0.0790	66
LSA	QVNKEKEKF	1869	9	1	100		67
LSA	SLYDEHIKKY	1855	10	1	100		68
LSA	TVNISDVNDF	1746	10	1	100		69
SSP2	ALLACAGLAY	509	10	10	100		70
SSP2	ASCGVWDEW	242	9	10	100		71
SSP2	ATPYAGEPAPF	526	11	8	80		72
SSP2	CSGSIRRHNW	55	10	10	100		73
SSP2	DLDEPEQF	546	8	10	100		74
SSP2	EVCNDEVDLY	41	10	8	80		75
SSP2	EVEKTASCGVW	237	11	10	100		76
SSP2	FLIFFDLF	14	8	10	100		77
SSP2	FVVPGAATPY	520	10	8	80		78
SSP2	GIGQGINVAF	189	10	10	100		79
SSP2	GINVAFNRF	193	9	10	100		80
SSP2	GSIRRHNW	57	8	10	100		81
SSP2	IVFLIFFDLF	12	10	10	100		82
SSP2	KTASCGVW	240	8	10	100		83
SSP2	KTASCGVWDEW	240	11	10	100		84
SSP2	LLACAGLAY	510	9	10	100		85
SSP2	LLACAGLAYKF	510	11	10	100		86
SSP2	LLSTNLPY	121	8	9	90		87
SSP2	LVIVFLIF	10	8	10	100		88
SSP2	LVIVFLIFF	10	9	10	100		89
SSP2	NIVDEIKY	31	8	10	100		90
SSP2	NLYADSAW	213	8	10	100		91
SSP2	NVKNVIGPF	222	9	10	100		92
SSP2	NVKYLVIVF	6	9	10	100		93
SSP2	PSDGKCNLY	207	9	10	100	0.5400	94
SSP2	RLPEENEW	554	8	10	100		95
SSP2	SLLSTNLPY	120	9	9	90		96
SSP2	VIVFLIFF	11	8	10	100		97
SSP2	VIVFLIFFDLF	11	11	10	100		98
SSP2	VVPGAATPY	521	9	8	80		99
SSP2	YLVIVFLIF	9	9	10	100		100
SSP2	YLVIVFLIFF	9	10	10	100		101

TABLE VIII
Malaria A02 Motif Peptides With Binding Information

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*0201
CSP	HIEQYLKKI	350	9	15	79
CSP	KIQNSLST	361	8	15	79
CSP	YLKKIQNSL	358	9	15	79
CSP	YLKKIQNSLST	358	11	15	79
CSP	NANANNAV	335	8	16	84
CSP	NVDENANANNA	331	11	16	84
CSP	ELNYDNAGI	37	9	18	95
CSP	ELNYDNAGINL	37	11	18	95
CSP	GINLYNEL	44	8	18	95
CSP	GINLYNELEM	44	10	18	95
CSP	NAGINLYNEL	42	10	18	95
CSP	SLSTEWSPCSV	365	11	18	95
CSP	AILSVSSFL	6	9	19	100	0.0220
CSP	AILSVSSFLFV	6	11	19	100
CSP	DIEKKICKM	402	9	19	100
CSP	GIQVRIKPGSA	380	11	19	100
CSP	GLIMVLSFL	425	9	19	100	0.0630
CSP	GLIMVLSFLFL	425	11	19	100
CSP	ILSVSSFL	7	8	19	100
CSP	ILSVSSFLFV	7	10	19	100	0.0300
CSP	IMVLSFLFL	427	9	19	100	0.0007
CSP	IQVRIKPGSA	381	10	19	100
CSP	KICKMEKCSSV	406	11	19	100
CSP	KLAILSVSSFL	4	11	19	100
CSP	KLRICPICHKKL	104	10	19	100	0.0001
CSP	KMEKCSSV	409	8	19	100
CSP	KMEKCSSVFNV	409	11	19	100
CSP	KQENWYSL	58	8	19	100
CSP	LAILSVSSFL	5	10	19	100
CSP	LIMVLSFL	426	8	19	100
CSP	LIMVLSFLFL	426	10	19	100	0.0019
CSP	MMRKLAIL	1	8	19	100
CSP	MMRKLAILSV	1	10	19	100	0.0012
CSP	MVLSFLFL	428	8	19	100
CSP	NVDPNANPNA	300	10	19	100
CSP	NANPNVDPNA	196	10	19	100
CSP	NLYNELEM	46	8	19	100
CSP	NMPNDPNRNV	323	10	19	100	0.0007
CSP	NQGNGQGHNM	315	10	19	100
CSP	NTRVLNEL	31	8	19	100
CSP	NVDENANA	331	8	19	100
CSP	NVDPNANPNA	200	10	19	100
CSP	NVDPNANPNV	128	10	19	100
CSP	NVVNSSIGL	418	9	19	100
CSP	NVVNSSIGLI	418	10	19	100
CSP	NVVNSSIGLIM	418	11	19	100
CSP	QVRIKPGSA	382	9	19	100
CSP	RVLNELNYDNA	33	11	19	100
CSP	SIGLIMVL	423	8	19	100
CSP	SIGLIMVLSFL	423	11	19	100
CSP	SLKKNSRSL	64	9	19	100	0.0001
CSP	STEWSPCSV	367	9	19	100
CSP	STEWSPCSVT	367	10	19	100
CSP	SVFNVVNSSI	415	10	19	100	0.0005
CSP	SVSSFLFV	9	8	19	100
CSP	SVSSFLFVEA	9	10	19	100
CSP	SVSSFLFVEAL	9	11	19	100
CSP	SVTCQNGI	374	8	19	100
CSP	SVTCQNGIQV	374	10	19	100
CSP	VLNELNYDNA	34	10	19	100
CSP	VTCGNGIQV	375	9	19	100	0.0011
CSP	VTCGNGIQVRI	375	11	19	100
CSP	VVNSSIGL	419	8	19	100
CSP	VVNSSIGLI	419	9	19	100
CSP	VVNSSIGL1M	419	10	19	100
CSP	VVNSSIGLIMV	419	11	19	100
CSP	YQCYGSSSNT	23	10	19	100
EXP	ATSVLAGL	77	8	1	100
Exp	ATSVLAGLL	77	9	1	100
EXP	DMIKKEEEL	56	9	1	100
EXP	DNMUCEEELV	56	10	1	100
EXP	DVHDLISDM	49	9	1	100
EXP	DVHDLISDMI	49	10	1	100
EXP	EQPQGDDNINIL	147	10	1	100
EXP	EQPQGDDNNLV	147	11	1	100
EXP	EVNKRKSKYKL	66	11	1	100
EXP	FIIFNICESL	13	9	1	100
EXP	FIIFNKESLA	13	10	1	100
EXP	FLALFFII	8	8	1	100
EXP	GLLGNVST	83	8	1	100
EXP	GLLGNVSTV	83	9	1	100	0.0160
EXP	GLLGNVSTVL	83	10	1	100	0.0380
EXP	GLLGNVSTVLL	83	11	1	100
EXP	GVGLVLYNT	95	9	1	100
EXP	IIFNKESL	14	8	1	100
EXP	IIFNKESLA	14	9	1	100
EXP	ILSVFFLA	3	8	1	100
EXP	ILSVFFLAL	3	9	1	100	0.0058
EXP	KIGSSDPA	111	8	1	100
EXP	KIGSSDPADNA	111	11	1	100
EXP	KILSVFFL	2	8	1	100
EXP	KILSVFFLA	2	9	1	100	0.8500
EXP	KILSVFFLAL	2	10	1	100
EXP	KLATSVLA	75	8	1	100
EXP	KLATSVLAGL	75	10	1	100	0.0047
EXP	KLATSVLAGLL	75	11	1	100
EXP	KTNKGTGSGV	24	10	1	100
EXP	LABCTNKGT	21	9	1	100
EXP	LAGLLGNV	81	8	1	100
EXP	LAGLLGNVST	81	10	1	100
EXP	LAGLLGNVSTV	81	11	1	100
EXP	LATSVLAGL	76	9	1	100
EXP	LATSVLAGLL	76	10	1	100
EXP	LIDVHDLI	47	8	1	100
EXP	LIDVHDLISDM	47	11	1	100
EXP	LLGGVCLV	92	8	1	100
EXP	LLGGVCLVL	92	9	1	100	0.0038
EXP	LLGNVSTV	84	8	1	100
EXP	LLGNVSTVL	84	9	1	100	0.0350
EXP	LLGNVSTVLL	84	10	1	100	0.0059
EXP	MIKKEEEL	37	8	1	100
EXP	MIKKEEELV	57	9	1	100
EXP	MIKKEEELVEV	37	11	1	100
EXP	NADPQVTA	134	8	1	100
EXP	NADPQVTAQDV	134	11	1	100
EXP	NTEKGRHPFKI	102	11	1	100
EXP	NVSTVLLGGV	87	10	1	100
EXP	PADNANPDA	117	9	1	100
EXP	PLIDVHDL	46	8	1	100
EXP	PLIDVHDLI	46	9	1	100
EXP	PQGDDNNL	149	8	1	100
EXP	PQGDDNNLV	149	9	1	100
EXP	PQVTAQDV	137	8	1	100
EXP	PQVTAQDVT	137	9	1	100
EXP	QVTAQDVT	138	8	1	100
EXP	SLAEKTNKGT	20	10	1	100
EXP	STVLLGGV	89	8	1	100
EXP	STVLLGQVGL	89	10	1	100
EXP	STVLLGGVGLV	89	11	1	100
EXP	SVFFLALFFI	5	10	1	100	0.0017
EXP	SVPFLALFFH	5	11	1	100
EXP	SVLACLLGNV	79	10	1	100	0.0022
EXP	TVLLGGVGL	90	9	1	100
EXP	TVLLGGVCLV	90	10	1	100
EXP	TVLLGGVGLVL	90	11	1	100
EXP	VLAGLLGNV	80	9	1	100	0.0210
EXP	VLAGLLGNVST	80	11	1	100
EXP	VLLGGVCL	91	8	1	100
EXP	VLLGOVGLV	91	9	1	100	0.0290
EXP	VLLGGVCLVL	91	10	1	100	0.0290
LSA	DIQNHILET	1138	9	1	100
LSA	DIQNHTLETV	1738	10	1	100
LSA	DITKYFMKL	1901	9	1	100
LSA	DUDEFKPI	1781	8	1	100
LSA	DLDEFKPIV	1781	9	1	100	0.0001
LSA	DLEEKAAKET	148	10	1	100
LSA	DLEEKAAKETL	148	11	1	100
LSA	DLEQDRLA	1388	8	1	100
LSA	DLEQERLA	1609	8	1	100
LSA	DLEQERRA	1575	8	1	100
LSA	DLEMADT	1626	9	1	100
LSA	DUERTXASKET	1184	11	1	100
LSA	DLYGRLEI	1651	8	1	100
LSA	DLYGRLEIPA	1651	10	1	100
LSA	DLYGRLEIPAI	1651	11	1	100
LSA	DVLAEDLYGRL	1646	11	1	100
LSA	EILQIVDEL	1890	9	1	100
LSA	EISAEYDDSL	1763	10	1	100
LSA	EISAEYDDSLI	1763	11	1	100
LSA	EISIIEKT	1692	8	1	100
LSA	ELSEDITKYFM	1897	11	1	100
LSA	ELTMSNVKNV	83	10	1	100
LSA	EQDRLWEKL	1390	10	1	100
LSA	EQERLAKEKL	1611	10	1	100
LSA	EQERLANEKL	1526	10	1	100
LSA	EQERRAKEKL	1577	10	1	100
LSA	EQKEDKSA	1730	8	1	100
LSA	EQKEDKSADI	1730	10	1	100
LSA	EQQRDLEQERL	1605	11	1	100
LSA	EQQRDLEQRKA	1622	11	1	100
LSA	EQQSDLEQDRL	1384	11	1	100
LSA	EQQSDLEQERL	1588	11	1	100
LSA	EQQSDLERT	1180	9	1	100
LSA	EQQSDLERTKA	1180	11	1	100
LSA	EQQSDSEQERL	517	11	1	100
LSA	EQRKADTKKNL	1628	11	1	100
LSA	ETLQEQQSDL	1193	10	1	100
LSA	ETLWQQSDL	156	10	1	100
LSA	ETVNISDV	1745	8	1	100
LSA	FIKSLFHI	1877	8	1	100
LSA	FILVNLLI	11	8	1	100
LSA	FILVNLLIFIT	11	11	1	100
LSA	FQDEENIGI	1794	9	1	100
LSA	FQISKYEDE1	1755	10	1	100
LSA	GIOCSSEEL	1822	9	1	100
LSA	GIYKELEDL	1801	9	1	100
LSA	GIYKELEDLI	1801	10	1	100
LSA	GQDENRQEDL	140	10	1	100
LSA	GQQSDIEQISRL	1129	11	1	100
LSA	GVSENTFL	105	8	1	100
LSA	HIFDGDNEI	1883	9	1	100
LSA	HIFDGDNEIL	1883	10	1	100
LSA	HIKKYKNDKQV	1860	11	1	100
LSA	HILYISFYFI	3	10	1	100	0.0033
LSA	HILYISFYFIL	3	11	1	100
LSA	HLEEKKDGSI	1718	10	1	100
LSA	HTLETVNI	1742	8	1	100
LSA	HTLETVNISDV	1742	11	1	100
LSA	HVLSHNSYEKT	59	11	1	100
LSA	IIDONRESI	1695	10	1	100
LSA	IIEKTNRESIT	1695	11	1	100
LSA	IIKNSEKDEI	25	10	1	100
LSA	IIKNSEKDEII	25	11	1	100
LSA	ILQIVDEL	1891	8	1	100
LSA	ILVNLLIFHI	12	10	1	100	0.0076
LSA	ILYISFYFI	4	9	1	100	0.0023
LSA	ILYISFYFIL	4	10	1	100	0.0035
LSA	ILYISFYFILV	4	11	1	100
LSA	IQNHTLET	1739	8	1	100
LSA	IQNHTLETV	1739	9	1	100
LSA	IQNHTLETVN1	1739	11	1	100
LSA	IKYFMKL	1902	8	1	100
LSA	ITTNVEGRRDI	1704	11	1	100
LSA	IVDELSEDI	1894	9	1	100
LSA	IVDELSEDIT	1894	10	1	100
LSA	KADTICKNI	1631	8	1	100
LSA	KIIKNSEKDEI	24	11	1	100
LSA	KIKKGKKYEICT	1834	11	1	100
LSA	KLNKEGKL	116	8	1	100
LSA	KLNKEGKLI	116	9	1	100
LSA	KLQEQQRDL	1619	9	1	100
LSA	KLQGQQSDL	1585	9	1	100	0.0019
LSA	KLQGQQSDL	1126	9	1	100
LSA	KQVNKEKEKFI	1868	11	1	100
LSA	KTNRESIT	1698	8	1	100
LSA	KTINIRESITT	1698	9	1	100
LSA	KTNRESITNV	1698	11	1	100
LSA	LAEDLYGRL	1648	9	1	100
LSA	LAEDLYGRLEI	1648	11	1	100
LSA	LIDEEEDDEDL	1772	11	1	100
LSA	LIEICNENL	1809	8	1	100
LSA	LIEKNENLDDL	1809	11	1	100
LSA	LIFHJNGKI	17	9	1	100
LSA	LIFHINGKII	17	10	1	100	0.0002
LSA	LLIFHINGKI	16	10	1	100
LSA	LLIFHINGKII	16	11	1	100
LSA	LLRNLGVSENI	100	11	1	100
LSA	LQEQQRDL	1620	8	1	100
LSA	LQEQQSDL	1586	8	1	100
LSA	LQEQQSDLERT	1178	11	1	100
LSA	LQOQQSDL	1127	8	1	100
LSA	LQIVDELSEDI	1892	11	1	100
LSA	LTMSNVKNV	84	9	1	100	0.0010
LSA	LVNLLIFHI	13	9	1	100	0.0006
LSA	N1FLKENKL	109	9	1	100
LSA	NIGIYKEL	1799	8	1	100
LSA	NIGIYKELEDL	1799	11	1	100
LSA	NISDVNDFQI	1748	10	1	100
LSA	NLDDLDEGI	1815	9	1	100
LSA	NLERKKEHGDY	1637	11	1	100
LSA	NLGVSEN1	103	8	1	100
LSA	NLOVSENIFL	103	10	1	100
LSA	NLLIFHINGKI	15	11	1	100
LSA	NVEGRRDI	1707	8	1	100
LSA	NVKNVSQT	88	8	1	100
LSA	NVSQTNFKSL	91	10	1	100
LSA	NVSQTNFKSLL	91	11	1	100
LSA	QISKYEDEI	1756	9	1	100
LSA	QISKYEDEISA	1756	11	1	100
LSA	QIVDELSEDI	1893	10	1	100
LSA	QIVDELSEDIT	1893	11	1	100
LSA	QQRDLEQERL	1606	10	1	100
LSA	QQRDLEQERLA	1606	11	1	100
LSA	QQRDLEQERRA	1538	11	1	100
LSA	QQRDLEQRKA	1623	10	1	100
LSA	QQSDLEQDRL	1385	10	1	100
LSA	QQSDLEQDRLA	1385	11	1	100
LSA	QQSDLEQERL	1589	10	1	100
LSA	QQSDLEQDRLA	1589	11	1	100
LSA	QQSDLEQERRA	1572	11	1	100
LSA	QQSDLERT	1181	8	1	100
LSA	QQ6DLERTKA	1181	10	1	100
LSA	QQSDSEQERL	518	10	1	100
LSA	QQSDSEQERLA	518	11	1	100
LSA	QINFKSLL	94	8	1	100
LSA	QTNFKSLLRNL	94	11	1	100
LSA	QVNKEKEKFI	1869	10	1	100
LSA	RLEIPA1EL	1655	9	1	100
LSA	RQEDLEEKA	145	9	1	100
LSA	RQEDLEEKAA	145	10	1	100
LSA	RTKASKET	1187	8	1	100
LSA	RTKASKETL	1187	9	1	100
LSA	SADIQNHT	1736	8	1	100
LSA	SADIQNHTL	1736	9	1	100
LSA	SADIONITTLET	1736	11	1	100
LSA	SAEYDDSL	1765	8	1	100
LSA	SAEYDDSLI	1765	9	1	100
LSA	SIIEKTNRESI	I694	11	1	100
LSA	SLLRNLGV	99	8	1	100
LSA	SQTNFKSL	93	8	1	100
LSA	SQTNFKSLL	93	9	1	100
LSA	TLETVRISOV	1743	10	1	100
LSA	TLQEQQSDL	1194	9	1	100
LSA	TLQGQQSDL	157	9	1	100
LSA	TMSNVKNV	85	8	1	100
LSA	TMSNVICNVSQT	85	11	1	100
LSA	TTNVEGRRDI	1705	10	1	100
LSA	VLAEDLYGRL	1647	10	1	100
LSA	VLSHNSYEKT	60	10	1	100
LSA	YIPHQSSL	1672	8	1	100
LSA	YISFYFIL	6	8	1	100
LSA	YISFYFILV	6	9	1	100	0.0016
LSA	YISFYFILVNL	6	11	1	100
SSP2	AATPYAGEPA	525	10	8	80
SSP2	ATPYAGEPA	526	9	8	80
SSP2	EILHEGCTSEL	267	11	8	80
SSP2	EVCNDEVDL	41	9	8	80
SSP2	EVCNDEVDLVL	41	11	8	80
SSP2	EVDLYLLM	46	8	8	80
SSP2	FVVPGAATPYA	520	11	8	80
SSP2	GAATPYAGEPA	524	11	8	80
SSP2	ILHEGCTSEL	268	10	8	80
SSP2	LLSTNLPYGRT	121	11	8	80
SSP2	NLPYGRTNL	125	9	8	80
SSP2	SIRRHNWVNHA	58	11	8	80
SSP2	STNLPYGRT	123	9	8	80
SSP2	STNLPYQRTNI	123	11	8	80
SSP2	VVPGAATPYA	521	10	8	80
SSP2	WVNHAVPL	64	8	8	80
SSP2	WVNHAVPLA	64	9	8	80	0.0008
SSP2	WVNHAVPLAM	64	10	8	80
SSP2	YAGEPAPFDET	529	11	8	80
SSP2	ALLQVRKHL	136	9	9	90	0.0010
SSP2	DALLQVRKHL	135	10	9	90
SSP2	DAWNKEKALI	106	11	9	90
SSP2	DQPRPRGDNFA	302	11	9	90
SSP2	EIKYREEV	35	8	9	90
SSP2	IQDSLKESRKL	168	11	9	90
SSP2	IVDEIKYREEV	32	11	9	90
SSP2	LLQVRKHL	137	8	9	90
SSP2	LQVRKHLNDRI	138	11	9	90
SSP2	QVRKHLNDRI	139	10	9	90	0.0001
SSP2	SLICESRKL	171	8	9	90
SSP2	ALLACAGL	509	8	10	100
SSP2	ALLACAGLA	509	9	10	100	0.0006
SSP2	AMICLIQQL	72	8	10	100
SSP2	AMICLIQQLNL	72	10	10	100	0.0006
SSP2	AVCVEVEKT	233	9	10	100
SSP2	AVCVEVEKTA	233	10	10	100
SSP2	AVFGIGQGI	186	9	10	100	0.0001
SSP2	AVFGIGQGINV	186	11	10	100
SSP2	AVPLAMKL	68	8	10	100
SSP2	AVPLAMKLI	68	9	10	100	0.0001
SSP2	CAGLAYKFV	513	9	10	100
SSP2	CAGLAYKFVV	513	10	10	100	0.0015
SSP2	CVEVEKTA	235	8	10	100
SSP2	DASKNKEKA	106	9	10	100
SSP2	DASKNKD(AL	106	10	10	100
SSP2	DLDEPEQFRL	546	10	10	100	0.0001
SSP2	DLFLVNGRDV	19	10	10	100
SSP2	DVQNNIVDEI	27	10	10	100
SSP2	EIIRLHSDA	99	9	10	100
SSP2	ELHEGCT	267	8	10	100
SSP2	ETLGEEDKDL	538	10	10	100
SSP2	EVEKTASCGV	237	10	10	100
SSP2	FLIFFDLFL	14	9	10	100	1.2000
SSP2	FLIFFDLFLV	14	10	10	100	0.8000
SSP2	FLVNGRDV	21	8	10	100
SSP2	FMKAVCVEV	230	9	10	100	0.0290
SSP2	FVVPQAAT	520	8	10	100
SSP2	GIAGGLAL	503	8	10	100
SSP2	GIAGGLALL	503	9	10	100	0.0022
SSP2	GIAGGLALLA	503	10	10	100
SSP2	GIGQGTNV	189	8	10	100
SSP2	GIGQGINVA	189	9	10	100
SSP2	GINVAFNRFL	193	10	10	100
SSP2	GINVAFNRFLV	193	11	10	100
SSP2	GIPDSIQDSL	163	10	10	100
SSP2	GLALLACA	507	8	10	100
SSP2	GLALLACAGL	507	10	10	100	0.0170
SSP2	GLALLACAGLA	507	11	10	100
SSP2	GLAYKFVV	515	8	10	100
SSP2	GLAYKFVVPGA	515	11	10	100
SSP2	GTRSRKREI	260	9	10	100
SSP2	GTRSRKREIL	260	10	10	100
SSP2	GVKIAVFGI	182	9	10	100
SSP2	GVWDEWSPCSV	245	11	10	100
SSP2	HAVPLAMKL	67	9	10	100
SSP2	HAVPLAMKLI	67	10	10	100
SSP2	HLGNVKYL	3	8	10	100
SSP2	HLGNVKYLV	3	9	10	100	0.0017
SSP2	HLGNVKYLVI	3	10	10	100
SSP2	HLGNVKYLVIV	3	11	10	100
SSP2	HLNDRINRENA	143	11	10	100
SSP2	HVPNSEDRET	445	10	10	100
SSP2	LAGGIAGGL	500	9	10	100
SSP2	IAGGIAGGLA	500	10	10	100
SSP2	IAGGIAGGLAL	500	11	10	100
SSP2	LAGGLALL	504	8	10	100
SSP2	LAGGLALLA	504	9	10	100	0.0001
SSP2	IACTGLALLACA	504	11	10	100
SSP2	IAVFGIGQGI	185	10	10	100
SSP2	IIRLHSDA	100	8	10	100
SSP2	ILTDGIPDSI	159	10	10	100
SSP2	IVFLIFFDL	12	9	10	100	0.0024
SSP2	IVFLIFFDLFL	12	11	10	100
SSP2	KAVCVEVEKT	232	10	10	100
SSP2	KAVCVEVEKTA	232	11	10	100
SSP2	KIAGGIAGGL	499	10	10	100
SSP2	KIAGGIAGGLA	499	11	10	100
SSP2	KIAVFGIGQI	184	11	10	100
SSP2	KLIQQLNL	74	8	10	100
SSP2	LACAGLAYKFV	511	11	10	100
SSP2	LALLACAGL	508	9	10	100
SSP2	LALLACAGLA	508	10	10	100
SSP2	LAMKLIQQL	71	9	10	100
SSP2	LAMKLIQQLNL	71	11	10	100
SSP2	LAYKFVVPGA	516	10	10	100
SSP2	LAYICFVVPGAA	516	11	10	100
SSP2	LIFFDLFL	I5	8	10	100
SSP2	LIFFDLFLV	15	9	10	100	0.0890
SSP2	LLACAGLA	510	8	10	100
SSP2	LLMDCSGSI	51	9	10	100	0.0460
SSP2	LMDCSGSI	52	8	10	100
SSP2	LTDGIPDSI	160	9	10	100
SSP2	LVIVFLIFFDL	10	11	10	100
SSP2	LVNGRDVQNNI	22	11	10	100
SSP2	LVVILTDGI	156	9	10	100
SSP2	NANQLVVI	152	8	10	100
SSP2	NANQLVVIL	152	9	10	100
SSP2	NANQLVVILT	152	10	10	100
SSP2	NIPEDSEKEV	366	10	10	100
SSP2	NLYADSAWENV	213	11	10	100
SSP2	NQLVVILT	154	8	10	100
SSP2	NQLVVILTDGI	154	11	10	100
SSP2	NVAFNRFL	195	8	10	100
SSP2	NVAFNRFLV	195	9	10	100	0.0001
SSP2	NVIGPFMKA	225	9	I0	100	0.0002
SSP2	NVIGPFMKAV	225	10	10	100	0.0008
SSP2	NVKNVIGPFM	222	10	10	100
SSP2	NVKYLVIV	6	8	10	100
SSP2	NVKYLVIVFL	6	10	10	100
SSP2	NVKYLVIVFLI	6	11	10	100
SSP2	PAPFDETL	533	8	10	100
SSP2	PLANIKLIQQL	70	10	10	100
SSP2	QLVVILIDGI	155	10	10	100	0.0002
SSP2	RINRENANQL	147	10	10	100
SSP2	RINRENANQLV	147	11	10	100
SSP2	SAWENVKNV	218	9	10	100	0.0019
SSP2	SAWENVKNVI	218	10	10	100
SSP2	SIRRHNWV	58	8	10	100
SSP2	SQDNNGNRHV	437	10	10	100
SSP2	SVTCGKGT	254	8	10	100
SSP2	TLGEEDKDL	539	9	10	100	0.0001
SSP2	VAFNRFLV	196	8	10	100
SSP2	VIGPFMKA	226	8	10	100
SSP2	VIGPFMKAV	226	9	10	100	0.0004
SSP2	VIGPFMKAVCV	226	11	10	100
SSP2	VILTDGIPDSI	158	11	10	100
SSP2	VIVFLIFFDL	11	10	10	100	0.0038
SSP2	VQNNIVDEI	28	9	10	100
SSP2	VVILTDGI	157	8	10	100
SSP2	YADSAWENV	215	9	10	100
SSP2	YLLMDCSGSI	50	10	10	100	0.1700
SSP2	YLVIVFLI	9	8	10	100

Protein	A*0202	A*0203	A*0206	A*6802	Seq. Id
CSP					102
CSP					103
CSP					104
CSP					105
CSP					106
CSP					107
CSP					108
CSP					109
CSP					110
CSP					111
CSP					112
CSP					113
CSP					114
CSP					115
CSP					116
CSP					117
CSP					118
CSP					119
CSP					120
CSP					121
CSP					122
CSP					123
CSP					124
CSP					125
CSP					126
CSP					127
CSP					128
CSP					129
CSP					130
CSP					131
CSP					132
CSP					133
CSP					134
CSP					135
CSP					136
CSP					137
CSP					138
CSP					139
CSP					140
CSP					141
CSP					142
CSP					143
CSP					144
CSP					145
CSP					146
CSP					147
CSP					148
CSP					149
CSP					150
CSP					151
CSP					152
CSP					153
CSP					154
CSP					155
CSP					156
CSP					157
CSP					158
CSP					159
CSP					160
CSP					161
CSP					162
CSP					163
CSP					164
CSP					165
CSP					166
CSP					167
CSP					168
EXP					169
EXP					170
EXP					171
EXP					172
EXP					173
EXP					174
EXP					175
EXP					176
EXP					177
EXP					178
EXP					179
EXP					180
EXP					181
EXP					182
EXP					183
EXP					184
EXP					185
EXP					186
EXP					187
EXP					188
EXP					189
EXP					190
EXP					191
EXP					192
EXP					193
EXP					194
EXP					195
EXP					196
EXP					197
EXP					198
EXP					199
EXP					200
EXP					201
EXP					202
EXP					203
EXP					204
EXP					205
EXP					206
EXP					207
EXP					208
EXP					209
EXP					210
EXP					211
EXP					212
EXP					213
EXP					214
EXP					215
EXP					216
EXP					217
EXP					218
EXP					219
EXP					220
EXP					221
EXP					222
EXP					223
EXP					224
EXP					225
EXP					226
EXP					227
EXP					228
EXP					229
EXP					230
EXP					231
EXP					232
EXP					233
EXP					234
DT					235
EXP					236
EXP					237
EXP					238
EXP					239
EXP					240
EXP					241
LSA					242
LSA					243
LSA					244
LSA					245
LSA					246
LSA					247
LSA					248
LSA					249
LSA					250
LSA					251
LSA					252
LSA					253
LSA					255
LSA					256
LSA					257
LSA					258
LSA					259
LSA					260
LSA					261
LSA					262
LSA					263
LSA					264
LSA					265
LSA					266
LSA					267
LSA					268
LSA					269
LSA					270
LSA					271
LSA					272
LSA					273
LSA					274
LSA					275
LSA					276
LSA					277
LSA					278
LSA					279
LSA					280
LSA					281
LSA					282
LSA					283
LSA					284
LSA					285
LSA					286
LSA					287
LSA					288
LSA					289
LSA					290
LSA					291
LSA					292
LSA					293
LSA					294
LSA					295
LSA					296
LSA					297
LSA					298
LSA					299
LSA					300
LSA					301
LSA					302
LSA					303
LSA					304
LSA					305
LSA					306
LSA					307
LSA					308
LSA					309
LSA					310
LSA					311
LSA					312
LSA					313
LSA					314
LSA					315
LSA					316
LSA					317
LSA					318
LSA					319
LSA					320
LSA					321
LSA					322
LSA					323
LSA					324
LSA					325
LSA					326
LSA					327
LSA					328
LSA					329
LSA					330
LSA					331
LSA					332
LSA					333
LSA					334
LSA					335
LSA					336
LSA					337
LSA					338
LSA					339
LSA					340
LSA					341
LSA					342
LSA					343
LSA					344
LSA					345
LSA					346
LSA					347
LSA					348
LSA					349
LSA					350
LSA					351
LSA					352
LSA					353
LSA					354
LSA					355
LSA					356
LSA					357
LSA					258
LSA					359
LSA					360
LSA					361
LSA					362
LSA					363
LSA					364
LSA					365
LSA					366
LSA					367
LSA					368
LSA					369
LSA					370
LSA					371
LSA					372
LSA					373
LSA					374
LSA					375
LSA					376
LSA					377
LSA					378
LSA					379
LSA					380
LSA					381
LSA					382
LSA					383
LSA					384
LSA					385
LSA					386
LSA					387
LSA					388
LSA					389
LSA					390
LSA					391
LSA					392
LSA					393
LSA					394
LSA					395
LSA					396
LSA					397
LSA					398
LSA					399
LSA					400
LSA					401
LSA					402
LSA					403
LSA					404
LSA					405
SSP2					406
SSP2					407
SSP2					408
SSP2					409
SSP2					410
SSP2					411
SSP2					412
SSP2					413
SSP2					414
SSP2					415
SSP2					416
SSP2					417
SSP2					418
SSP2					419
SSP2					420
SSP2					421
SSP2					422
SSP2					423
SSP2					424
SSP2					425
SSP2					426
SSP2					427
SSP2					428
SSP2					429
SSP2					430
SSP2					431
SSP2					432
SSP2					433
SSP2					434
SSP2					435
SSP2					436
SSP2					437
SSP2					438
SSP2					439
SSP2					440
SSP2					441
SSP2					442
SSP2					443
SSP2					444
SSP2					445
SSP2					446
SSP2					447
SSP2					448
SSP2					449
SSP2					450
SSP2					451
SSP2					452
SSP2					453
SSP2					454
SSP2					455
SSP2					456
SSP2					457
SSP2					458
SSP2					459
SSP2					460
SSP2					461
SSP2					462
SSP2					463
SSP2					464
SSP2					465
SSP2					466
SSP2					467
SSP2					468
SSP2					469
SSP2					470
SSP2					471
SSP2					472
SSP2					473
SSP2					474
SSP2					475
SSP2					476
SSP2					477
SSP2					478
SSP2					479
SSP2					480
SSP2					481
SSP2					482
SSP2					483
SSP2					484
SSP2					485
SSP2					486
SSP2					487
SSP2					488
SSP2					489
SSP2					490
SSP2					491
SSP2					492
SSP2					493
SSP2					494
SSP2					495
SSP2					496
SSP2					497
SSP2					498
SSP2					499
SSP2					500
SSP2					501
SSP2					502
SSP2					503
SSP2					504
SSP2					505
SSP2					506
SSP2					507
SSP2					508
SSP2					509
SSP2					510
SSP2					511
SSP2					512
SSP2					513
SSP2					514
SSP2					515
SSP2					516
SSP2					517
SSP2					518
SSP2					519
SSP2					520
SSP2					521
SSP2					522
SSP2					523
SSP2					524
SSP2					525
SSP2					526
SSP2					327
SSP2					528
SSP2					529
SSP2					530
SSP2					531
SSP2					532
SSP2					533
SSP2					534
SSP2					535
SSP2					536
SSP2					337
SSP2					538
SSP2					339
SSP2					540
SSP2					541
SSP2					542
SSP2					543
SSP2					544
SSP2					545
SSP2					546
SSP2					547
SSP2					548
SSP2					549
SSP2					550
SSP2					551
SSP2					552
SSP2					553
SSP2					554
SSP2					555
SSP2					556
SSP2					557

TABLE IX
Malaria A03 Super Motif Peptides With Binding Data

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*301
CSP	DIEKKICK	402	8	19	100
CSP	DIEKKICKMEK	402	11	19	100
CSP	ELEMNYYGK	50	9	19	100	0.0001
CSP	KLRKPKHK	104	8	19	100
CSP	KLRKPKHKK	104	9	19	100	0.1300
CSP	KLRKPKHKKLK	104	11	19	100
CSP	NANANNAVK	335	9	16	84	0.0001
CSP	NANPNANPNK	304	10	19	100	0.0005
CSP	NMPNDPNR	323	8	19	100
CSP	SVTCGNGIQVR	374	11	19	100
CSP	VTCGNGIQVR	375	10	19	100	0.0005
CSP	YSLKKNSR	63	8	19	100
EXP	ALFFIIFNK	10	9	1	100	1.1000
EXP	DLISDMIK	52	8	1	100
EXP	DLISDMIKK	52	9	1	100	0.0001
EXP	DVHDLISDMIK	49	11	1	100
EXP	ELVEVNKR	63	8	1	100
EXP	ELVEVNKRK	63	9	1	100	0.0001
EXP	ELVEVNKRKSK	63	11	1	100
EXP	ESLAEKTNK	19	9	1	100	0.0001
EXP	EVNKRKSK	66	8	1	100
EXP	EVNKRKSKYK	66	10	1	100	0.0005
EXP	FLALFFIIFNK	8	11	1	100
EXP	GLVLYNTEK	97	9	1	100	0.0069
EXP	GLVLYNTEKGR	97	11	1	100
EXP	GSGVSSKK	30	8	1	100
EXP	GSGVSSKKK	30	9	1	100	0.0003
EXP	GSGVSSKKKNK	30	11	1	100
EXP	GTGSGVSSK	28	9	1	100	0.0039
EXP	GTGSGVSSKK	28	10	1	100	0.0071
EXP	GTGSGVSSKKK	28	11	1	100
EXP	GVGLVLYNTEK	95	11	1	100
EXP	GVSSKKKNK	32	9	1	100	0.0001
EXP	GVSSKKKNKK	32	10	1	100	0.0011
EXP	IIFNKESLAEK	14	11	1	100
EXP	LALFFTIIFNK	9	10	1	100	0.014
EXP	LISDMIKK	53	8	1	100
EXP	LVEVNKRK	64	8	1	100
EXP	LVEVNKRKSK	64	10	1	100	0.0005
EXP	LVLYNTEK	98	8	1	100
EXP	LVLYNTEKGR	98	10	1	100	0.0005
EXP	NTEKGRHPFK	102	10	1	100	0.0047
EXP	SLAEKTNK	20	8	1	100
EXP	SSKKKNKK	34	8	1	100
EXP	VLYNTEKGRS	99	9	1	100	0.0110
EXP	VSSKKKNK	33	8	1	100
EXP	VSSKKKNKK	33	9	1	100	0.0001
LSA	AIELPSENER	1660	10	1	100	0.0001
LSA	DIHKGHLEEK	1713	10	1	100	0.0004
LSA	DIHKGHLEEKK	1713	11	1	100
LSA	DITKYFMK	1901	8	1	100
LSA	DLDEGIEK	1818	8	1	100
LSA	DLEEKAAK	148	8	1	100
LSA	DLEQDRLAK	1388	9	1	100	0.0001
LSA	DLEQDRLAKEK	1388	11	1	100
LSA	DLEQERLAK	1609	9	1	100	0.0001
LSA	DLEQERLAKEK	1609	11	1	100
LSA	DLEQERLANEK	1524	11	1	100

LSA	DLEQERRAK	1575	9	1	100	0.0001
LSA	DLEQERRAIUEK	1575	11	1	100
LSA	DLEQRKADTK	1626	10	1	100	0.0001
LSA	DLEQRKADTKK	1626	11	1	100
LSA	DLERTICASK	1184	9	1	100	0.0001
LSA	DSEQERLAK	521	9	1	100	0.0001
LSA	CGEQERLAKEK	521	11	1	100
LSA	DSKEISIIEK	1689	10	1	100	0.0001
LSA	DTKKNLER	1633	8	1	100
LSA	DTKKNLERK	1633	9	1	100	0.0001
LSA	DTKKKNLERKK	1633	10	1	100	0.0001
LSA	DVLAEDLYGR	1646	10	1	100	0.0001
LSA	DVNDFQISK	1751	9	1	100	0.0001
LSA	EIIKSNLR	33	8	1	100
LSA	EISIIEKTNR	1692	10	1	100	0.0001
LSA	ELEDLIEK	1805	8	1	100
LSA	ELPSENER	1662	8	1	100
LSA	ELSEDITK	1897	8	1	100
LSA	ELSEEKIK	1829	8	1	100
LSA	ELSEEKIKK	1829	9	1	100	0.0002
LSA	ELSEEKIKKGK	1829	11	1	100
LSA	ELTMSNVK	83	8	1	100
LSA	ESITTNVEGR	1702	10	1	100	0.0001
LSA	ESITTNVEGRR	1702	11	1	100
LSA	FLKENKLNK	111	9	1	100	0.0260
LSA	GSIKPEQK	1725	8	1	100
LSA	GSIKPEQKEDK	1725	11	1	100
LSA	GSSNSRNR	42	8	1	100
LSA	GVSENIFLK	105	9	1	100	0.2700
LSA	HIINDDDDK	126	9	1	100	0.0002
LSA	HIINDDDDKK	126	10	1	100	0.0001
LSA	HIINDDDDKKK	126	11	1	100
LSA	HIKKYKNDK	1860	9	1	100	0.0002
LSA	HINGKIIK	20	8	1	100
LSA	HLEEKICDGSIK	1718	11	1	100
LSA	HVLSHNSYEK	59	10	1	100	0.0170
LSA	QNDDDDK	127	8	1	100
LSA	IINDDDDKK	127	9	1	100	0.0002
LSA	IINDDDDIUCK	127	10	1	100	0.0001
LSA	ISDVNDFQISK	1749	11	1	100
LSA	ISIIEKTNR	1693	9	1	100	0.0001
LSA	ITTNVEGR	1704	8	1	100
LSA	ITINVEGRR	1704	9	1	100	0.0002
LSA	IVDELSEDMC	1894	11	1	100
LSA	ICADIKKNLER	1631	10	1	100	0.0001
LSA	KADTKKNLERK	1631	11	1	100
LSA	KIIKNSEK	24	8	1	100
LSA	ICQUCGKKYEK	1834	10	1	100	0.0081
LSA	KLQEQQSDLER	1177	11	1	100
LSA	KSLYDEHIK	1854	9	1	100	0.0005
LSA	KSLYDEHIKIC	1854	10	1	100	0.0094
LSA	KSSEELSEEK	1825	10	1	100	0.0001
LSA	KTKDNNFK	1843	8	1	100
LSA	KTKNNENNK	68	9	1	100	0.0028
LSA	LAEDLYGR	1648	8	1	100
LSA	LAKEKLQEQQR	1615	11	1	100
LSA	LANEKLQEQQR	1530	11	1	100
LSA	LIFHINGK	17	8	1	100
LSA	LIGHINKKIIK	17	11	1	100
LSA	LLIFHINKGK	16	9	1	100	0.0260
LSA	LSEDITKYFMK	1898	11	1	100
LSA	LSEEKIKK	1830	8	1	100
LSA	LSEEKIKKGK	1830	10	1	100	0.0004
LSA	LSEEKIKKGKK	1830	11	1	100
LSA	LSHNSYEK	61	8	1	100
LSA	LSHNSYEKTK	61	10	1	100	0.0004
LSA	NIFLKENK	109	8	1	100
LSA	NKFLKENKLNK	109	11	1	100
LSA	LNDDLDEGIEK	1815	11	1	100
LSA	NLGVSENTFLK	103	11	1	100
LSA	NLLIGHINGK	15	10	1	100	0.0049
LSA	NLRSGSSNSR	38	10	1	100	0.0004
LSA	NSEKDETIK	28	9	1	100	0.0002
LSA	NSRNRINEEK	45	10	1	100	0.0004
LSA	NVEGRRDIHK	1707	10	1	100	0.0004
LSA	NVKNVSQTNFK	88	11	1	100
LSA	NVSQTNFK	91	8	1	100
LSA	PAIELPSENER	1659	11	1	100
LSA	QSDLEQDR	1386	8	1	100
LSA	QSDLEQDRLAK	1386	11	1	100
LSA	QSKLEQER	1590	8	1	100
LSA	QSDLEQERLAK	1590	11	1	100
LSA	QSKLEQERR	1573	9	1	100	0.0002
LSA	QSDLEQERRAK	1573	11	1	100
LSA	QSDLERTK	1182	8	1	100
LSA	QSDLERTKASK	1182	11	1	100
LSA	QSDSEQER	519	8	1	100
LSA	QSDSEQERLAK	519	11	1	100
LSA	QSSLPQDNR	1676	9	1	100	0.0002
LSA	QTNFKSLLR	94	9	1	100	0.0320
LSA	QVNKEKEK	1869	8	1	100
LSA	QVNKEKEKFIK	1869	11	1	100
LSA	RINEEKHEK	49	9	1	100	0.0033
LSA	RINEEKHEKK	49	10	1	100	0.0024
LSA	RSGSSNSR	40	8	1	100
LSA	RSGSSNSRNR	40	10	1	100	0.0011
LSA	SIIEKTNR	1694	8	1	100
LSA	SIKPEQKEDK	1726	10	1	100	0.0002
LSA	SITTNVEGR	1703	9	1	100	0.0002
LSA	SITTNVEGRR	1703	10	1	100	0.0002
LSA	SLPQDNRDNSR	1678	11	1	100
LSA	SLYDEHIK	1855	8	1	100
LSA	SLYDEHIKK	1855	9	1	100	0.0460
LSA	SLYDEHIKKYK	1855	11	1	100
LSA	SSEELSEEK	1826	9	1	100	0.0002
LSA	SSEELSEEKIK	1826	11	1	100
LSA	SSLPQDNR	1677	8	1	100
LSA	TTNVEGRR	1705	8	1	100
LSA	VLAEDLYGR	1647	9	1	100	0.0013
LSA	VLSHNSYEK	60	9	1	100	0.0280
LSA	VLSHNSYEKTK	60	11	1	100
LSA	VSENTIFLK	106	8	1	100
LSA	VSENIFLKENK	106	11	1	100
LSA	VSQTNFKSLLR	92	11	1	100
LSA	YIKGQDENR	137	9	1	100	0.0025
SSP2	ALLACAGLAYK	509	11	10	100
SSP2	AVCVEVEK	233	8	10	100
SSP2	CSVTCGKGTR	253	10	10	100	0.0002
SSP2	DALLQVRK	135	8	9	90
SSP2	DASKNKEK	106	8	10	100
SSP2	DIPKKPENK	392	9	10	100	0.0004
SSP2	DLDEPEQFR	546	9	10	100	0.0002
SSP2	DLFLVNGR	19	8	10	100
SSP2	DSAWENVK	217	8	10	100
SSP2	DSIQDSLK	166	8	10	100
SSP2	DSIQDSLKESR	166	11	10	100
SSP2	DSLKESRK	170	8	9	90
SSP2	DVPKNPEDDR	378	10	10	100	0.0002
SSP2	DVQNNIVDEIK	27	11	10	100
SSP2	EIIRLHSDASK	99	11	10	100
SSP2	ELQEQCEEER	276	10	8	80	0.0002
SSP2	ETLGEEDK	538	8	10	100
SSP2	EVPSDVPK	374	8	10	100
SSP2	FLVGCHPSDCK	201	11	10	100
SSP2	FMKAVCVEVEK	230	11	10	100
SSP2	GINVAFNR	193	8	10	100
SSP2	GIPDSIQDSLK	163	11	10	100
SSP2	HAVPLAMK	67	8	10	100
SSP2	HLNDRINR	143	8	10	100
SSP2	HSDASKNK	104	8	10	100
SSP2	HSDASKNKEK	104	10	10	100	0.0004
SSP2	HVPNSEDR	445	8	10	100
SSP2	HVPNSEDRETR	445	11	9	90
SSP2	IIRLHSDASK	100	10	10	100	0.0230
SSP2	1VDEIKYR	32	8	9	90
SSP2	KAVCVEVEK	232	9	10	100	0.0004
SSP2	KVLDNERK	421	8	8	80
SSP2	LACAGLAYK	511	9	10	100	0.0240
SSP2	LLACAGLAYK	510	10	10	100	0.9500
SSP2	LLMDCSGSIR	51	10	10	100	0.0004
SSP2	LLMDCSGSIRR	51	11	10	100
SSP2	LLQVRKHLNDR	137	11	9	90
SSP2	LLSTNLPYGR	121	10	8	80	0.0017
SSP2	LMDCSGSIR	52	9	10	100	0.0004
SSP2	LMDCSGSIRR	52	10	10	100	0.0015
SSP2	LSTNLPYGR	122	9	8	80	0.0004
SSP2	LVGCHPSDGK	202	10	10	100	0.0004
SSP2	NIPEDSEK	366	8	10	100
SSP2	NIVDEIKYR	31	9	9	90	0.0005
SSP2	NLPNDKSDR	406	9	10	100	0.0005
SSP2	NSEDRETFT	448	8	9	90
SSP2	NVIGPFMK	225	8	10	100
SSP2	NVICNVIGPFMK	222	11	10	100
SSP2	PSPNPEEGK	328	9	10	100	0.0005
SSP2	QSQDNNGNR	436	9	10	100	0.0005
SSP2	QVRKHLNDR	139	9	9	90	0.0005
SSP2	RLHSDASK	102	8	10	100
SSP2	RLHSDASKNK	102	10	10	100	0.0240
SSP2	SIQDSLKESR	167	10	10	100	0.0004
SSP2	SIQDSLKESRK	167	11	9	90
SSP2	SLLSTNLPYGR	120	11	8	80
SSP2	STNLPYGR	123	8	8	80
SSP2	SVTCGKGTR	254	9	10	100	0.0005
SSP2	SVTCGKGTRSR	254	11	10	100
SSP2	VTCGKGTR	255	8	10	100
SSP2	VPCGKGTISR	255	10	10	100	0.0004
SSP2	VTCGKGTRSRK	255	11	10	100
SSP2	WSPCSVTCGK	250	10	10	100	0.0004
SSP2	WVNHAVPLAMK	64	11	8	80
SSP2	YADSAWENVK	215	10	10	100	0.0004
SSP2	YLLMDCSGSIR	50	11	10	100

Protein	A*1101	A*3101	A*3301	A*6801	Seq id.
CSP					558
CSP					559
CSP	0.0003				560
CSP					561
CSP	0.0037				562
CSP					563
CSP	0.0002	0.0006	0.0096	0.0210	564
CSP	0.0021	0.0009	0.0009	0.0054	565
CSP					566
CSP					567
CSP	0.0340				568
CSP					569
EXP	1.2000				570
EXP					571
EXP	0.0003				572
EXP					573
EXP					574
EXP	0.0002				575
EXP					576
EXP	0.0002	0.0004	0.0110	0.0260	577
EXP					578
EXP	0.0002				579
EXP					580
EXP	0.0055				581
EXP					582
EXP					583
EXP	0.0065	0.0004	0.0010	0.0002	584
EXP					585
EXP	0.0180				586
EXP	0.0340				587
EXP					588
EXP					589
EXP	0.0002				590
EXP	0.0002				591
EXP					592
EXP	0.0530	0.0072	0.0076	0.0039	593
EXP					594
EXP					595
EXP	0.0002				596
EXP					597
EXP	0.0002				598
EXP	0.0080				599
EXP					600
EXP					601
EXP	0.0007	0.0039	0.0055	0.0022	602
EXP					603
EXP	0.0002	0.0004	0.0010	0.0002	604
LSA	0.0002	0.0009	0.0008	0.0029	605
LSA	0.0002	0.0009	0.0055	0.0046	606
LSA					607
LSA					608
LSA					609
LSA					610
LSA	0.0002				611
LSA					612
LSA	0.0002				613
LSA					614
LSA					615
LSA	0.0002				616
LSA					617
LSA	0.0002				618
LSA					619
LSA	0.0002				620
LSA	0.0002	0.0004	0.0010	0.0002	621
LSA					622
LSA	0.0002				623
LSA					624
LSA	0.0002				625
LSA	0.0002				626
LSA	0.0002				627
LSA	0.0018				628
LSA					629
LSA	0.0002				630
LSA					631
LSA					632
LSA					633
LSA					634
LSA	0.0002				635
LSA					636
LSA					637
LSA	0.0002				638
LSA					639
LSA	0.0005				640
LSA					641
LSA					642
LSA					643
LSA	0.6600				644
LSA	0.0002				645
LSA	0.0002	0.0009	0.0009	0.0003	646
LSA					647
LSA	0.0002				648
LSA					649
LSA					650
LSA	0.0140				651
LSA					652
LSA	0.0002				653
LSA	0.0002				654
LSA					655
LSA	0.0008	0.0320	0.0150	0.0054	656
LSA					657
LSA	0.0007	0.0025	0.0043	0.3200	658
LSA					659
LSA	0.0002	0.0086	0.0011	0.0003	660
LSA					661
LSA					662
LSA	0.0007	0.0042	0.0009	0.0003	663
LSA					664
LSA	0.0340	0.0004	0.0010	0.0002	665
LSA	0.0490				666
LSA	0.0009				667
LSA					668
LSA	0.0038				669
LSA					670
LSA					671
LSA					672
LSA					673
LSA					674
LSA	0.0100				675
LSA					676
LSA					677
LSA	0.0002				678
LSA					679
LSA					680
LSA	0.0002				681
LSA					682
LSA					683
LSA					684
LSA					685
LSA	0.0008				686
LSA	0.0002				687
LSA	0.0002	0.0004	0.0010	0.0002	688
LSA	0.0002				689
LSA	0.0002				690
LSA					691
LSA					692
LSA					692
LSA					694
LSA					695
LSA					696
LSA					697
LSA	0.0002	0.0006	0.0005	0.0005	698
LSA					699
LSA					700
LSA					701
LSA					702
LSA					703
LSA	0.0013	0.0150	0.014	0.0480	704
LSA	0.0440	0.0820	0.0180	0.1300	705
LSA					706
LSA					707
LSA	0.0370				708
LSA	0.0018	0.0009	0.0009	0.0003	709
LSA					710
LSA	0.0002				711
LSA					712
LSA	0.0002	0.0009	0.0009	0.0003	713
LSA	0.0027				714
LSA	0.0002				715
LSA					716
LSA					717
LSA	0.4100				718
LSA					719
LSA	0.0017	0.0004	0.0010	0.0002	720
LSA					721
LSA					722
LSA					723
LSA	0.0004	0.0083	0.0220	0.0032	724
LSA	0.0280				725
LSA					726
LSA					727
LSA					728
LSA					729
LSA	0.0002				730
SSP2					731
SSP2					732
SSP2	0.0002				733
SSP2					734
SSP2					735
SSP2	0.0002				736
SSP2	0.0002	0.0004	0.0170	0.0002	737
SSP2					738
SSP2					739
SSP2					740
SSP2					741
SSP2					742
SSP2	0.0002				743
SSP2					744
SSP2					745
SSP2	0.0002				746
SSP2					747
SSP2					748
SSP2					749
SSP2					750
SSP2					751
SSP2					752
SSP2					753
SSP2					754
SSP2					755
SSP2	0.0002				756
SSP2					757
SSP2					758
SSP2	0.0002	0.0009	0.0009	0.0013	759
SSP2					760
SSP2	0.0076	0.0009	0.0005	0.0029	761
SSP2					762
SSP2	0.0290	0.0150	0.3200	0.1100	763
SSP2	0.0870				764
SSP2	0.0005				765
SSP2					766
SSP2					767
SSP2	0.0025				768
SSP2	0.0002	0.0370	0.0430	0.0010	769
SSP2	0.0002				770
SSP2	0.0100	0.2900	0.0760	0.2700	771
SSP2	0.0002				772
SSP2					773
SSP2	0.0002				774
SSP2	0.0002				775
SSP2					776
SSP2					777
SSP2					778
SSP2	0.0002	0.0004	0.0010	0.0002	779
SSP2	0.0002	0.0020	0.0093	0.0018	780
SSP2	0.0002	0.0041	0.0570	0.0002	781
SSP2					782
SSP2	0.0002				783
SSP2	0.0009				784
SSP2					785
SSP2					786
SSP2					787
SSP2	0.0009	0.0031	0.0039	0.0310	788
SSP2					789
SSP2					790
SSP2	0.0017				791
SSP2					792
SSP2	0.0002				793
SSP2					794
SSP2	0.0002	0.0009	0.0009	0.0077	795
SSP2					796

TABLE X
Malaria A24 Super Motif Peptides With Binding Information

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*201	Seq Id.

CSP	AILSVSSF	6	8	18	95		797
CSP	AILSVSSFL	6	9	19	100		798
CSP	AILSVSSFLF	6	10	19	100		799
CSP	ALFQEYQCY	18	9	19	100		800
CSP	CYGSSSNTRVL	25	11	19	100		801
CSP	DIEKKICKM	402	9	19	100		802
CSP	DYENDIEKKI	398	10	18	95		803
CSP	ELNYDNAGI	37	9	18	95		804
CSP	ELNYDNAGINL	37	11	18	95		805
CSP	EMNYYGKQENW	52	11	19	100		806
CSP	FLFVEALF	13	8	19	100		807
CSP	FLFVEALFQEY	13	11	19	100		808
CSP	FVEALFQEY	15	9	19	100		809
CSP	GINLYNEL	44	8	18	95		810
CSP	GINLYNELEM	44	10	18	95		811
CSP	GLIMVLSF	425	8	19	100		812
CSP	GLIMVLSFL	425	9	19	100		813
CSP	GLIMVLSFLF	425	10	19	100		814
CSP	GLIMVLSFLFL	425	11	19	100		815
CSP	HIEQYLKKI	350	9	15	79		816
CSP	ILSVSSFL	7	8	19	100		817
CSP	ILSVSSFLF	7	9	19	100		818
CSP	IMVLSFLF	427	8	19	100		819
CSP	IMVLSFLFL	427	9	19	100	0.0008	820
CSP	KIQNSLSTEW	361	10	15	79		821
CSP	KLAILSVSSF	4	10	19	100		822
CSP	KLAILSVSSFL	4	11	19	100		823
CSP	KLRKPICHICKL	104	10	19	100		824
CSP	KMEKCSSVF	409	9	19	100		825
CSP	LFQEYQCY	19	8	19	100		826
CSP	LFVEALFQEY	14	10	19	100		827
CSP	LIMVLSFL	426	8	19	100		828
CSP	LIMVLSFLF	426	9	19	100		829
CSP	LIMVLSFLFL	426	10	19	100		830
CSP	LYNELEMNY	47	9	19	100		831
CSP	LYNELEMNYY	47	10	19	100		832
CSP	MMRKLAIL	1	8	19	100		833
CSP	MVLSFLFL	428	8	19	100		834
CSP	NLYNELEM	46	8	19	100		835
CSP	NLYNELEIINY	46	10	19	100		836
CSP	NLYNELINNYY	46	11	19	100		837
CSP	NTRVLNEL	31	8	19	100		838
CSP	NTRYLNELNY	31	10	19	100		839
CSP	NVVNSSIGL	418	9	19	100		840
CSP	NVVNSSIGLI	418	10	19	100		841
CSP	NVVNSSIGLIM	418	11	19	100		842
CSP	NYDNAGINL	39	9	18	95	0.0004	843
CSP	NYDNAGINLY	39	10	18	95		844
CSP	NYYGKQENW	54	9	19	100		845
CSP	NYYGKQENWY	54	10	19	100		846
CSP	RVLNELNY	33	8	19	100		847
CSP	SFLFVEAL	12	8	19	100		848
CSP	SFLFVEALF	12	9	19	100		849
CSP	SIGLIMVL	423	8	19	100		850
CSP	SIGLIMVLSF	423	10	19	100		851
CSP	SIGLIMVLSFL	423	11	19	100		852
CSP	SLKKNSRSL	64	9	19	100		853
CSP	SVFNVVNSSI	415	10	19	100		854
CSP	SVSSFLFVEAL	9	11	19	100		855
CSP	SVTCGNGI	374	8	19	100		856
CSP	VFNVVNSSI	416	9	19	100		857
CSP	VFNVVNSSIGL	416	11	19	100		858
CSP	VTCGNGIQVRI	375	11	19	100		859
CSP	VVNSSIGL	419	8	19	100		860
CSP	VVNSSIGLI	419	9	19	100		861
CSP	VVNSSIGL1M	419	10	19	100		862
CSP	WYSLKKNSRSL	62	11	19	100		863
CSP	YLKKIQNSL	358	9	15	79		864
CSP	YYGKQENW	55	8	19	100		865
CSP	YYGKQENWY	55	9	19	100		866
CSP	YYGKQENWYSL	55	11	19	100		867
EXP	ATSVLAGL	77	8	1	100		868
EXP	ATSVLAGLL	77	9	1	100		869
EXP	DMIKKEEEL	56	9	1	100		870
EXP	DVHDLISDM	49	9	1	100		871
EXP	DVHDLISDMI	49	10	1	100		872
EXP	EVNKRKSKY	66	9	1	100		873
EXP	EVNKRICSKYKL	66	11	1	100		874
EXP	FFIIFNKESL	12	10	1	100		875
EXP	FFLALFFI	7	8	1	100		876
EXP	FFLALFFII	7	9	1	100		877
EXP	FFLALFFIIF	7	10	1	100		878
EXP	FITFNKESL	13	9	1	100		879
EXP	FLALFFII	8	8	1	100		880
EXP	FLALFFIIF	8	9	1	100		881
EXP	GLLGNVSTVL	83	10	1	100		882
EXP	GLLGNVSTVLL	83	11	1	100		883
EXP	IIFNKESL	14	8	1	100		884
EXP	ILSVFFLAL	3	9	1	100		885
EXP	ILSVFFLALF	3	10	1	100		886
EXP	ILSVFFLALFF	3	11	1	100		887
EXP	KILSVFFL	2	8	1	100		888
EXP	KILSVFFLAL	2	10	1	100		889
EXP	KILSVFFLALF	2	11	1	100		890
EXP	KLATSVLAGL	75	10	1	100		891
EXP	KLATSVLAGLL	75	11	1	100		892
EXP	KYKLATSVL	73	9	1	100	0.0960	893
EXP	LFFIIFNICESL	11	11	1	100		894
EXP	LIDVHDLI	47	8	1	100		895
EXP	LIDVHDLISDM	47	11	1	100		896
EXP	LLGGVGLVL	92	9	1	100		897
EXP	LLGGVGLVLY	92	10	1	100		898
EXP	LLGNVSTVL	84	9	1	100		899
EXP	LLGNVSTVLL	84	10	1	100		900
EXP	LVEVNICRICSKY	64	11	1	100		901
EXP	LYNTEKGRHPF	100	11	1	100		902
EXP	MIKKEEEL	57	8	1	100		903
EXP	NTEKGRHPF	102	9	1	100		904
EXP	NTEKGRHPFKI	102	11	1	100		905
EXP	PLIDVHDL	46	8	1	100		906
EXP	PLIDVHDLI	46	9	1	100		907
EXP	STVLLGGVGL	89	10	1	100		908
EXP	SVFFLALF	5	8	1	100		909
EXP	SVFFLALFF	5	9	1	100		910
EXP	SVFFLALFFI	5	10	1	100		911
EXP	SVFFLALFFII	5	11	1	100		912
EXP	TVLLGGVGL	90	9	1	100		913
EXP	TVLLGGVQLVL	90	11	1	100		914
EXP	VFFLALFF	6	8	1	100		915
EXP	VFFLALFFI	6	9	1	100		916
EXP	VFFLALFFII	6	10	1	100		917
EXP	VFFLALFFIIF	6	11	1	100		918
EXP	VLLCrGVGL	91	8	1	100		919
EXP	VLLGGVGLVL	91	10	1	100		920
EXP	VLLGGVGLVLY	91	11	1	100		921
LSA	DFQISKYEDEI	1754	11	1	100		922
LSA	DITKYFMKI	1901	9	1	100		923
LSA	DLDEFKPI	1781	8	1	100		924
LSA	DLDEFKFIVQY	1781	11	1	100		925
LSA	DLEEXAAKETL	148	11	1	100		926
LSA	DLIEXNENL	1808	9	1	100		927
LSA	DLYGRLEI	1651	8	1	100		928
LSA	DLYGRLEIPAI	1651	11	1	100		929
LSA	DVLAEDLY	1646	8	1	100		930
LSA	DVLAEDLYGRL	1646	11	1	100		931
LSA	DVNDFQISKY	1751	10	1	100		932
LSA	EFXPIVQY	1784	8	1	100		933
LSA	EFKPIVQYDNF	1784	11	1	100		934
LSA	ERQIVDEL	1890	9	1	100		935
LSA	EISAEYDDSL	1763	10	1	100		936
LSA	EISAEYDDSLI	1763	11	1	100		937
LSA	ELPSENERGY	1662	10	1	100		938
LSA	ELPSENERGYY	1662	11	1	100		939
LSA	ELSEDTIKY	1897	9	1	100		940
LSA	ELSEDTIKYF	1897	10	1	100		941
LSA	ELSEDIDCYFM	1897	11	1	100		942
LSA	ETLQBQQSDL	1193	10	1	100		943
LSA	ETLQGQQSDL	156	10	1	100		944
LSA	ETVNISDVNDF	1745	11	1	100		945
LSA	FFDKDKEL	77	8	1	100		946
LSA	FFDKDKELTM	77	10	1	100		947
LSA	FIKSLFHI	1877	8	1	100		948
LSA	FIKSLFH1F	1877	9	1	100		949
LSA	FILVNLLI	11	8	1	100		950
LSA	FILVNLLIF	11	9	1	100		951
LSA	FILVNLLIFHI	11	11	1	100		952
LSA	FYF1LVNL	9	8	1	100		953
LSA	FYFILVNLL	9	9	1	100	7.5000	954
LSA	FYFILVNLLI	9	10	1	100		955
LSA	FYFILVNLLIF	9	11	1	100		956
LSA	GIEKSSEEL	1822	9	1	100		957
LSA	GIYKELEDL	1801	9	1	100		958
LSA	GIYKELEDL1	1801	10	1	100		959
LSA	GVSEN1FL	105	8	1	100		960
LSA	GYYIPHQSSL	1670	10	1	100	0.0074	961
LSA	HIFDGDNEI	1883	9	1	100		962
LSA	HIFDGDNEIL	1883	10	1	100		963
LSA	HILYISFY	3	8	1	100		964
LSA	HILYISFYF	3	9	1	100		965
LSA	NILYISFYFI	3	10	1	100		966
LSA	LIILYISFYFIL	3	11	1	100		967
LSA	HLEEKKDOS1	1718	10	1	100		968
LSA	FITLETVNI	1742	8	1	100		969
LSA	HVLSHNSY	59	8	1	100		970
LSA	IFDGDNEI	1884	8	1	100		971
LSA	IFDGDNEIL	1884	9	1	100		972
LSA	IFDODNEILQI	1884	11	1	100		973
LSA	IFHINGKI	18	8	1	100		974
LSA	IFHINGKII	18	9	1	100		975
LSA	IFLKENKL	110	8	1	100		976
LSA	IIEKTNRESI	1695	10	1	100		977
LSA	IIKNSEKDEI	25	10	1	100		978
LSA	IIKNSEKDEII	25	11	1	100		979
LSA	IINDDDDYKKY	127	11	1	100		980
LSA	ILQIVDEL	1891	8	1	100		981
LSA	ILVNLLIF	12	8	1	100		982
LSA	ILVNLLIFHI	12	10	1	100		983
LSA	ILYISFYF	4	8	1	100		984
LSA	ILYISFYFI	4	9	1	100		985
LSA	ILYISFYFIL	4	10	1	100		986
LSA	IIKYFMKL	1902	8	1	100		987
LSA	ITINVEGRRDI	1704	11	1	100		988
LSA	IVDELSEDI	1894	9	1	100		989
LSA	IYKELEDL	1802	8	1	100		990
LSA	IYKELEDLI	1802	9	1	100		991
LSA	KFFDKDKEL	76	9	1	100		992
LSA	KFFDKDKELTM	76	11	1	100		993
LSA	KFIKSLFHI	1876	9	1	100		994
LSA	KFIKSLFHIF	1876	10	1	100		995
LSA	KIIKNSEKDEI	24	11	1	100		996
LSA	KIKKGKKY	1834	8	1	100		997
LSA	KLNKEGKL	116	8	1	100		998
LSA	KLNKEGKLI	116	9	1	100		999
LSA	KLQEQQRDL	1619	9	1	100		1000
LSA	KLQEQQSDL	1585	9	1	100		1001
LSA	KLQGQQSDL	1126	9	1	100		1002
LSA	KTKNNENNKF	68	10	1	100		1003
LSA	KTKNNENNKFF	68	11	1	100		1004
LSA	KYEDEISAEY	1759	10	1	100		1005
LSA	KYEKTKDNNF	1140	10	1	100	0.0004	1006
LSA	LFHTFDODNEI	1881	11	1	100		1007
LSA	LIDEEEDDEDL	1772	11	1	100		1008
LSA	LISCNENL	1809	8	1	100		1009
LSA	LIEKNENLDDL	1809	11	1	100		1010
LSA	LIFHINGKI	17	9	1	100		1011
LSA	LIFHINGKII	17	10	1	100		1012
LSA	LLIFHINGKI	16	10	1	100		1013
LSA	LLIFHINGKII	16	11	1	100		1014
LSA	LLRNLGVSENI	100	11	1	100		1015
LSA	LVNLLIFHI	13	9	1	100		1016
LSA	LYDEHIKKY	1856	9	1	100		1017
LSA	LYGRLEIPAI	1652	10	1	100		1018
LSA	LYISFYFI	5	8	1	100		1019
LSA	LYISFYFIL	5	9	1	100	0.0088	1020
LSA	NFIONDKSL	1848	9	1	100		1021
LSA	NFKPNDKSLY	1848	10	1	100		1022
LSA	NFKSLLRNL	96	9	1	100		1023
LSA	NFQDEENI	1793	8	1	100		1024
LSA	NFQDEENIGI	1793	10	1	100		1025
LSA	NFQDEENIG1Y	1793	11	1	100		1026
LSA	NIFLKENKL	109	9	1	100		1027
LSA	MGIYKEL	1799	8	1	100		1028
LSA	MGIYKELEDL	1799	11	1	100		1029
LSA	MSDVNDF	1748	8	1	loo		1030
LSA	NISDVNDFQI	1748	10	1	100		1031
LSA	NLDDLDEGI	1815	9	1	100		1032
LSA	NLGVSENI	103	8	1	100		1033
LSA	NLGVSENIF	103	9	1	100		1034
LSA	NLGVSEN1FL	103	10	1	100		1035
LSA	NLLIFHINGKI	15	11	1	100		1036
LSA	NVEGRRDI	1707	8	1	100		1037
LSA	NVKNVSQTNF	88	10	1	100		1038
LSA	NVSQTNFKSL	91	10	1	100		1039
LSA	NVSQTNFKSLL	91	11	1	100		1040
LSA	PIVQYDNF	1787	8	1	100		1041
LSA	QISKYEDEI	1756	9	1	100		1042
LSA	QtVDELSEDI	1893	10	1	100		1043
LSA	QTNFKSLL	94	8	1	100		1044
LSA	QTNFKSLLFINL	94	11	1	100		1045
LSA	QVNKEKEKF	1869	9	1	100		1046
LSA	QVNKEKEKF1	1869	10	1	100		1047
LSA	QYDNFQDEENI	1790	11	1	100		1048
LSA	RLEIPAIEL	1655	9	1	100		1049
LSA	RIKASKETL	1187	9	1	100		1050
LSA	SFYFILVNL	8	9	1	100		1051
LSA	SFYFILVNLL	8	10	1	100		1052
LSA	SFYFILVNLLI	8	11	1	100		1053
LSA	SIIEKTNRESI	1694	11	1	100		1054
LSA	SLYDEHIKKY	1855	10	1	100		1055
LSA	TLQEQQSDL	1194	9	1	100		1056
LSA	TLQGQQSDL	157	9	1	100		1057
LSA	TTNVEGRRDI	1705	10	1	100		1058
LSA	TVNISDVNDF	1746	10	1	100		1059
LSA	VLAEDLYGRL	1647	10	1	100		1060
LSA	YFILVNLL	10	8	1	100		1061
LSA	YFILVNLLI	10	9	1	100		1062
LSA	YFILVNLLIF	10	10	1	100		1063
LSA	YIPHQSSL	1672	8	1	100		1064
LSA	YISFYFIL	6	8	1	100		1065
LSA	YISFYFILVNL	6	11	1	100		1066
LSA	YYIPHQSSL	1671	9	1	100	4.3000	1067
SSP2	ALLACAGL	509	8	10	100		1068
SSP2	ALLACAGLAY	509	10	10	100		1069
SSP2	ALLQVRKHL	136	9	9	90		1070
SSP2	AMKLIQQL	72	8	10	100		1071
SSP2	AMKLIQQLNL	72	10	10	100	0.0006	1072
SSP2	ATPYAGEPAPF	526	11	8	80		1073
SSP2	AVFGIGQI	186	9	10	100		1074
SSP2	AVPLAMKL	68	8	10	100		1075
SSP2	AVPLAMKLI	68	9	10	100		1076
SSP2	AWENVKNVI	219	9	10	100		1077
SSP2	DLDEPEQF	546	8	10	100		1078
SSP2	DLDEPEQFRL	546	10	10	100		1079
SSP2	DVQNNIVDEI	27	10	10	100		1080
SSP2	EILHEGCTSEL	267	11	8	80		1081
SSP2	ETLGEEDKDL	538	10	10	100		1082
SSP2	EVCNDEVDL	41	9	8	80		1083
SSP2	EVCNDEVDLY	41	10	8	80		1084
SSP2	EVCNDEVDLYL	41	11	8	80		1085
SSP2	EVDLYLLM	46	8	8	80		1086
SSP2	EVEKTASCGVW	237	11	10	100		1087
SSP2	FLIFFDLF	14	8	10	100		1088
SSP2	FLIFFDLFL	14	9	10	100		1089
SSP2	FVVPGAATPY	520	10	8	80		1090
SSP2	GIAGGLAL	503	8	10	100		1091
SSP2	GIAGGLALL	503	9	10	100		1092
SSP2	GIGQGINVAF	189	10	10	100		1093
SSP2	GINVAFNRF	193	9	10	100		1094
SSP2	GNVAFNRFL	193	10	10	100		1095
SSP2	GIPDSIQDSL	163	10	10	100		1096
SSP2	GLALLACAGL	507	10	10	100		1097
SSP2	GTRSRXREI	260	9	10	100		1098
SSP2	GTRSRKREIL	260	10	10	100		1099
SSP2	GVKIAVFGI	182	9	10	100		1100
SSP2	HLGNVKYL	3	8	10	100		1101
SSP2	HLGNVKYLVI	3	10	10	100		1102
SSP2	ILHEOCTSEL	268	10	8	80		1103
SSP2	ILTDGIPDSI	159	10	10	100		1104
SSP2	IVFLWFDL	12	9	10	100		1105
SSP2	IVFLIFFDLF	12	10	10	100		1106
SSP2	IVFLIFFDLFL	12	11	10	100		1107
SSP2	KFVVPGAATPY	519	11	8	80		1108
SSP2	KIAGGIAGOL	499	10	10	100		1109
SSP2	KIAVFGIGQGI	184	11	10	100		1110
SSP2	KLIQQLNL	74	8	10	100		1111
SSP2	KTASCGVW	240	8	10	100		1112
SSP2	KTASCGVWDEW	240	11	10	100		1113
SSP2	KYKIAGGI	497	8	9	90		1114
SSP2	KYLVIVFL	8	8	10	100		1115
SSP2	KYLVIVFLI	8	9	10	100	4.6000	1116
SSP2	KYLVIVFLIF	8	10	10	100	0.0003	1117
SSP2	KYLVIVFLIFF	8	11	10	100		1118
SSP2	LIFFDLFL	15	8	10	100		1119
SSP2	LLACAGLAY	510	9	10	100		1120
SSP2	LLACAGLAYKF	510	11	10	100		1121
SSP2	LLMDCSGSI	51	9	10	100		1122
SSP2	LLQVRKHL	137	8	9	90		1123
SSP2	LLSTNLPY	121	8	9	90		1124
SSP2	LMDCSGSI	52	8	10	100		1125
SSP2	LIDGIPDSI	160	9	10	100		1126
SSP2	LVTVFLIF	10	8	10	100		1127
SSP2	LVIVFLIFF	10	9	10	100		1128
SSP2	LVIVFLIFFDL	10	11	10	100		1129
SSP2	LVNGRDVQNNI	22	11	10	100		1130
SSP2	LVVILTDQI	156	9	10	100		1131
SSP2	LYLLMDCSGSI	49	11	9	90		1132
SSP2	NIVDEIKY	31	8	10	100		1133
SSP2	NLPYGRTNL	125	9	8	80		1134
SSP2	NLYADSAW	213	8	10	100		1135
SSP2	NVAFNRFL	195	8	10	100		1136
SSP2	NVKNVIGPF	222	9	10	100		1137
SSP2	NVKNVIGPFM	222	10	10	100		1138
SSP2	NVKYLVIVF	6	9	10	100		1139
SSP2	NVKYLVIIVFL	6	10	10	100		1140
SSP2	NVKYLVIVFLI	6	11	10	100		1141
SSP2	NWVNHAVPL	63	9	8	80		1142
SSP2	NWVNHAVPLAM	63	11	8	80		1143
SSP2	PLAMKLIQQL	70	10	10	100		1144
SSP2	PYAQEPAPF	528	9	8	80	0.0370	1145
SSP2	QFRLPEENEW	552	10	10	100		1146
SSP2	QLVVILIDGI	155	10	10	100		1147
SSP2	QVRKHLNDFTI	139	10	9	90		1148
SSP2	RINRENANQL	147	10	10	100		1149
SSP2	RLPEENEW	554	8	10	100		1150
SSP2	SLKESRKL	171	8	9	90		1151
SSP2	SLLSTNLPY	120	9	9	90		1152
SSP2	STNLPYGRTNL	123	11	8	80		1153
SSP2	TLGEEDKDL	539	9	10	100		1154
SSP2	VFGIGQGI	187	8	10	100		1155
SSP2	VFLIFFDL	13	8	10	100		1156
SSP2	VFLIFFDLF	13	9	10	100		1157
SSP2	VFLIFFDLFL	13	10	10	100		1158
SSP2	VILTDGIPDSI	158	11	10	100		1159
SSP2	VIVFLIFF	11	8	10	100		1160
SSP2	VIVFLIFFDL	11	10	10	100		1161
SSP2	VIVFLIFFDLF	11	11	10	100		1162
SSP2	VVILTDGI	157	8	10	100		1163
SSP2	VVPGAATPY	521	9	8	80		1164
SSP2	WVNHAVPL	64	8	8	80		1165
SSP2	WVNHAVPLAM	64	10	8	80		1166
SSP2	YLLMDCSGSI	50	10	10	100		1167
SSP2	YLVIVFLI	9	8	10	100		1168
SSP2	YLVIVFLIF	9	9	10	100		1169
SSP2	YLVIVFLIFF	9	10	10	100		1170

TABLE XI
Malaria B07 Super Motif Peptides With Binding Information

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	B*0702	Seq. Id.

CSP	EPSDKHIEQY	345	10	15	79		171
CSP	EPSDKHIEQYL	345	11	15	79		172
CSP	DPNANPNA	202	8	19	100		173
CSP	DPNANPNV	130	8	19	100		174
CSP	DPNRNVDBIA	327	10	19	100	0.0002	175
CSP	MPNDPNRNV	324	9	19	100	0.0001	176
CSP	NPDPNANPNV	120	10	19	100	0.0001	177
CSP	NPNANPNA	302	8	19	100	0.0001	178
CSP	NPNVDPNA	198	8	19	100	0.0001	179
CSP	QPGDGNPDPNA	115	11	19	100		180
CSP	SPCSVTCGNGI	371	11	19	100		181
EXP	DPADNANPDA	116	10	1	100	0.0002	182
EXP	DPQVTAQDV	136	9	1	100	0.0001	183
EXP	EPLIDVHDL	45	9	1	100	0.0001	184
EXP	EPLIDVHDLI	45	10	1	100	0.0002	185
EXP	EPNADPQV	132	8	1	100	0.0001	186
EXP	EPNADPQVTA	132	10	1	100	0.0002	187
EXP	HPFKIGSSDPA	108	11	1	100		188
EXP	QPQGDDNNL	148	9	1	100	0.0001	189
EXP	QPQGDDNNLV	148	10	1	100	0.0002	190
LSA	KPEQKEDKSA	1728	10	1	100	0.0002	191
LSA	KPIVQYDNF	1786	9	1	100	0.0001	192
LSA	KPNDKSLY	1850	8	1	100	0.0004	193
LSA	LPSENERGY	1663	9	1	100	0,0001	194
LSA	LPSENERGYY	1663	10	1	100	0.0001	195
LSA	LPSENERGYYI	1663	11	1	100		196
SSP2	EPAPFDETL	532.	9	10	100	0.0001	197
SSP2	GPFMKAVCV	228	9	10	100	0.0023	198
SSP2	GFFMKAVCVEV	228	11	10	100		199
SSP2	HPSDGKCNL	206	9	10	100	0.0220	200
SSP2	HPSDGKCNLY	206	10	10	100	0.0001	201
SSP2	HPSDGKCNLYA	206	11	10	100		202
SSP2	IPDSIQDSL	164	9	10	100	0.0022	203
SSP2	IPEDSEKEV	367	9	10	100	0.0001	204
SSP2	LPYGRTNL	126	8	8	80	0.1100	205
SSP2	NPEDDREENF	382	10	10	100	0.0001	206
SSP2	QPRPRGDNF	303	9	9	90	0.0160	207
SSP2	QPRPRGDNFA	303	10	9	90	0.0009	208
SSP2	QPRPRGDNFAV	303	11	9	90		209
SSP2	RPRGDNFA	305	8	9	90	0.0110	210
SSP2	RPRGDNFAV	305	9	9	90	0.4800	211
SSP2	TPYAGEPA	527	8	8	80		212
SSP2	TPYAGEPAPF	527	10	8	80	0.0990	213
SSP2	VPGAATPY	522	8	8	80		214
SSP2	VPGAAIPYA	522	9	8	80	0.0001	215
SSP2	VPLAMKLI	69	8	10	100	0.0001	216
SSP2	VPLAMKLIQQL	69	11	10	100		217

TABLE XII
Malaria B27 Super Motif Peptides

			No. of	Sequence	Conservancy	Seq.
Protein	Sequence	Position	Amino Acids	Frequency	(%)	Id

CSP	CKMEKCSSVF	408	10	19	100	1218
CSP	DKHIEQYL	348	8	15	79	1219
CSP	DKHIEQYLKKI	348	11	15	79	1220
CSP	EKLRKPKHKKL	103	11	19	100	1221
CSP	GKQENWYSL	57	9	19	100	1222
CSP	KHIEQYLKKI	349	10	15	79	1223
CSP	KKIQNSLSTEW	360	11	15	79	1224
CSP	LKKIQNSL	359	8	15	79	1225
CSP	LKICNSRSL	65	8	19	100	1226
CSP	LRKPKHKKL	105	9	19	100	1227
CSP	RKLAILSVSSF	3	11	19	100	1228
CSP	RKPKHKKL	106	8	19	100	1229
CSP	TRVLNELNY	32	9	19	100	1230
EXP	EKGRHPFKI	104	9	1	100	1231
EXP	KKGSGEPL	40	8	1	100	1232
EXP	KKGSGEPLI	40	9	1	100	1233
EXP	KKNKKGSGEPL	37	11	1	100	1234
EXP	KRKSKYKL	69	8	1	100	1235
EXP	MKILSVFF	1	8	1	100	1236
EXP	MKILSVFFL	1	9	1	100	1237
EXP	MK1LSVFFLAL	1	11	1	100	1238
EXP	NKKGSGEPL	39	9	1	100	1239
EXP	NKKGSGEPLI	39	10	1	100	1240
EXP	NKRKSKYKL	68	9	1	100	1241
EXP	SKYKLATSVL	72	10	1	100	1242
EXP	VHDLISDM	50	8	1	100	1243
EXP	VHDLISDMI	50	9	1	100	1244
EXP	YKLATSVL	74	8	1	100	1245
EXP	YKLATSVLAGL	74	11	1	100	1246
LSA	DKDKELIM	79	8	1	100	1247
LSA	DKQVNKEKEICF	1867	11	1	100	1248
LSA	DKSADIQNHIL	1734	11	1	100	1249
LSA	DKSLYDEHI	1853	9	1	100	1250
LSA	DRLAKEKL	1392	8	1	100	1251
LSA	EHGDVLAEDL	1643	10	1	100	1252
LSA	EHODVIAEDLY	1643	11	1	100	1253
LSA	EKAAKEIL	151	8	1	100	1254
LSA	EKDEIIKSNL	30	10	1	100	1255
LSA	EKEKFIKSL	873	9	1	100	1256
LSA	EKEXFIKSLF	873	10	1	100	1257
LSA	EKFIKSLF	875	8	1	100	1258
LSA	EKFIKSLFHI	875	10	1	100	1259
LSA	EKFIKSLFHIF	875	11	1	100	1260
LSA	EXHECKHVL	53	9	1	100	1261
LSA	EKIKKGKKY	833	9	1	100	1262
LSA	DUCHVLSHNSY	56	11	1	100	1263
LSA	EKLQEQQRDL	618	10	1	100	1264
LSA	EKLQEQQSDL	584	10	1	100	1265
LSA	SCLQGQQSDL	125	10	1	100	1266
LSA	EISNENLDDL	811	9	1	100	1267
LSA	EKTICDNNF	842	8	1	100	1268
LSA	EKTKNNENNKF	67	11	1	100	1269
LSA	EXINRESI	697	8	1	100	1270
LSA	ERKKEHGDVL	639	10	1	100	1271
LSA	ERLAICEKL	613	8	1	100	1272
LSA	ERLANEKL	528	8	1	100	1273
LSA	ERRAKEKL	1579	8	1	100	1274
LSA	ERTKASKETL	1186	10	1	100	1275
LSA	FHIFDGDNEI	1882	10	1	100	1276
LSA	FHTFDGDNEIL	1882	11	1	100	1277
LSA	FHINGKII	19	8	1	100	1278
LSA	FKPIVQYDNF	1785	10	1	100	1279
LSA	FKPNDKSL	1849	8	1	100	1280
LSA	FIQNDKSLY	1849	9	1	100	1281
LSA	FKSLLRNL	97	8	1	100	1282
LSA	GHLEEKKDGSI	1717	11	1	100	1283
LSA	GKLIEHII	121	8	1	100	1284
LSA	GRLEIPAI	1654	8	1	100	1285
LSA	GRLEIPAIEL	1654	10	1	100	1286
LSA	GRRDIHKGHL	1710	10	1	100	1287
LSA	IKNSEKDEI	26	9	1	100	1288
LSA	IKNSEKDEII	26	10	1	100	1289
LSA	IKSLFHIF	1878	8	1	100	1290
LSA	KHEKKHVL	54	8	1	100	1291
LSA	KHILYISF	2	8	1	100	1292
LSA	KHILYISFY	2	9	1	100	1293
LSA	KHILYISFYF	2	10	1	100	1294

LSA	KHILYISFYFI	2	11	1	100	1295

LSA	KHVLSHNSY	58	9	1	100	1296
LSA	KKEHGDVL	1641	8	1	100	1297
LSA	KKHVLSHNSY	57	10	1	100	1298
LSA	KKYEKIKDNNF	1839	11	1	100	1299
LSA	LRNLGVSENI	101	10	1	100	1300
LSA	LRNLGVSENIF	101	11	1	100	1301
LSA	MKHILYISF	1	9	1	100	1302
LSA	MKHILYISFY	1	10	1	100	1303
LSA	MKHILYISFYF	1	11	1	100	1304
LSA	NHTLETVNi	1741	9	1	100	1305
LSA	NKEGKLIEH1	118	10	1	100	1306
LSA	NKEGKLIEHII	118	11	1	100	1307
LSA	NICEKEKSI	1871	8	1	100	1308
LSA	NKEKEKFRSL	1871	11	1	100	1309
LSA	NKFFDKDKEL	75	10	1	100	1310
LSA	NKLNKEGKL	115	9	1	100	1311
LSA	NKLNKEGKU	115	10	1	100	1312
LSA	NRGNSRDSKEI	1683	11	1	100	1313
LSA	QKEDILSADI	1731	9	1	100	1314
LSA	QRDLEQERL	1607	9	1	100	1315
LSA	QRKADTKKNL	1629	10	1	100	1316
LSA	RKADTKKNL	1630	9	1	100	1317
LSA	RKKEHGDVL	1640	9	1	100	1318
LSA	RRDIHKGHL	1711	9	1	100	1319
LSA	SKYEDEISAEY	1758	11	1	100	1320
LSA	SRDSKEISI	1687	9	1	100	1321
LSA	SRDSKEISII	1687	10	1	100	1322
LSA	TKASKEIL	1188	8	1	100	1323
LSA	TICNNENNKF	69	9	1	100	1324
LSA	TKNNENNKFF	69	10	1	100	1325
LSA	VKNVSQTNF	89	9	1	100	1326
LSA	YKELEDLI	1803	8	1	100	1327
SSP2	CHPSDGKCNL	205	10	10	100	1328
SSP2	CHPSDGKCNLY	205	11	10	100	1329
SSP2	DKDLDEPEQF	544	10	10	100	1330
SSP2	DREENFDI	386	8	10	100	1331
SSP2	DRGVKIAVF	180	9	9	90	1332
SSP2	DRGVKIAVEGI	180	11	9	90	1333
SSP2	DRINRENANQL	146	11	10	100	1334
SSP2	EKTASCGVW	239	9	10	100	1335
SSP2	FRLPEENEW	333	9	10	100	1336
SSP2	GKCNLYADSAW	210	11	10	100	1337
SSP2	GKGTRSRKREI	258	11	10	100	1338
SSP2	GRDVQNNI	25	8	10	100	1339
SSP2	GRNNENRSY	458	9	10	100	1340
SSP2	KHDNQNNL	400	8	10	100	1341
SSP2	LHEGCTSEL	269	9	8	80	1342
SSP2	MKLIQQLNL	73	9	10	100	1343
SSP2	NHAVPLAM	66	8	8	80	1344
SSP2	NHAVPLAMKL	66	10	8	80	1345
SSP2	NHAVPLAMKLI	66	11	8	80	1346
SSP2	NHLGNVKY	2	8	10	100	1347
SSP2	NHLGNVKYL	2	9	10	100	1348
SSP2	NHLGNVKYLVI	2	11	10	100	1349
SSP2	NKEKALII	110	8	9	90	1350
SSP2	NKEKALIII	110	9	9	90	1351
SSP2	NKHDNQNNL	399	9	10	100	1352
SSP2	NKYKIAGGI	496	9	9	90	1353
SSP2	NRENANQL	149	8	10	100	1354
SSP2	NRENANQLVVI	149	11	10	100	1355
SSP2	PHGRNNENRSY	456	11	10	100	1356
SSP2	PRPRGDNF	304	8	9	90	1357
SSP2	RHNWVNHAVPL	61	11	8	80	1358
SSP2	RKHLNDRI	141	8	10	100	1359
SSP2	SKNKEKAL	108	8	10	100	1360
SSP2	SKNKSCALI	108	9	9	90	1361
SSP2	SKNKEKALII	108	10	9	90	1362
SSP2	SKNKEKALIII	108	11	9	90	1363
SSP2	TRSRKREI	261	8	10	100	1364
SSP2	TRSRKREIL	261	9	10	100	1365
SSP2	VKIAVFGI	183	8	10	100	1366
SSP2	VKNVIGPF	223	8	10	100	1367
SSP2	VKNVIGPFM	223	9	10	100	1368
SSP2	VKYLVIVF	7	8	10	100	1369
SSP2	VKYLVIVFL	7	9	10	100	1370
SSP2	VKYLVIVFLI	7	10	10	100	1371
SSP2	VKYLVIVFLIF	7	11	10	100	1372
SSP2	VRKHLNDRI	140	9	10	100	1373
SSP2	YKIAGGIAGGL	498	11	10	100	1374

TABLE XIII
Malaria B58 Super Motif Peptides

			No. of	Sequence	Conservancy	Seq.
Protein	Sequence	Position	Amino Acids	Frequency	(%)	Id

CSP	CSSVFNVV	413	8	19	100	1375
CSP	CSVTCGNGI	373	9	19	100	1376
CSP	CSVTCGNGIQV	373	11	19	100	1377
CSP	EALFQEYQCY	17	10	19	100	1378
CSP	GSSSNTRV	27	8	19	100	1379
CSP	GSSSNTRVL	27	9	19	100	1380
CSP	LAILSVSSF	5	9	19	100	1381
CSP	LAILSVSSFL	5	10	19	100	1382
CSP	LAILSVSSFLF	5	11	19	100	1383
CSP	LSTEWSPCSV	366	10	18	95	1384
CSP	LSVSSFLF	8	8	19	100	1385
CSP	LSVSSFLFV	8	9	19	100	1386
CSP	NAGINLYNEL	42	10	18	95	1387
CSP	NANANNAV	335	8	16	84	1388
CSP	NSSIGLIM	421	8	19	100	1389
CSP	NSSIGLIMV	421	9	19	100	1390
CSP	NSSIGLIMVL	421	10	19	100	1391
CSP	NTRVLNEL	31	8	19	100	1392
CSP	NTRVLNELNY	31	10	19	100	1393
CSP	PSDKHIEQY	346	9	15	79	1394
CSP	PSDKHIEQYL	346	10	15	100	1395
CSP	SSFLFVEAL	11	9	19	100	1396
CSP	SSFLFVEALF	11	10	19	100	1397
CSP	SSIGLIMV	422	8	19	100	1398
CSP	SSIGLIMVL	422	9	19	100	1399
CSP	SSIGLIMVLSF	422	11	19	100	1400
CSP	SSNTRVLNEL	29	10	19	100	1401
CSP	SSSNTRVL	28	8	19	100	1402
CSP	SSSNTRVLNEL	28	11	19	100	1403
CSP	SSVFNVVNSSI	414	11	19	100	1404
CSP	STEWSPCSV	367	9	19	100	1405
CSP	VSSFLFVEAL	10	10	19	100	1406
CSP	VSSFLFVEALF	10	11	19	100	1407
CSP	VTCGNGIQV	375	9	19	100	1408
CSP	VTCGNGIQVRI	375	11	19	100	1409
CSP	YSLKKNSRSL	63	10	19	100	1410
EXP	ATSVLAGL	77	8	1	100	1411
EXP	ATSVLAGLL	77	9	1	100	1412
EXP	GSGEPLIDV	42	9	1	100	1413
EXP	ISDMIKKEEEL	54	11	1	100	1414
EXP	KSKYKLATSV	71	10	1	100	1415
EXP	KSKYKLATSVL	71	11	1	100	1416
EXP	KTNKGTGSGV	24	10	1	100	1417
EXP	LAGLLGNV	81	8	1	100	1418
EXP	LAGLLGNVSTV	81	11	1	100	1419
EXP	LALFFIIF	9	8	1	100	1420
EXP	LATSVLAGL	76	9	1	100	1421
EXP	LATSVLAGLL	76	10	1	100	1422
EXP	LSVFFLAL	4	8	1	100	1423
EXP	LSVFFLALF	4	9	1	100	1424
EXP	LSVFFLALFF	4	10	1	100	1425
EXP	LSVFFLALFFI	4	11	1	100	1426
EXP	NADPQVTAQDV	134	11	1	100	1427
EXP	NTEKGRHPF	102	9	1	100	1428
EXP	NTEKGRHPFKI	102	11	1	100	1429
EXP	STVLLGGV	89	8	1	100	1430
EXP	STVLIGGVGL	89	10	1	100	1431
EXP	STVLLGGVGLV	89	11	1	100	1432
EXP	TSVLAGLL	78	8	1	100	1433
EXP	TSVLAGLLGNV	78	11	1	100	1434
EXP	VSTVLLGGV	88	9	1	100	1435
EXP	VSTVLLGGVGL	88	11	1	100	1436
LSA	DSKEISII	1689	8	1	100	1437
LSA	ETLQEQQSDL	1193	10	1	100	1438
LSA	ETLQGQQSDL	156	10	1	100	1439
LSA	ETVNISDV	1745	8	1	100	1440
LSA	EIVNISDVNDF	1745	11	1	100	1441
LSA	GSSNSRNRI	42	9	1	100	1442
LSA	HTLETVNI	1742	8	1	100	1443
LSA	HTLETVNISDV	1742	11	1	100	1444
LSA	ISAEYDDSL	1764	9	1	100	1445
LSA	ISAEYDDSLI	1764	10	1	100	1446
LSA	ISDVNDFQI	1749	9	1	100	1447
LSA	ISFYFILV	7	8	1	100	1448
LSA	ISFYFILVNL	7	10	1	100	1449
LSA	ISFYFILVNLL	7	11	1	100	1450
LSA	ISKYEDEI	1757	8	1	100	1451
LSA	ITKYFMKL	1902	8	1	100	1452
LSA	ITTNVEGRRDI	1704	11	1	100	1453
LSA	KADTKKNL	1631	8	1	100	1454
LSA	KSADIQNHTL	1735	10	1	100	1455
LSA	KSLLRNLGV	98	9	1	100	1456
LSA	KSLYDEHI	1854	8	1	100	1457
LSA	KSLYDEHIKKY	1854	11	1	100	1458
LSA	KSSEELSEEKI	1825	11	1	100	1459
LSA	KTKNNENNKF	68	10	1	100	1460
LSA	KTKNNENNKFF	68	11	1	100	1461
LSA	KTNRESITTNV	1698	11	1	100	1462
LSA	LAEDLYGRL	1648	9	1	100	1463
LSA	LAEDLYGRLEI	1648	11	1	100	1464
LSA	LSEDITKY	1898	8	1	100	1465
LSA	LSEDITKYF	1898	9	1	100	1466
LSA	LSEDITKYFM	1898	10	1	100	1467
LSA	LTMSNVKNV	84	9	1	100	1468
LSA	NSEKDEII	28	8	1	100	1469
LSA	NSRDSKEI	1686	8	1	100	1470
LSA	NSRDSKEISI	1686	10	1	100	1471
LSA	NSRDSKEISII	1686	11	1	100	1472
LSA	PSENERGY	1664	8	1	100	1473
LSA	PSENERGYY	1664	9	1	100	1474
LSA	PSENERGYYI	1664	10	1	100	1475
LSA	QSDLEQDRL	1386	9	1	100	1476
LSA	QSDLEQERL	1590	9	1	100	1477
LSA	QSDSEQERL	519	9	1	100	1478
LSA	QTNFKSLL	94	8	1	100	1479
LSA	QTNFKSLLRNL	94	11	1	100	1480
LSA	RSGSSNSRNRI	40	11	1	100	1481
LSA	RTKASKETL	1187	9	1	100	1482
LSA	SADIQNHTL	1736	9	1	100	1483
LSA	SAEYDDSL	1765	8	1	100	1484
LSA	SAEYDDSLI	1765	9	1	100	1485
LSA	SSEELSEEKI	1826	10	1	100	1486
LSA	SSNSRNRI	43	8	1	100	487
LSA	TTNVEGRRDI	1705	10	1	100	488
LSA	VSQTNFKSL	92	9	1	100	489
LSA	VSQTNFKSLL	92	10	1	100	490
SSP2	ASCGVWDEW	242	9	10	100	491
SSP2	ASKNKEKAL	107	9	10	100	492
SSP2	ASKNKEKALI	107	10	9	90	493
SSP2	ASKNKEKALII	107	11	9	90	494
SSP2	AIPYAGEPAPF	526	11	8	80	495
SSP2	CAGLAYKF	513	8	10	100	496
SSP2	CAGLAYKFV	513	9	10	100	497
SSP2	CAGLAYKFVV	513	10	10	100	498
SSP2	CSGSIRRHNW	55	10	10	100	499
SSP2	CSGSIRRHNWV	55	11	10	100	500
SSP2	DALLQVRKHL	135	10	9	90	501
SSP2	DASKNKEKAL	106	10	10	100	502
SSP2	DASKNKEKALI	106	11	9	90	503
SSP2	DSAWENVKNV	217	10	10	100	504
SSP2	DSAWENVKNVI	217	11	10	100	505
SSP2	DSEKEVPSDV	370	10	10	100	506
SSP2	DSLKESRKL	170	9	9	90	507
SSP2	ETLGEEDKDL	538	10	10	100	508
SSP2	GSIRRHNW	57	8	10	100	509
SSP2	GSIRRHNWV	57	9	10	100	510
SSP2	GTRSRKREI	260	9	10	100	511
SSP2	GTRSRKREIL	260	10	10	100	512
SSP2	HAVPLAMKL	67	9	10	100	513
SSP2	HAVPLAMKLI	67	10	10	100	514
SSP2	IAGGIAGGL	500	9	10	100	515
SSP2	IAGGIAGGLAL	500	11	10	100	516
SSP2	IAGGLALL	504	8	10	100	517
SSP2	IAVFGIGQGI	185	10	10	100	518
SSP2	KTASCGVW	240	8	10	100	519
SSP2	KTASCGVWDEW	240	11	10	100	520
SSP2	LACAGLAY	511	8	10	100	521
SSP2	LACAGLAYKF	511	10	10	100	522
SSP2	LACAGLAYKFV	511	11	10	100	523
SSP2	LALLACAGL	508	9	10	100	524
SSP2	LALLACAGLAY	508	11	10	100	525
SSP2	LAMKLIQQL	71	9	10	100	526
SSP2	LAMKLIQQLNL	71	11	10	100	527
SSP2	LTDGIPDSI	160	9	10	100	528
SSP2	NANQLVVI	152	8	10	100	529
SSP2	NANQLVVIL	152	9	10	100	530
SSP2	PAPFDETL	533	8	10	100	531
SSP2	PSCGKCNL	207	8	10	100	532
SSP2	PSDGKCNLY	207	9	10	100	533
SSP2	QSQDNNGNRHV	436	11	10	100	534
SSP2	RSRKREIL	262	8	10	100	535
SSP2	SAWENVKNV	218	9	10	100	536
SSP2	SAWENVKNVI	218	10	10	100	537
SSP2	STNLPYGRTNL	123	11	8	80	538
SSP2	TASCGVWDEW	241	10	10	100	539
SSP2	VAFNRFLV	196	8	10	100	540
SSP2	YADSAWENV	215	9	10	100	541
SSP2	YAGEPAPF	529	8	8	80	1542

TABLE XIV
Malaria B62 Super Motif Peptides

			No. of	Sequence	Conservancy	Seq.
Protein	Sequence	Position	Amino Acids	Frequency	(%)	Id.

CSP	AILSVSSF	6	8	9	100	1543
CSP	AILSVSSFLF	6	10	9	100	1544
CSP	AILSVSSFLFV	6	11	9	100	1545
CSP	ALFQEYQCY	18	9	9	100	1546
CSP	DIEKKICKM	402	9	9	100	1547
CSP	DPNANPNV	130	8	9	100	1548
CSP	ELNYDNAGI	37	9	8	95	1549
CSP	EMNYYGKQENW	52	11	9	100	1550
CSP	EPSDKHIEQY	345	10	5	79	1551
CSP	FLFVEALF	13	8	9	100	1552
CSP	FLFVEALFQEY	13	11	9	100	1553
CSP	FVEALFQEY	1S	9	9	100	1554
CSP	GINLYNELEM	44	10	8	95	1555
CSP	GLIMVLSF	425	8	9	100	1556
CSP	GLIMVLSFLF	425	10	9	100	1557
CSP	HIEQYLKKI	350	9	5	79	1558
CSP	ILSVSSFLF	7	9	9	100	1559
CSP	ILSVSSFLFV	7	10	9	100	1560
CSP	IMVLSFLF	427	8	9	100	1561
CSP	IQNSLSTEW	362	9	5	79	1562
CSP	KICKMEKCSSV	406	11	9	100	1563
CSP	KIQNSLSTEW	361	10	5	79	1564
CSP	KLAILSVSSF	4	10	9	100	1565
CSP	KMEKCSSV	409	8	9	100	1566
CSP	KMEKCSSVF	409	9	9	100	1567
CSP	KMEKCSSVFNV	409	11	9	100	1568
CSP	LIMVLSFLF	426	9	9	100	1569
CSP	MMRKLAILSV	1	10	9	100	1570
CSP	MPNDPNRNV	324	9	9	100	1571
CSP	NLYNELEM	46	8	9	100	1572
CSP	NLYNELEMNY	46	10	9	100	1573
CSP	NLYNELEMNYY	46	11	9	100	1574
CSP	NMPNDPNRNV	323	10	9	100	1575
CSP	NPDPNANPNV	120	10	9	100	1576
CSP	NQGNGQGHNM	315	10	9	100	1577
CSP	NVDPNANPNV	128	10	9	100	1578
CSP	NVVNSSIGLI	418	10	9	100	1579
CSP	NVVNSSIGLIM	418	11	9	100	1580
CSP	RVLNELNY	33	8	9	100	1581
CSP	SIGLIMVLSF	423	10	9	100	1582
CSP	SLSTEWSPCSV	365	11	8	95	1583
CSP	SPCSVTCGNGI	371	11	9	100	1584
CSP	SVFNVVNSSI	415	10	9	100	1585
CSP	SVSSFLFV	9	8	9	100	1586
CSP	SVTCGNGI	374	8	9	100	1587
CSP	SVTCGNGIQV	374	10	9	100	1588
CSP	VVNSSIGLI	419	9	9	100	1589
CSP	VVNSSIGLIM	419	10	9	100	1590
CSP	VVNSSIGLIMV	419	11	9	100	1591
EXP	DMIKKEEELV	56	10	1	100	1592
EXP	DPQVTAQDV	136	9	1	100	1593
EXP	DVHDLISDM	49	9	1	100	1594
EXP	DVHDLISDMI	49	10	1	100	1595
EXP	EPLIDVHDLI	45	10	1	100	1596
EXP	EPNADPQV	132	8	1	100	1597
EXP	EQPQGDDNNLV	147	11	1	100	1598
EXP	EVNKRKSKY	66	9	1	100	1599
EXP	FLALFFII	8	8	1	100	1600
EXP	FLALFFIIF	8	9	1	100	1601
EXP	GLLGNVSTV	83	9	1	100	1602
EXP	ILSVFFLALF	3	10	1	100	1603
EXP	ILSVFFLALFF	3	11	1	100	1604
EXP	KILSVFFLALF	2	11	1	100	1605
EXP	LIDVHDLI	47	8	1	100	1606
EXP	LIDVHDLISDM	47	11	1	100	1607
EXP	LLGGVGLV	92	8	1	100	1608
EXP	LLGGVGLVLY	92	10	1	100	1609
EXP	LLGNVSTV	84	8	1	100	1610
EXP	LVEVNKRKSKY	64	11	1	100	1611
EXP	MIKKEEELV	57	9	1	100	1612
EXP	MIKKEEELVEV	57	11	1	100	1613
EXP	NVSTVLLGGV	87	10	1	100	1614
EXP	PLIDVHDLI	46	9	1	100	1615
EXP	PQGDDNNLV	149	9	1	100	1616
EXP	PQVTAQDV	137	8	1	100	1617
EXP	QPQGDDNNLV	148	10	1	100	1618
EXP	SVFFLALF	5	8	1	100	1619
EXP	SVFFLALFF	5	9	1	100	1620
EXP	SVFFLALFFI	5	10	1	100	1621
EXP	SVFFLALFFII	5	11	1	100	1622
EXP	SVLAGLLGNV	79	10	1	100	1623
EXP	TVLLGGVGLV	90	10	1	100	1624
EXP	VLAGLLGNV	80	9	1	100	1625
EXP	VLLGGVGLV	91	9	1	100	1626
EXP	VLLGGVGLVLY	91	11	1	100	1627
LSA	DIQNHTLETV	1738	10	1	100	1628
LSA	DLDEFKPI	1781	8	1	100	1629
LSA	DLDEFKPIV	1781	9	1	100	1630
LSA	DLDEFKPIVQY	1781	11	1	100	1631
LSA	DLYGRLEI	1651	8	1	100	1632
LSA	DLYGRLEIPAI	1651	11	1	100	1633
LSA	DVLAEDLY	1646	8	1	100	1634
LSA	DVNDFQISKY	1751	10	1	100	1635
LSA	EISAEYDDSLI	1763	11	1	100	1636
LSA	ELPSENERGY	1662	10	1	100	1637
LSA	ELPSENERGYY	1662	11	1	100	1638
LSA	ELSEDITKY	1897	9	1	100	1639
LSA	ELSEDITKYF	1897	10	1	100	1640
LSA	ELSEDRKYFM	1897	11	1	100	1641
LSA	ELTMSNVKNV	83	10	1	100	1642
LSA	EQKEDKSADI	1730	10	1	100	1643
LSA	FIKSLFHI	1877	8	1	100	1644
LSA	FIKSLFHIF	1877	9	1	100	1645
LSA	FILVNLLI	11	8	1	100	1646
LSA	FILVNLLIF	11	9	1	100	1647
LSA	FILVNLLIFFII	11	11	1	100	1648
LSA	FQDEENIGI	1794	9	1	100	1649
LSA	FQDEENIGIY	1794	10	1	100	1650
LSA	FQISKYEDE1	1755	10	1	100	1651
LSA	GIYKELEDLI	1801	10	1	100	1652
LSA	HIFDGDNEI	1883	9	1	100	1653
LSA	HIKKYKNDKQV	1860	11	1	100	1654
LSA	HILYISFY	3	8	1	100	1655
LSA	HILYISFYF	3	9	1	100	1656
LSA	HILYISFYFI	3	10	1	100	1657
LSA	HLEEKKDGSI	1718	10	1	100	1658
LSA	HVLSHNSY	59	8	1	100	1659
LSA	IIEKTNRESI	1695	10	1	100	1660
LSA	IIKNSEKDEI	25	10	1	100	1661
LSA	IIKNSEKDEII	25	11	1	100	1662
LSA	IINDDDDKKKY	127	11	1	100	1663
LSA	RILVNLLIF	12	8	1	100	1664
LSA	ILVNLLIFHI	12	10	1	100	1665
LSA	ILYYISFYF	4	8	1	100	1666
LSA	ILYISFYFI	4	9	1	100	1667
LSA	ILYISFYFILV	4	11	1	100	1668
LSA	IQNHTLETV	1739	9	1	100	1669
LSA	IQNHTLETVNI	1739	11	1	100	1670
LSA	IVDELSEDI	1894	9	1	100	1671
LSA	KIIKNSEKDEI	24	11	1	100	1672
LSA	KIKKGKKY	1834	8	1	100	1673
LSA	KLNKEGKLI	116	9	1	100	1674
LSA	KPIVQYDNF	1786	9	1	100	1675
LSA	KPNDKSLY	1850	8	1	100	1676
LSA	KQVNKEKEKF	1868	10	1	100	1677
LSA	KQVNKEKEKFI	1868	11	1	100	1678
LSA	LIFHINGKI	17	9	1	100	1679
LSA	LIFHINGKII	17	10	1	100	1680
LSA	LLIFHINGKI	16	10	1	100	1681
LSA	LLIFHINGKII	16	11	1	300	1682
LSA	LLRNLGVSENI	100	11	1	100	1683
LSA	LPSENERGY	1663	9	1	100	1684
LSA	LPSENERGYY	1663	10	1	100	1685
LSA	LPSENERGYYI	1663	11	1	100	1686
LSA	LQIVDELSEDI	1892	11	1	100	1687
LSA	LVNLLIFHI	13	9	1	100	1688
LSA	NISDVNDF	1748	8	1	100	1689
LSA	NISDVNDFQI	1748	10	1	100	1690
LSA	NLDDLDEGI	1815	9	1	100	1691
LSA	NLERKKEHGDV	1637	11	1	100	1692
LSA	NLGVSENI	103	8	1	100	1693
LSA	NLGVSENIF	103	9	1	100	1694
LSA	NLLIFHTNGKI	15	11	1	100	1695
LSA	NVEGRRDI	707	8	1	100	1696
LSA	NVKNVSQTNF	88	10	1	100	1697
LSA	PIVQYDNF	787	8	1	100	1698
LSA	QISKYEDEI	756	9	1	100	1699
LSA	QIVDELSEDI	893	10	1	100	1700
LSA	QVNKEKEKF	869	9	1	100	1701
LSA	QVINIKEKEKFI	869	10	1	100	1702
LSA	SIIEKTNRESI	694	11	1	100	1703
LSA	SLLRNLGV	99	8	1	100	1704
LSA	SLYDEHIKKY	855	10	1	100	1705
LSA	TLETVNISDV	743	10	1	100	1706
LSA	TMSNVKNV	85	8	1	100	1707
LSA	TVNISDVNDF	746	10	1	100	1708
LSA	YISFYFILV	6	9	1	100	1709
SSP2	ALLACAGLAY	509	10	10	100	1710
SSP2	AVFGIGQGI	186	9	10	100	1711
SSP2	AVFGIGQGINV	186	11	10	100	1712
SSP2	AVPLAMKLI	68	9	10	100	1713
SSP2	DLDEPDQF	546	8	10	100	1714
SSP2	DLFLVNGRDV	19	10	10	100	1715
SSP2	DQPRPRGDNF	302	10	9	90	1716
SSP2	DVQNNIVDEI	27	10	10	100	1717
SSP2	EIKYREEV	35	8	9	90	1718
SSP2	EQFRLPEENEW	551	11	10	100	1719
SSP2	EVCNDEVDLY	41	10	8	80	1720
SSP2	EVDLYLLM	46	8	8	80	1721
SSP2	EVEKTASCGV	237	10	10	100	1722
SSP2	EVEXTASCGVW	237	11	10	100	1723
SSP2	FLIFFDLF	14	8	10	100	1724
SSP2	FLIFFDLFLV	14	10	10	100	1725
SSP2	FLVNGRDV	21	8	10	100	1726
SSP2	FMKAVCVEV	230	9	10	100	1727
SSP2	FVVPGAATPY	520	10	8	80	1728
SSP2	GIGQGINV	189	8	10	100	1729
SSP2	GIGQGINVAF	189	10	10	100	1730
SSP2	GINVAFNRF	193	9	10	100	1731
SSP2	GINVAFNRFLV	193	11	10	100	1732
SSP2	GLAYKFVV	515	8	10	100	1733
SSP2	GPFMKAVCV	228	9	10	100	1734
SSP2	GPFMKAVCVEV	228	11	10	100	1735
SSP2	GQGINVAF	191	8	10	100	1736
SSP2	GQGINVAFNRF	191	11	10	100	1737
SSP2	GVKIAVFGI	182	9	10	100	1738
SSP2	GVWDEWSPCSV	245	11	10	100	1739
SSP2	HLGNVKYLV	3	9	10	100	1740
SSP2	HLGNVKYLVI	3	10	10	100	1741
SSP2	HLGNVKYLVIV	3	11	10	100	1742
SSP2	HPSDGKCNLY	206	10	10	100	1743
SSP2	ILTDGIPDSI	159	10	10	100	1744
SSP2	IPEDSEKEV	367	9	10	100	1745
SSP2	IVDEIKYREEV	32	11	9	90	1746
SSP2	IVFLIFFDLF	12	10	10	100	1747
SSP2	KIAVFGIGQGI	184	11	10	100	1748
SSP2	LIFFDLFLV	15	9	10	100	1749
SSP2	LLACAGLAY	510	9	10	100	1750
SSP2	LLACAGLAYKF	510	11	10	100	1751
SSP2	LLMDCSGSI	51	9	10	100	1752
SSP2	LLSTNLPY	121	8	9	90	1753
SSP2	LMDCSGSI	52	8	10	100	1754
SSP2	LQVRKHLNDRI	138	11	9	90	1755
SSP2	LVIVFLIF	10	8	10	100	1756
SSP2	LVIVFLIFF	10	9	10	100	1757
SSP2	LVNGRDVQNNI	22	11	10	100	1758
SSP2	LVVILTDGI	156	9	10	100	1759
SSP2	NIPEDSEKEV	366	10	10	100	1760
SSP2	NIVDEIKY	31	8	10	100	1761
SSP2	NLYADSAW	213	8	10	100	1762
SSP2	NLYADSAWENV	213	11	10	100	1763
SSP2	NPEDDREENF	382	10	10	100	1764
SSP2	NQLVVILTDGI	154	11	10	100	1765
SSP2	NVARAFIN	195	9	10	100	1766
SSP2	NVIGPFMKAV	225	10	10	100	1767
SSP2	NVKNVIGPF	222	9	10	100	1768
SSP2	NVKNVIGPFM	222	10	10	100	1769
SSP2	NVKYLVIV	6	8	10	100	1770
SSP2	NVKYLVIVF	6	9	10	100	1771
SSP2	NVKYLVIVFLI	6	11	10	100	1772
SSP2	QLVVILTDGI	155	10	10	100	1773
SSP2	QPRPRGDNF	303	9	9	90	1774
SSP2	QPRPRGDNFAV	303	11	9	90	1775
SSP2	QVRKHLNDR1	139	10	9	90	1776
SSP2	RINRENANQLV	147	11	10	100	1777
SSP2	RLPEENEW	554	8	10	100	1778
SSP2	RPRGDNFAV	305	9	9	90	1779
SSP2	SIRRHNWV	58	8	10	100	1780
SSP2	SLLSTNLPY	120	9	9	90	1781
SSP2	SQDNNGNRHV	437	10	10	100	1782
SSP2	TPYAGEPAPF	527	10	8	80	1783
SSP2	VIGPFMKAV	226	9	10	100	1784
SSP2	VIGPFMKAVCV	226	11	10	100	1785
SSP2	VILIDGIPDSI	158	11	10	100	1786
SSP2	VIVFLIFF	11	8	10	100	1787
SSP2	VIVFLIFFDLF	11	11	10	100	1788
SSP2	VPGAATPY	522	8	8	80	1789
SSP2	VPLAMKLI	69	8	10	100	1790
SSP2	VQNNIVDEI	28	9	10	100	1791
SSP2	VQNNIVDE1KY	28	11	10	100	1792
SSP2	VVILTDM	157	8	10	100	1793
SSP2	VVPGAATPY	521	9	8	80	1794
SSP2	WVNHAVPLAM	64	10	8	80	1795
SSP2	YLLMDCSGS1	50	10	10	100	1796
SSP2	YLVIVFLI	9	8	10	100	1797
SSP2	YLV1VFLIF	9	9	10	100	1798
SSP2	YLVIVFLIFF	9	10	10	100	1799

TABLE XV
Malaria A01 Motif Peptides With Binding Information

			No. of	Sequence	Conservancy		Seq.
Protein	Sequence	Pos	Amino Acids	Freq.	(%)	A*0101	Id.

CSP	DNAGINLY	41	8	19	100		1800
CSP	EPSDKHIEQY	345	10	15	79		1801
CSP	FVEALFQEY	15	9	19	100	3.4000	1802
CSP	NTRVLNELNY	31	10	19	100	0.0096	1803
CSP	NYDNAGINLY	39	10	18	95	0.0012	1804
CSP	PSDKHIEQY	346	9	15	79		1805
CSP	VEALFQEY	16	8	19	100		1806
CSP	VEALFQEYQCY	16	11	19	100		1807
CSP	YNELEMNY	48	8	19	100		1808
CSP	YNELEMNYY	48	9	19	100		1809
EXP	LVEVNKRKSKY	64	11	1	100		1810
LSA	DDDDKKKY	130	8	1	100		1811
LSA	DEENIGIY	1796	8	1	100		1812
LSA	DLDEFKPIVQY	1781	11	1	100		1813
LSA	EDEISAEY	1761	8	1	100		1814
LSA	ELSEDIAY	1897	9	1	100		1815
LSA	FQDEENIGIY	1794	10	1	100	1.1000	1816
LSA	HGDVLAEDLY	1644	10	1	100	0.0012	1817
LSA	INDDDDKKKY	128	10	1	100		1818
LSA	KSLYDEHIKKY	1854	11	1	100		1819
LSA	KYEDEISAEY	1759	10	1	100	0.0011	1820
LSA	LDEFKPIVQY	1782	10	1	100		1821
LSA	LPSENERGY	1663	9	1	100	0.6700	1822
LSA	LPSENERGYY	1663	10	1	100	0.0011	1823
LSA	LSEDIMY	1898	8	1	100		1824
LSA	LYDEHIKKY	1856	9	1	100	0.0011	1825
LSA	NDDDDKKKY	129	9	1	100		1826
LSA	PSENERGY	1664	8	1	100		1827
LSA	PSENERGYY	1664	9	1	100	0.0790	1828
LSA	QDEENIGIY	1795	9	1	100		1829
LSA	SEEKIKKGKKY	1831	11	1	100		1830
LSA	VDELSEDITKY	1895	11	1	100		1831
LSA	VNDFQISKY	1752	9	1	100		1832
LSA	YDEHGCY	1857	8	1	100		1833
LSA	YEDEISAEY	1760	9	1	100	0.0012	1834
SSP2	CNDEVDLY	43	8	8	80		1835
SSP2	HPSDGKCNLY	206	10	10	100	0.0260	1836
SSP2	LLACAGLAY	510	9	10	100		1837
SSP2	LLSTNLPY	121	8	9	90		1838
SSP2	PSDGKCNLY	207	9	10	100	0.5400	1839

TABLE XVI
Malaria A3 Motif Peptides With Binding Information

			No. of	Sequence	Conservancy		SEQ.
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*0301	Id.

CSP	NMPNDPNR	323	8	19	100		1897
CSP	NIRVLNELNY	31	10	19	100	0.0005	1898
CSP	NVDENANA	331	8	19	100		1899
CSP	NVDENANANNA	331	11	16	84		1900
CSP	NVDPNANPNA	200	10	19	100		1901
CSP	PGDGNPDPNA	116	10	19	100		1902
CSP	PSDKHIEQY	346	9	15	79		1903
CSP	PSDICHIEQYLK	346	11	15	79		1904
CSP	QCYGSSSNTR	24	10	19	100		1905
CSP	QGHNMPNDPNR	320	11	19	100		1906
CSP	QVRIKPGSA	382	9	19	100		1907
CSP	RDGNNEDNEK	95	10	19	100	0.0005	1908
CSP	RVLNEHNY	33	8	19	100		1909
CSP	RVLNELNYDNA	33	11	19	100		1910
CSP	SDKHIEQY	347	8	15	79		1911
CSP	SDKHIEQYLK	347	10	15	79		1912
CSP	SDKHIEQYLKK	347	11	15	79		1913
CSP	SFLFVEALF	12	9	19	100		1914
CSP	StGLIMVLSF	423	10	19	100		1915
CSP	SSFLFVEA	11	8	19	100		1916
CSP	SSFLFVEALF	11	10	19	100		1917
CSP	SSIGLIMVLSF	422	11	19	100		1918
CSP	SVSSFLFVEA	9	10	19	100		1919
CSP	SVTCGNGIQVR	374	11	19	100		1920
CSP	TCGNGIQVR	376	9	19	100		1921
CSP	TCGNGIQVRIK	376	11	19	100		1922
CSP	VDENANANNA	332	10	16	84		1923
CSP	VDPNANPNA	201	9	19	100		1914
CSP	VLNEINYDNA	34	10	19	100		1925
CSP	VSSFLFVEA	10	9	19	100		1926
CSP	VSSFLFVEALF	10	11	19	100		1927
CSP	VTCGNGIQVR	375	10	19	100	0.0005	1928
CSP	YDNAGINLY	40	9	18	95		1929
CSP	YGKQENWY	56	8	19	100		1930
CSP	YGKQENWYSLK	56	11	19	100		1931
CSP	YGSSSNTR	26	8	19	100		1932
CSP	YSLKKNSR	63	8	19	100		1933
EXP	ADNANPDA	118	8	1	100		1934
EXP	ADSESNGEPNA	125	11	1	100		1935
EXP	ALFFITFNIC	10	9	1	100	1.1000	1936
EXP	DDNNLVSGPEH	152	11	1	100		1937
EXP	DLISDMIK	52	8	1	100		1938
EXP	DLISDMIKK	52	9	1	100	0.0001	1939
EXP	DSESNGEPNA	126	10	1	100		1940
EXP	DVHDLISDMIK	49	11	1	100		1941
EXP	ELYEVNKR	63	8	1	100		1942
EXP	ELVEVNKRK	63	9	1	100	0.0001	1943
EXP	ELVEVNKRKSK	63	11	1	100		1944
EXP	ESLAEKTNIC	19	9	1	100	0.0001	1945
EXP	ESNGEPNA	128	8	1	100		1946
EXP	EVNKRKSK	66	8	1	100		1947
EXP	EVNKRKSKY	66	9	1	100	0.0001	1948
EXP	EVNKRKSKYK	66	10	1	100	0.0005	1949
EXP	FFIIFNKESLA	12	11	1	100		1950
EXP	FFLALFFIIF	7	10	1	100		1951
EXP	FFIFNKESLA	13	10	1	100		1952
EXP	FLALFFIIF	8	9	1	100		1953
EXP	FLALFFIIFNK	8	11	1	100		1954
EXP	GGVGLVLY	94	8	1	100		1955
EXP	GLVLYNTEK	97	9	1	100	0.0069	1956
EXP	GLVLYNTEKGR	97	11	1	100		1957
EXP	GSGEPLIDVH	42	10	1	100	0.0005	1958
EXP	GSGVSSKK	30	8	1	100		1959
EXP	GSGVSSKKK	30	9	1	100	0.0003	1960
EXP	GSGVSSKKKNK	30	11	1	100		1961
EXP	GSSDPADNA	113	9	1	100		1962
EXP	GTGSGVSSK	28	9	1	100	0.0039	1963
EXP	GTGSGVSSKX	28	10	1	100	0.0071	1964
EXP	GTGSGVSSKKK	28	11	1	100		1965
EXP	GVGLVLYNTEK	95	11	1	100		1966
EXP	GVSSKKKNK	32	9	1	100	0.0001	1967
EXP	GVSSKKKNKK	32	10	1	100	0.0011	1968
EXP	HDLISDMIK	51	9	1	100	0.0001	1969
EXP	HDLISDMIKK	51	10	1	100	0.0009	1970
EXP	IFNKESLA	15	8	1	100		1971
EXP	IFNKESLAEK	15	10	1	100	0.0005	1972
EXP	IGSSDPADNA	112	10	1	100		1973
EXP	IIFNKESLA	14	9	1	100		1974
EXP	IIFNKESLAEK	14	11	1	100		1975
EXP	ILSVFFLA	3	8	1	100		1976
EXP	ILSVFFLALF	3	10	1	100		1977
EXP	ILSVFFLALFF	3	11	1	100		1978
EXP	KGSGEPLIDVH	41	11	1	100		1979
EXP	KGTGSGVSSK	27	10	1	100	0.0005	1980
EXP	KGTGSOVSSKK	27	11	1	100		1981
EXP	KIGSSDPA	111	8	1	100		1982
EXP	KIGSSDPADNA	111	11	1	100		1983
EXP	KILSVFFLA	2	9	1	100	0.1400	1984
EXP	KILSVFFLALF	2	11	1	100		1985
EXP	KLATSVLA	75	8	1	100		1986
EXP	LALFFIIF	9	8	1	100		1987
EXP	LALFFIIFNK	9	10	1	100	0.0140	1988
EXP	LFFIIFNK	11	8	1	100		1989
EXP	LGGVGLVLY	93	9	1	100	0.0001	1990
EXP	LISDMIKK	53	8	1	100		1991
EXP	LLGGVGLVLY	92	10	1	100	0.0034	1992
EXP	LSVFFLALF	4	9	1	100		1993
EXP	LSVFFLALFF	4	10	1	100		1994
EXP	LVEVNKRK	64	8	1	100		1995
EXP	LVEVNKRKSK	64	10	1	100	0.0005	1996
EXP	LVEVNKRKSKY	64	11	1	100		1997
EXP	LVLYNIEK	98	8	1	100		1998
EXP	LVLYNTEKGR	98	10	1	100	0.0005	1999
EXP	LVLYNTEKGRH	98	11	1	100		2000
EXP	NADPQVTA	134	8	1	100		2001
EXP	NLVSGPEH	155	8	1	100		2002
EXP	NTEKGRHPF	102	9	1	100		2003
EXP	NTEKGFHPFK	102	10	1	100	0.0047	2004
EXP	PADNANPDA	117	9	1	100		2005
EXP	PFKIGSSDPA	109	10	1	100		2006
EXP	SDPADNANPDA	115	11	1.	100		2007
EXP	SGEPLIDVH	43	9	1	100	0.0001	2008
EXP	SGVSSKKK	31	8	1	100		2009
EXP	SGVSSKKKNK	31	10	1	100	0.0005	2010
EXP	SGVSSKKKNKK	31	11	1	100		2011
EXP	SLAEKTINIK	20	8	1	100		2012
EXP	SSDPADNA	114	8	1	100		2013
EXP	SSKKKNKK	34	8	1	100		2014
EXP	SVFFLALF	S	8	1	100		2015
EXP	SVFFLALFF	5	9	1	100		2016
EXP	TGSGVSSK	29	8	1	100		2017
EXP	TGSGVSSKK	29	9	1	100	0.0001	2018
EXP	TGSGVSSKKK	29	10	1	100	0.0005	2019
EXP	VFFLALFF	6	8	1	100		2020
EXP	VFFLALFFIIF	6	11	1	100		2021
EXP	VGLVLYNIEK	96	10	1	100	0.0005	2022
EXP	VLLGGVGLVLY	91	11	1	100		2023
EXP	VLYNTEKGR	99	9	1	100	0.0110	2024
EXP	VLYNIEKGRH	99	10	1	100	0.0029	2025
EXP	VSSKKKNK	33	8	1	100		2026
EXP	VSSKKKNKK	33	9	1	100	0.0001	2027
LSA	ADTKKNLER	1632	9	1	100		2028
LSA	ADTKKNLERK	1632	10	1	100	0.0001	2029
LSA	ADTKKNLERKK	1632	11	1	100		2030
LSA	AIELPSENER	1660	10	1	100	0.0001	2031
LSA	DDDDKKKY	130	8	1	100		2032
LSA	DDDDKKKYIK	130	10	1	100	0.0001	2033
LSA	DDDKKKYIK	131	9	1	100	0.0001	2034
LSA	DDEDLDEF	1778	8	1	100		2035
LSA	DDEDLDEFK	1778	9	1	100	0.0001	2036
LSA	DDKKKYIK	132	8	1	100		2037
LSA	DDIDEGIEK	1817	9	1	100	0.0001	2038
LSA	DGSIKPEQK	1724	9	1	100	0.0001	2039
LSA	DIHKGHLEEK	1713	10	1	100	0.0004	2040
LSA	DIHKGHLEEKK	1713	11	1	100		2041
LSA	DITKYFMK	1901	8	1	100		2042
LSA	DLDEFKPIVQY	1781	11	1	100		2043
LSA	DLDEGIEK	1818	8	1	100		2044
LSA	DLEEKAAK	148	8	1	100		2045
LSA	DLEQDRLA	1388	8	1	100		2046
LSA	DLEQDRLAK	1388	9	1	100	0.0001	2047
LSA	DLEQDRLAKEK	1388	11	1	100		2048
LSA	DLEQERLA	1609	8	1	100		2049
LSA	DLEQERLAK	1609	9	1	100	0.0001	2050
LSA	DLEQERLAKEK	1609	11	1	100		2051
LSA	DLEQERLANEK	1524	11	1	100		2052
LSA	DLEpERRA	1575	8	1	100		2053
LSA	DLEQERRAK	1575	9	1	100	0.0001	2054
LSA	DLEQERRAKEK	1575	11	1	100		2055
LSA	DLEQRKADTK	1626	10	1	100	0.0001	2056
LSA	DLEQRKADIKK	1626	11	1	100		2057
LSA	DLERTKASK	1184	9	1	100	0.0001	2058
LSA	DLYGRLEIPA	1651	10	1	100		2059
LSA	DSEQERLA	521	8	1	100		2060
LSA	DSEQERLAK	521	9	1	100	0.0001	2061
LSA	DSEQERLAKEK	521	11	1	100		2062
LSA	DSKEISIIEK	1689	10	1	100	0.0001	2063
LSA	DTKKNLER	1633	8	1	100		2064
LSA	DTKIMERK	1633	9	1	100	0.0001	2065
LSA	DTKKNLERKK	1633	10	1	100	0.0001	2066
LSA	DVLAEDLY	1646	8	1	100		2067
LSA	DVLAEDLYGR	1646	10	1	100	0.0001	2068
LSA	DVNDFQISK	1751	9	1	100	0.0001	2069
LSA	DVNDFQISKY	1751	10	1	100	0.0003	2070
LSA	EDDEDLDEF	1777	9	1	100		2071
LSA	EDDEDLDEFK	1777	10	1	100	0.0001	2072
LSA	EDEISAEY	1761	8	1	100		2073
LSA	EDITKYFMK	1900	9	1	100	0.0001	2074
LSA	EDKSADIQNH	1733	10	1	100		2075
LSA	EDLEEKAA	147	8	1	100		2076
LSA	EDLEEKAAK	147	9	1	100	0.0002	2077
LSA	EDLYGRLEIPA	1650	11	1	100		2078
LSA	EFKPIVQY	1784	8	1	100		2079
LSA	EFPIVQYDNF	1784	11	1	100		2080
LSA	EGRRDIHK	709	8	1	100		2081
LSA	EGRRDIHKGH	1709	10	1	100	0.0001	2082
LSA	EIIKSNLR	33	8	1	100		2083
LSA	EISIIEKTNR	1692	10	1	100	0.0001	2084
LSA	ELEDLIEK	1805	8	1	100		2085
LSA	ELPSENER	1662	8	1	100		2086
LSA	ELPSENERGY	1662	10	1	100	0.0001	2087
LSA	ELPSENERGYY	1662	11	1	100		2088
LSA	ELSEDITK	1897	8	1	100		2089
LSA	ESLSEDITKY	1897	9	1	100	0.0002	2090
LSA	ELSEDITKYF	1897	10	1	100		2091
LSA	ELSEEKIK	1829	8	1	100		2092
LSA	ELSEEKIKK	1829	9	1	100	0.0002	2093
LSA	ELSEEKIKKGK	1829	11	1	100		2094
LSA	ELTMSNVK	83	8	1	100		2095
LSA	ESITTNVEGR	1702	10	1	100	0.0001	2096
LSA	ESITTNVEGRR	1702	11	1	100		2097
LSA	ETVNISDVNDF	1745	11	1	100		2098
LSA	FIKSLFHIF	1877	9	1	100		2099
LSA	FILVNLLIF	11	9	1	100		2100
LSA	FILVNLLIFH	11	10	1	100	0.0310	2101
LSA	FLKENKLNK	111	9	1	100	0.0260	2102
LSA	GDVLAEDLY	1645	9	1	100		2103
LSA	GDVLAEDLYGR	1645	11	1	100		2104
LSA	GSIKPEQK	1725	8	1	100		2105
LSA	GSIKPEQKEDK	1725	11	1	100		2106
LSA	GSSNSRNR	42	8	1	100		2107
LSA	GVSENIFLK	105	9	1	100	0.2700	2108
LSA	HGDVLAEDLY	1644	10	1	100	0.0001	2109
LSA	HIINDDDDK	126	9	1	100	0.0002	2110
LSA	HIINDDDDKK	126	10	1	100	0.0001	2111
LSA	HIINDDDDKKK	126	11	1	100		2112
LSA	HIKKYKNDK	1860	9	1	100	0.0002	2113
LSA	HILYISFY	3	8	1	100		2114
LSA	HILYISFYF	3	9	1	100		2115
LSA	HINGKIIK	20	8	1	100		2116
LSA	HLEEKKDGSIK	1718	11	1	100		2117
LSA	HVLSHNSY	59	8	1	100		2118
LSA	HVLSHNSYEK	59	10	1	100	0.0170	2119
LSA	IFHINGKIIK	18	10	1	100	0.0001	2120
LSA	IFLKENKLNK	110	10	1	100	0.0001	2121
LSA	IINDDDDK	127	8	1	100		2122
LSA	IINDDDDKK	127	9	1	100	0.0002	2123
LSA	IINDDDDKKK	127	10	1	100	0.0001	2124
LSA	IINDDDDKKKY	127	11	1	100		2125
LSA	ILVNLLIF	12	12	8	100		2126
LSA	ILVNLLIFH	12	9	1	100	0.0150	2127
LSA	ILYISFYF	4	8	1	100		2128
LSA	ISDVNDMISK	749	11	1	100		2129
LSA	ISHEKTNR	693	9	1	100	0.0001	2130
LSA	ISKYEDEISA	757	10	1	100		2131
LSA	ITTNVEGR	704	8	1	100		2132
LSA	ITTNVEGRR	704	9	1	100	0.0002	2133
LSA	DAMESEDITK	894	11	1	100		2134
LSA	KADTKKNLER	631	10	1	100	0.0001	2135
LSA	KADTKKNLERK	631	11	1	100		2136
LSA	KDEGIKSNIR	31	10	1	100		2137
LSA	KDGSIKPEQK	723	10	1	100	0.0004	2138
LSA	KDKELTMSNVK	80	11	1	100		2139
LSA	KDNNFKPNDK	845	10	1	100	0.0001	2140
LSA	KFIKSLFH	876	8	1	100		2141
LSA	KFIKSLFHIF	876	10	1	100		2142
LSA	KGHLEEKK	716	8	1	100		2143
LSA	KGKKYEKIK	837	9	1	100	0.0002	2144
LSA	KIIKNSEK	24	8	1	100		2145
LSA	KKKKGKKY	834	8	1	100		2146
LSA	KIKKGKKYEK	834	10	1	100	0.0081	2147
LSA	KLNKEGKLIEN	116	1t	1	100		2148
LSA	KLQEQQSDLER	177	11	1	100		2149
LSA	KSADIQNH	735	8	1	100		2150
LSA	KSLYDEIHK	854	9	1	100	0.0005	2151
LSA	KSLYDMIKK	854	10	1	100	0.0094	2152
LSA	KSLYDEHIKKY	854	11	1	100		2153
LSA	KSSEELSEEK	825	10	1	100	0.0001	2154
LSA	KTKDNNFK	843	8	1	100		2155
LSA	KTKNNENNK	68	9	1	100	0.0028	2156
LSA	KTKNNENNKF	68	10	1	100		2157
LSA	KTKNNENNKFF	68	11	1	100		2158
ISA	LAEDLYGR	1648	8	1	100		2159
LSA	LAKEKLQEQQR	1615	11	1	100		2160
LSA	LANEKLQEQQR	1530	11	1	100		2161
LSA	LDDLDEGIEK	1816	10	1	100	0.0001	2162
LSA	LDEFKPIVQY	1782	10	1	100		2163
LSA	LGVSENIF	104	8	1	100		2164
LSA	LGVSENIFLK	104	10	1	100	0.0001	2165
LSA	LIFHINGK	17	8	1	100		2166
LSA	LIFHINGKIIK	17	11	1	100		2167
LSA	LLIFNINGK	16	9	1	100	0.0260	2168
LSA	LSEDITKY	1898	8	1	100		2169
LSA	LSEDITKYF	1898	9	1	100		2170
LSA	LSEDITKYDAK	1898	11	1	100		2171
LSA	LSEEKIKK	1830	8	1	100		2172
ISA	LSEEKIKKGK	1830	10	1	100	0.0004	2173
LSA	LSEEKIKKGKK	1830	11	1	100		2174
LSA	LSHNSYEK	61	8	1	100		2175
LSA	LSFINSYEKTK	61	10	1	100	0.0004	2176
LSA	LVNLLIFH	13	8	1	100		2177
LSA	NDDDDKKK	129	8	1	100		2178
LSA	NDDDDKKKY	129	9	1	100		2179
LSA	NDDDDKKKYIK	129	11	1	100		2180
LSA	NDFQISKY	1753	8	1	100		2181
LSA	NDKQVNKEK	1866	9	1	100	0.0002	2182
LSA	NDKQVNKEKEK	1866	11	1	100		2183
LSA	NDKSLYDEH	1852	9	1	100		2184
LSA	NDKSLYDEHIK	1852	11	1	100		2185
LSA	NFKPNDKSLY	1848	10	1	100		2186
LSA	NFQDEENIGIY	1793	11	1	100		2187
ISA	NGKIIKNSEK	22	10	1	100	0.0004	2188
LSA	NIFLKENK	109	8	1	100		2189
LSA	NIFLKENKLNK	109	11	1	100		2190
LSA	NISDVNDF	1748	8	1	100		2191
LSA	NLDDLDEGIEK	1815	11	1	100		2192
LSA	NLERKKEH	1637	8	1	100		2193
LSA	NLGVSENIF	103	9	1	100		2194
LSA	NLGVSENIFLK	103	11	1	100		2195
LSA	NLLIFHINGK	15	10	1	100	0.0049	2196
LSA	NLRSGSSNSR	38	10	1	100	0.0004	2197
LSA	NSEKDFIKK	28	9	1	100	0.0002	2198
LSA	NSRNRKNEEK	45	10	1	100	0.0004	2199
LSA	NSRNRINEEKH	45	11	1	100		2200
LSA	NVEGRRDIH	1707	9	1	100	0.0002	2201
LSA	NVEGRRDIHK	1707	10	1	100	0.0004	2202
LSA	NVKNVSQINF	88	10	1	100		2203
LSA	NVKNVSQINFK	88	11	1	100		2204
LSA	NVSQTNFK	91	8	1	100		2205
LSA	PAIELPSENER	659	11	1	100		2206
LSA	PIVQYDNF	787	8	1	100		2207
LSA	PSENERGY	664	8	1	100		2208
LSA	PSENERGYY	664	9	1	100	0.0001	2209
LSA	QDEENIGIY	795	9	1	100		2210
LSA	QDEENIGIYK	795	10	1	100	0.0004	2211
LSA	QDNRGNSR	681	8	1	100		2212
LSA	QDNRGNSRDSK	681	11	1	100		2213
LSA	QDRLAKEK	391	8	1	100		2214
LSA	QGWISCLEM	128	11	1	100		2215
LSA	QISKYEDEISA	756	11	1	100		2216
LSA	QSDLEQDR	386	8	1	100		2217
LSA	QSDLEQDRLA	386	10	1	100		2218
LSA	QSDLEQDRLAK	386	11	1	100		2219
LSA	QSDLEQER	590	8	1	100		2220
LSA	QSDLEQERLA	590	10	1	100		2221
LSA	QSDLEQERLAK	590	11	1	100		2222
LSA	QSDLEQERR	573	9	1	100	0.0002	2223
LSA	QSDLEQERRA	573	10	1	100		2224
LSA	QSDLEQDRLAK	573	11	1	100		2225
LSA	QSDLERTK	182	8	1	100		2226
LSA	QSDLERTKA	182	9	1	100		2227
LSA	QSDLERTKASK	182	11	1	100		2228
LSA	QSDSEQER	519	8	1	100		2229
LSA	QSDSEQERLA	519	10	1	100		2230
LSA	QSDLEQDRLAK	519	11	1	100		2231
LSA	QSSLPQDNR	1676	9	1	100	0.0002	2232
LSA	QTNFKSLLR	94	9	1	100	0.0320	2233
ISA	QVNKEKEK	1869	8	1	100		2234
ISA	QVNKEIEKF	1869	9	1	100		2235
LSA	QVNKEKEKFIK	1869	11	1	100		2236
LSA	RDIHKGHLEIEK	1712	11	1	100		2237
ISA	RDLEQERLA	1608	9	1	100		2238
LSA	RDLEQERLAK	608	10	1	100	0.0004	2239
LSA	RDLEQERR	540	8	1	100		2240
LSA	RDLEQERRA	540	9	1	100		2241
LSA	RDLEQERRAK	540	10	1	100	0.0004	2242
LSA	RDLEQRKA	625	8	1	100		2243
ISA	RDLEQRKADTK	625	11	1	100		2244
ISA	RDSKEISIIEK	688	11	1	100		2245
ISA	RGNSRDSK	684	8	1	100		2246
LSA	RINEEKHEK	49	9	1	100	0.0033	2247
LSA	RINEEKNEKK	49	10	1	100	0.0024	2248
ISA	RINEEKHEKKH	49	11	1	100		2249
LSA	RSGSSNSR	40	8	1	100		2250
ISA	RSGSSNSRNR	40	10	1	100	0.0011	2251
LSA	SDLEQDRLA	1387	9	1	100		2252
ISA	SDLBQDRLAK	1387	10	1	100	0.0002	2253
LSA	SDLEQERLA	1591	9	1	100		2254
ISA	SDLEQERLAK	1591	10	1	100	0.0002	2255
ISA	SDLEQERR	1574	8	1	100		2256
LSA	SDLEQERRA	1574	9	1	100		2257
LSA	SDLEQERRAK	1574	10	1	100	0.0002	2258
LSA	SDLERTKA	1183	8	1	100		2259
ISA	SDLERTKASK	1183	10	1	100	0.0002	2260
LSA	SDSEQERLA	520	9	1	100		2261
ISA	SDSEQERLAK	520	10	1	100	0.0002	2262
ISA	SDVNDFQISK	1750	10	1	100	0.0002	2263
LSA	SDVNDFQISKY	1750	11	1	100		2264
LSA	SGSSNSRNR	41	9	1	100	0.0002	2265
LSA	SIIEKTNR	1694	8	1	100		2266
LSA	SIKPEQKEDK	1726	10	1	100	0.0002	2267
LSA	MTTNVEGR	1703	9	1	100	0.0002	2268
LSA	MTTNVEGRR	1703	10	1	100	0.0002	2269
LSA	SLPQDNRGNSR	1678	11	1	100		2270
LSA	SLYDEHKK	1855	8	1	100		2271
LSA	SLYDEHIKK	1855	9	1	100	0.0460	2272
LSA	SLYDEHIKKY	1855	10	1	100	0.0015	2273
ISA	SLYDEHIKKYK	1855	11	1	100		2274
LSA	SSEELSEEK	1826	9	1	100	0.0002	2275
LSA	SSEEBEDUK	1826	11	1	100		2276
LSA	SSLPQDNR	1677	8	1	100		2277
LSA	TTNVEGRR	1705	8	1	100		2278
LSA	TTNVEGRRIMH	1705	11	1	100		2279
ISA	TVNISDVNDF	1746	10	1	100		2280
ISA	VDESEDITK	1895	10	1	100	0.0002	2281
LSA	VDELSEDITKY	1895	11	1	100		2282
ISA	VLAEDLYGR	1647	9	1	100	0.0013	2283
LSA	VLSHNSYEK	60	9	1	100	0.0280	2284
LSA	VLSHNSYEKTK	60	11	1	100		2285
LSA	VSENIFLK	106	8	1	100		2286
LSA	VSENIFLKENK	106	11	1	100		2287
ISA	VSQTNFKSLLR	92	11	1	100		2288
LSA	YEEHDUCY	1857	8	1	100		2289
LSA	YDEHIKKYK	1857	9	1	100	0.0005	2290
LSA	YFILVNLLIF	10	10	1	100		2291
LSA	YFILVNLLWH	10	11	1	100		2292
LSA	YGRLEIPA	1653	8	1	100		2293
LSA	YIKGQDENR	137	9	1	100	0.0025	2294
SSP2	AATPYAGEPA	525	10	8	80		2295
SSP2	ACAGLAYK	512	8	10	100		2296
SSP2	ACAGLAYKF	512	9	10	100		2297
SSP2	ADSAWENVK	216	9	10	100	0.0002	2298
SSP2	AFNRFLVGCH	197	10	10	100		2299
SSP2	AGGIAGGLA	501	9	10	100		2300
SSP2	AGGLALLA	505	8	10	100		2301
SSP2	AGGLALLACA	505	10	10	100		2302
SSP2	ALLACAGLA	509	9	10	100	0.0002	2303
SSP2	ALLACAGLAY	509	10	10	100	0.0630	2304
SSP2	ALLACAGLAYK	509	11	10	100		2305
SSP2	ALLQVRKH	136	8	9	90		2306
SSP2	ASKNKEKA	107	8	10	100		2307
SSP2	ATPYAGEPA	526	9	8	80		2308
SSP2	ATPYAGEPAPF	526	11	8	80		2309
SSP2	AVCVEVEK	233	8	10	100		2310
SSP2	AVCVEVEKTA	233	10	10	100		2311
SSP2	CAGLAYKF	513	8	10	100		2312
SSP2	CGKGTRSR	257	8	10	100		2313
SSP2	CGKGTRSRK	257	9	10	100	0.0002	2314
SSP2	CGKGIRSRKR	257	10	10	100	0.0002	2315
SSP2	CSGSIRRH	55	8	10	100		2316
SSP2	CSVTCGKGTR	253	10	10	100	0.0002	2317
SSP2	CVEVEKTA	235	8	10	100		2318
SSP2	DALLQVRK	135	8	9	90		2319
SSP2	DALLQVRKH	135	9	9	90	0.0004	2320
SSP2	DASKNKEK	106	8	10	100		2321
SSP2	DASKNKEKA	106	9	10	100		2322
SSP2	DCSGSIRR	54	8	10	100		2323
SSP2	DCSGSIRRH	54.	9	10	100		2324
SSP2	DDQPRPRGDNF	301	11	9	90		2325
SSP2	DDREENFDIPK	385	11	10	100		2326
SSP2	CCKCNLYA	209	8	10	100		2327
SSP2	DGKCNLYADSA	209	11	10	100		2328
SSP2	DIPKKPENK	392	9	10	100	0.0004	2329
SSP2	DIPICKPENKH	392	10	10	100	0.0002	2330
SSP2	DLDEPEQF	546	8	10	100		2331
SSP2	DLDEPEQFR	546	9	10	100	0.0002	2332
SSP2	DLFLVNGR	19	8	10	100		2333
SSP2	DSAWENVK	217	8	10	100		2334
SSP2	DSIQDSLK	166	8	10	100		2335
SSP2	DSIQDSLKESR	166	11	10	100		2336
SSP2	DSLKESRK	170	8	9	90		2337
SSP2	DVPKNPEDDR	378	10	10	100	0.0002	2338
SSP2	DVQNNIVDBK	27	11	10	100		2339
SSP2	EDDQPRPR	300	8	10	100		2340
SSP2	EDDREENF	384	8	10	100		2341
SSP2	EDKDLDEPEQF	543	11	10	100		2342
SSP2	EDRETRPH	450	8	9	90		2343
SSP2	EDRETRPHGR	450	10	9	90		2344
SSP2	EIIRLHSDA	99	9	10	100		2345
SSP2	EIIRLHSDASK	99	11	10	100		2346
SSP2	ELQEQCEEER	276	10	8	80	0.0002	2347
SSP2	ETLGEEDK	538	8	10	100		2348
SSP2	EVCNDEVDLY	41	10	8	80	0.0002	2349
SSP2	EVPSDVPK	374	8	10	100		2350
SSP2	FDETLGEEDK	536	10	10	100	0.0002	2351
SSP2	FDIPKKPENK	391	10	10	100	0.0002	2352
SSP2	FDIPKKPENKH	391	11	10	100		2353
SSP2	FDLFLVNGR	18	9	10	100		2354
SSP2	FFDLFLVNGR	17	10	10	100		2335
SSP2	FGIGQGINVA	188	10	10	100		2356
SSP2	FGIGQGINVAF	188	11	10	100		2357
SSP2	FLIFFDLF	14	8	10	100		2358
SSP2	FLVGCHPSDGK	201	11	10	100		2359
SSP2	FMKAVCVEVEK	230	11	10	100		2360
SSP2	FVVPGAATPY	520	10	8	80	0.0002	2361
SSP2	FVVPGAATPYA	520	11	8	80		2362
SSP2	GAATPYAGEPA	524	11	8	80		2363
SSP2	GCHPSDGK	204	8	10	100		2364
SSP2	GDNFAVEK	308	8	9	90		2365
SSP2	GGIAGGLA	502	8	10	100		2366
SSP2	GGIAGGLALLA	502	11	10	100		2367
SSP2	GGLALLACA	506	9	10	100		2368
SSP2	GIAGGLALLA	503	10	10	100		2369
SSP2	GIGQGINVA	189	9	10	100		2370
SSP2	GIGQGINVAF	189	10	10	100		2371
SSP2	GINVAFNR	193	8	10	100		2372
SSP2	GINVAFNRF	193	9	10	100		2373
SSP2	GIPDSIQDSLK	163	11	10	100		2374
SSP2	GLALLACA	507	8	10'	100		2375
SSP2	GLALLACAGLA	507	11	10	100		2376
SSP2	GLAYKFVVPGA	515	11	10	100		2377
SSP2	GSIRRHNWVNH	37	11	8	80		2378
SSP2	GTRSRKRELH	260	11	10	100		2379
SSP2	HAVPLAMK	67	8	10	100		2380
SSP2	HDNQNNLPNDK	401	11	10	100		2381
SSP2	HGRNNENR	457	8	10	100		2382
SSP2	HGRNNENRSY	457	10	10	100	0.0004	2383
SSP2	HLNDRINR	143	8	10	100		2384
SSP2	HLNDRINRENA	143	11	10	100		2385
SSP2	HSDASKNK	104	8	10	100		2386
SSP2	HSDASKNKEK	104	10	10	100	0.0004	2387
SSP2	HSDASKNKEKA	104	11	10	100		2388
SSP2	HVPNSEDR	445	8	10	100		2389
SSP2	HVPNSEDRE1R	445	11	9	90		2390
SSP2	IAGGIAGGLA	500	10	10	100		2391
SSP2	IAGGLALLA	504	9	10	100	0.0002	2392
SSP2	IAGGLALLACA	504	11	10	100		2393
SSP2	IFFDLFLVNGR	16	11	10	100		2394
SSP2	IGQGINVA	190	8	10	100		2395
SSP2	IGQGINVAF	190	9	10	100		2396
SSP2	IGQGINVAFNR	190	11	10	100		2397
SSP2	RRLHSDA	100	8	10	100		2398
SSP2	IIRLHSDASK	100	10	10	100	0.0230	2399
SSP2	IVDEIKYR	32	8	9	90		2400
SSP2	IVFLIFFDLF	12	10	10	100		2401
SSP2	KAVCVEVEK	232	9	10	100	0.0004	2402
SSP2	KAVCVEVEKTA	232	11	10	100		2403
SSP2	KCNLYADSA	211	9	10	100		2404
SSP2	KDLDEPEQF	545	9	10	100		2405
SSP2	KDLDEPEQFR	545	10	10	100		2406
SSP2	KFVVPGAA	519	8	10	100		2407
SSP2	KFVVPGAAIPY	519	11	8	80		2408
SSP2	KGIRSRICR	259	8	10	100		2409
SSP2	KIAGGIAGGLA	499	11	10	100		2410
SSP2	KVLDNERK	421	8	8	80		2411
SSP2	LACACLAY	511	8	10	100		2412
SSP2	LACAGLAYK	511	9	10	100	0.0240	2413
SSP2	LACAGLAYKF	511	10	10	100		2414
SSP2	LALLACAGLA	508	10	10	100		2415
SSP2	LALLACAGIAY	508	11	10	100		2416
SSP2	LAYKFVVPGA	516	10	10	100		2417
SSP2	LAYKFVVPGAA	516	11	10	100		2418
SSP2	LDEPEQFR	547	8	10	100		2419
SSP2	LGNVKYLVIVF	4	11	10	100		2420
SSP2	LLACAGLA	510	8	10	100		2421
SSP2	LLACAGLAY	510	9	10	100	0.0120	2422
SSP2	LLACAGLAYK	510	10	10	100	0.9500	2423
SSP2	LLACAGLAYKF	510	11	10	100		2424
SSP2	LLMDCSGSIR	51	10	10	100	0.0004	2425
SSP2	LLMDCSGSIRR	51	11	10	100		2426
SSP2	LLQVRKHLNDR	137	11	9	90		2427
SSP2	LLSINLPY	121	8	9	90		2428
SSP2	LLSTNLPYGR	121	10	8	80	0.0017	2429
SSP2	LMDCSGSIR	52	9	10	100	0.0004	2430
SSP2	LMDCSGSIRR	52	10	10	100	0.0015	2431
SSP2	LMDCSGSIRRH	52	11	10	100		2432
SSP2	LSTNLPYGR	122	9	8	80	0.0004	2433
SSP2	LVGCHPSDOK	202	10	10	100	0.0004	2434
SSP2	LVIVFLIF	10	8	10	100		2435
SSP2	LVIVFLIFF	10	9	10	100		2436
SSP2	MDCSGSIR	53	8	10	100		2437
SSP2	MDCSGSIRR	53	9	10	100		2438
SSP2	MDCSGSIRRH	53	10	10	100		2439
SSP2	NDRINRENA	145	9	10	100		2440
SSP2	NFDIPKKPENK	390	11	10	100		2441
SSP2	NIPEDSEK	366	8	10	100		2442
SSP2	NIVDSKY	31	8	10	100		2443
SSP2	NIVDEIKYR	31	9	9	90	0.0005	2444
SSP2	NLPNDKSDR	406	9	10	100	0.0005	2445
SSP2	NSEDRETR	448	8	9	90		2446
SSP2	NSEDRETRPH	448	10	9	90	0.0004	2447
SSP2	NVIGPFMK	225	8	10	100		2448
SSP2	NVIGPFMKA	225	9	10	100	0.0002	2449
SSP2	NVKNVIGPF	222	9	10	100		2450
SSP2	NVKNVIGPFMK	222	11	10	100		2451
SSP2	NVKYLVIVF	6	9	10	100		2452
SSP2	PCSVTCGK	252	8	10	100		2453
SSP2	PCSVTCGKGTR	252	11	10	100		2454
SSP2	PDSIQDSLK	165	9	10	100	0.0005	2455
SSP2	PFDETLGEEDK	535	11	10	100		2456
SSP2	PGAATPYA	523	8	8	80		2457
SSP2	PSDGKCNLY	207	9	10	100	0.0002	2458
SSP2	PSDOKCNLYA	207	10	10	1013		2459
SSP2	PSPNPEEGK	328	9	10	100	0.0005	2460
SSP2	QCEEERCPPK	280	10	8	80	0.0004	2461
SSP2	QDNNGNRH	438	8	10	100		2462
SSP2	QDSLKESR	169	8	10	100		2463
SSP2	QDSLKESRK	169	9	9	90	0.0005	2464
SSP2	QGINVAFNR	192	9	10	100	0.0009	2465
SSP2	QGINVAFNRF	192	10	10	100		2466
SSP2	QSQDNNGNR	436	9	10	100	0.0005	2467
SSP2	QSQDNNONRH	436	10	10	100	0.0004	2468
SSP2	QVRICHLNDR	139	9	9	90	0.0005	2469
SSP2	RGDNFAVEK	307	9	9	90	0.0005	2470
SSP2	RGVKIAVF	181	8	9	90		2471
SSP2	RLHSDASK	102	8	10	100		2472
SSP2	RLHSDASKNK	102	10	10	100	0.0240	2473
SSP2	RSRKREILH	262	9	10	100	0.0110	2474
SSP2	SDASICNKEK	105	9	10	100	0.0005	2475
SSP2	SDASICNICEKA	105	10	10	100		2476
SSP2	SDGKCNLY	208	8	10	100		2477
SSP2	SDGKCNLYA	208	9	10	100		2478
SSP2	SDNKYKIA	494	8	9	90		2479
SSP2	SDVPKNPEDDR	377	11	10	100		2480
SSP2	SIQDSLKESR	167	10	10	100	0.0004	2481
SSP2	SIQDSLKESRK	167	11	9	90		2482
SSP2	SIRRHNWVNH	58	10	8	80	0.0011	2483
SSP2	SIRRHNWVNHA	58	11	8	80		2484
SSP2	SLLSTNLPY	120	9	9	90	0.0280	2485
SSP2	SLLSTNLPYGR	120	11	8	80		2486
SSP2	STNLPYGR	123	8	8	80		2487
SSP2	SVTCGKGTR	254	9	10	100	0.0005	2488
SSP2	SVICGKGTRSR	254	11	10	100		2489
SSP2	TCGKGTRSR	256	9	10	100		2490
SSP2	TCGKGTRSRK	256	10	10	100	0.0004	2491
SSP2	TCGKGIRSRKR	256	11	10	100		2492
SSP2	VAFNRFLVGCH	196	11	10	100		2493
SSP2	VCNDEVDLY	42	9	8	80		2494
SSP2	VCVEVEKTA	234	9	10	100		2495
SSP2	VFGIGQGINVA	187	11	10	100		2496
SSP2	VFLIFFDLF	13	9	10	100		2497
SSP2	VGCHPSDGK	203	9	10	100	0.0005	2498
SSP2	VIGPFMKA	226	8	10	100		2499
SSP2	VIVFLIFF	11	8	10	100		2500
SSP2	VIVFLIFFDLF	11	11	10	100		2501
SSP2	VTCGKGTR	255	8	10	100		2502
SSP2	VTCGKGTRSR	255	10	10	100	0.0004	2503
SSP2	VTCGKGTRSRK	255	11	10	100		2504
SSP2	VVPGAATPY	521	9	8	80	0.0005	2505
SSP2	VVPGAATPYA	521	10	8	80		2506
SSP2	WSPCSVTCGK	250	10	10	100	0.0004	2507
SSP2	WVNHAVPLA	64	9	8	80	0.0002	2508
SSP2	WVNHAVPLAMK	64	11	8	80		2509
SSP2	YADSAWENVIC	215	10	10	100	0.0004	2510
SSP2	YAGEPAPF	529	8	8	80		2511
SSP2	YLLMDCSGSIR	50	11	10	100		2512
SSP2	YLVIVFLIF	9	9	10	100		2513
SSP2	YLVIVFLIFF	9	10	10	100		2514

TABLE XVII
Malaria All Motif Peptides With Binding Information

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*1101	Seq. Id.

CSP	ALFQEYQCY	18	9	19	100	0.0021	2515
CSP	ANANNAVK	336	8	16	84		2516
CSP	ANPNANKNK	305	9	19	100		2517
CSP	CGNGIQVR	377	8	19	100		2518
CSP	CGNGIQVRIK	377	10	19	100	0.0002	2519
CSP	DGNNEDNEX	96	9	19	100	0.0002	2520
CSP	DGNNEDNEKLR	96	11	19	100		2521
CSP	DGNNNNGDNGR	77	11	17	89		2522
CSP	DIEKKICK	402	8	19	100		2523
CSP	DIEKKICKMEK	402	11	19	100		2524
CSP	DNAGINLY	41	8	18	95		2525
CSP	DNEKLRKPK	101	9	19	100		2526
CSP	DNEKLRKPKH	101	10	19	100		2527
CSP	DNEKLRKPKHK	101	11	19	100		2528
CSP	DNGREGKDEDK	84	11	19	100		2529
CSP	EALFQEYQCY	17	10	19	100	0.0002	2530
CSP	EDNEKLRK	100	8	19	100		2531
CSP	EDNEKLRKPK	100	10	19	100	0.0002	2532
CSP	EDNEKLRKPKH	100	11	19	100		2533
CSP	EGKDEDKR	88	8	19	100		2534
CSP	ELEMNYYGK	50	9	19	100	0.0003	2535
CSP	ENANANNAVK	334	10	16	84		2536
CSP	ENKIEKKICK	400	10	19	100		2537
CSP	ENWYSLKK	60	8	19	100		2538
CSP	ENWYSLKKNSR	60	11	19	100		2539
CSP	FLFVEALFQEY	13	11	19	100		2540
CSP	FVEALFQEY	15	9	19	100	0.0003	2541
CSP	GDNGREGK	83	8	19	100		2542
CSP	GNGIQVRIK	378	9	19	100		2543
CSP	GNNEDNEK	97	8	19	100		2544
CSP	GNNEDNEKLR	97	10	19	100		2545
CSP	GNNEDNEKLRK	97	11	19	100		2546
CSP	GNNNNGDNGR	78	10	19	100		2547
CSP	HIEQYLKK	350	8	15	79		2548
CSP	HNMPNDPNR	322	9	19	100		2549
CSP	INLYNELEMNY	45	11	18	95		2550
CSP	KLRKPKHK	104	8	19	100		2551
CSP	KLRKPKHKK	104	9	19	100	0.0037	2552
CSP	KLRKPKHKKLK	104	11	19	100		2553
CSP	KNNNNEEPSDK	343	11	19	100		2554
CSP	KNNQGNGQGH	313	10	19	100		2555
CSP	LDYENDIEK	397	9	18	95	0.0002	2556
CSP	LDYENDIEKK	397	10	18	95	0.0002	2557
CSP	LFQEYQCY	19	8	19	100		2558
CSP	LFVEALFQEY	14	10	19	100		2559
CSP	LNYDNAGINLY	38	11	18	95		2560
CSP	MNYYGKQENWY	53	11	19	100		2561
CSP	NANANNAVK	335	9	16	1984	0.0002	2562
CSP	NANPNANPNK	304	10	19	100	0.0021	2563
CSP	NDIEKKICK	401	9	19	100	0.0002	2564
CSP	NGDNGREGK	82	9	19	100	0.0002	2565
CSP	NGIQVRIK	379	8	19	100		2566
CSP	NGREGKDEDK	85	10	19	100	0.0002	2567
CSP	NGEGKDEDKR	85	11	19	100		2568
CSP	NLYNELEMNY	46	10	19	100	0.0002	2569
CSP	NLYNELEMNYY	46	11	19	100		2570
CSP	NMPNDPNR	323	8	19	100		2571
CSP	NNEDNEKIR	98	9	19	100		2572
CSP	NNEDNEXLRK	98	10	19	100		2373
CSP	NNEEPSDK	346	8	19	100		2574
CSP	NNEEPSDKH	346	9	19	100		2575
CSP	NNGDNGREGK	81	10	19	100		2576
CSP	NNNEEPSDK	345	9	19	100		2577
CSP	NNNEEPSDKH	345	10	19	100		2578
CSP	NNNGDNGR	80	8	19	100		2579
CSP	NNNGDNGREGK	80	11	19	100		2580
CSP	NNNNEEPSDK	344	10	19	100		2581
CSP	NNNNEEPSDKH	344	11	19	100		2582
CSP	NNNNGDNGR	79	9	19	100		2583
CSP	NNQGNGQGH	314	9	19	100		2584
CSP	NTRVLNELNY	31	10	19	100	0.0002	2585
CSP	PNANPNANPNK	303	11	19	100		2586
CSP	PSDKHIEQY	346	9	15	79		2587
CSP	PSDKHIEQYLK	346	11	15	79		2588
CSP	QCYGSSSNTR	24	10	19	100		2589
CSP	QGHNMPNDPNR	320	11	19	100		2590
CSP	RDGNNEDNEK	95	10	19	100	0.0002	2591
CSP	RVLNELNY	33	8	19	100		2592
CSP	SDICHIEQY	347	8	15	79		2593
CSP	SDKHIEQYLK	347	10	15	79		2594
CSP	SDKHIEQYLKK	347	11	15	79		2595
CSP	SNIRVLNELNY	30	11	19	100		2596
CSP	SVTCGNGIQVR	374	11	19	100		2597
CSP	TCGNGIQVR	376	9	19	100		2598
CSP	TCGNGIQVRDC	376	11	19	100		2599
CSP	VTCGNGIQVR	375	10	19	100	0.0340	2600
CSP	YDNAGINLY	40	9	18	95		2601
CSP	YGKQENWY	56	8	19	100		2602
CSP	YGKQENWYSLK	56	11	19	100		2603
CSP	YGSSSNTR	26	8	19	100		2604
CSP	YNELEMNY	48	8	19	100		2605
CSP	YNELEMNYY	48	9	19	100		2606
CSP	YNELEMNYYGK	48	11	19	100		2607
CSP	YSLKKNSR	63	8	19	100		2608
EXP	ALFFIIFNK	10	9	1	100	1.2000	2609
EXP	DDNNLVSGPEH	152	11	1	100		2610
EXP	DLISDMIK	52	8	1	100		2611
EXP	DLISDMIKK	52	9	1	100	0.0003	2612
EXP	DNNLVSGPEH	153	10	1	100		2613
EXP	DVHDLISDMIK	49	11	1	100		2614
EXP	ELVEVNKR	63	8	1	100		2615
EXP	ELVEVNKRK	63	9	1	100	0.0002	2616
EXP	ELVEVNKRKSK	63	11	1	100		2617
EXP	EMADCTNK	19	9	1	100	0.0002	2618
EXP	EVNKRKSK	66	8	1	100		2619
EXP	EVNKRKSKY	66	9	1	100	0.0002	2620
EXP	EVNKRKSKYK	66	10	1	100	0.0002	2621
EXP	FLALFFIIFNK	8	11	1	100		2622
EXP	FNKESLAEK	16	9	1	100		2623
EXP	GGVGLVLY	94	8	1	100		2624
EXP	GLVLYNIEK	97	9	1	100	0.0055	2625
EXP	GLVLYNTEKGR	97	11	1	100		2626
EXP	GSGEPLIDVH	42	10	1	00	0.0002	2627
EXP	GSGVSSKK	30	8	1	00		2628
EXP	GSOVSSKKK	30	9	1	00	0.0065	2629
EXP	GSGVSSKKKNK	30	11	1	00		2630
EXP	GTGSGVSSK	28	9	1	00	0.0180	2631
EXP	GTGSGVSSKK	28	10	1	00	0.0340	2632
EXP	GTGSGVSSKKK	28	11	1	00		2633
EXP	GVGLVLYNIEK	95	11	1	00		2634
EXP	GVSSKKKNK	32	9	1	00	0.0002	2635
EXP	GVSSKKKNKK	32	10	1	00	0.0002	2636
EXP	HDLISDMIK	51	9	1	00	0.0002	2637
EXP	HDLISDMIKK	51	10	1	00	0.0002	2638
EXP	IFNKESLAEK	15	10	1	00	0.0003	2639
EXP	IIFNKESLAEK	14	11	1	00		2640
EXP	KGSGEPLDVH	41	11	1	00		2641
EXP	KGTGSGVSSK	27	10	1	00	0.0009	2642
EXP	KGTGSGVSSKK	27	11	1	00		2643
EXP	LALFFIIFNK	9	10	1	00	0.0530	2644
EXP	LFFIIFNK	11	8	1	00		2645
EXP	LGGVGLVLY	93	9	1	00	0.0002	2646
EXP	LISDMIKK	53	8	1	00		2647
EXP	LLGGVGLVLY	92	10	1	00	0.0003	2648
EXP	LVEVNKRK	64	8	1	00		2649
EXP	LVEVNKRKSK	64	10	1	00	0.0002	2650
EXP	LVEVNKRKSKY	64	11	1	00		2651
EXP	LVLYNIEK	98	8	1	00		2652
EXP	LVLYNTEKGR	98	10	1	00	0.0002	2653
EXP	LVLYNTEKGRH	98	11	1	00		2654
EXP	NLVSGPEH	155	8	1	00		2655
EXP	NNLVSGPEH	154	9	1	00		2656
EXP	NTEKGRHPFK	102	10	1	00	0.0080	2657
EXP	SGEPLIDVH	43	9	1	00	0.0002	2658
EXP	SGVSSKKK	31	8	1	00		2659
EXP	SGVSSKKKNK	31	10	1	00	0.0002	2660
EXP	SGVSSKKKNKK	31	11	1	00		2661
EXP	SLAEKTNK	20	8	1	00		2662
EXP	SSKKKNKK	34	8	1	00		2663
EXP	TGSGVSSK	29	8	1	00		2664
EXP	TGSGVSSKK	29	9	1	00	0.0016	2665
EXP	TGSGVSSKKK	29	10	1	00	0.0002	2666
EXP	VGLVLYNTEK	96	10	1	00	0.0052	2667
EXP	VLLGGVGLVLY	91	11	1	00		2668
EXP	VLYNTEKGR	99	9	1	00	0.0007	2669
EXP	VLYNTEXGRH	99	10	1	00	0.0002	2670
EXP	VNKRKSKY	67	8	1	00		2671
EXP	VNKFRKSKYK	67	9	1	00		2672
EXP	VSSKKKNK	33	8	1	00		2673
EXP	VSSKKKNKK	33	9	1	00	0.0002	2674
EXP	YNTEKGRH	101	8	1	00		2675
EXP	YNTEKGRHPFK	101	11	1	00		2676
LSA	ADTKKNLER	1632	9	1	00		2677
LSA	ADTKKNLERK	1632	10	1	00	0.0003	2678
LSA	ADTKKNLERKK	1632	11	1	00		2679
LSA	AIELPSENER	1660	10	1	00	0.0002	2680
LSA	ANEKLQBQQR	1531	10	1	00		2681
LSA	DDDDKKKY	130	8	1	00		2682
LSA	DDDDKKKYIK	130	10	1	100	0.0002	2683
LSA	DDDKKKYIK	131	9	1	100	0.0002	2684
LSA	DDEDLDEFK	1778	9	1	100	0.0002	2685
LSA	DDKKKYIK	132	8	1	100		2686
LSA	DDLDEGIEK	1817	9	1	100	0.0002	2687
LSA	DGSIKPEQK	1724	9	1	100	0.0002	2688
LSA	DIHKGHLEEK	1713	10	1	100	0.0002	2689
LSA	DIHKGHLEEXK	1713	11	1	100		2690
LSA	DITKYFMK	1901	8	1	100		2691
LSA	DLDEFKPIVQY	1781	11	1	100		2692
LSA	DLDEOIEK	1818	8	1	100		2693
LSA	DLEEKAAK	148	8	1	100		2694
LSA	DLEQDRLAK	1388	9	1	100	0.0002	2695
LSA	DLEQDRLAKEK	1388	11	1	100		2696
LSA	DLEQDRLAK	1609	9	1	100	0.0002	2697
LSA	DLEQERLAKEK	1609	11	1	100		2698
LSA	DLEQERLANEK	1524	11	1	100		2699
LSA	DLEQBIRAK	1575	9	1	100	0.0002	2700
LSA	DLEQERRAKEK	1575	11	1	100		2701
LSA	DLEQRKADTK	1626	10	1	100	0.0002	2702
LSA	DLEQRKADTKK	1626	11	1	100		2703
LSA	DLERTKASK	1184	9	1	100	0.0002	2704
LSA	DNNFKPNDK	1846	9	1	100		2705
LSA	DNRGNSRDSK	1682	10	1	100		2706
LSA	DSEQERLAK	521	9	1	100	0.0002	2707
LSA	DSEQERLAKEK	521	11	1	100		2708
LSA	DSKEISIIEK	1689	10	1	100	0.0002	2709
LSA	DTKKNLER	1633	8	1	100		2710
LSA	DTKKNLERK	1633	9	1	100	0.0002	2711
LSA	DTKKNLERKK	1633	10	1	100	0.0002	2712
LSA	DVLAEDLY	1646	8	1	100		2713
LSA	DVLAEDLYGR	1646	10	1	100	0.0002	2714
LSA	DVNDFQISK	1751	9	1	100	0.0018	2715
LSA	DVNDFQISKY	1751	10	1	100	0.0002	2716
LSA	EDDEDLDEFK	1777	10	1	100	0.0002	2717
LSA	EDEISAEY	1761	8	1	!CO		2718
LSA	EDMCYFMK	1900	9	1	100	0.0003	2719
LSA	EDKSADIQNH	1733	10	1	100		2720
LSA	EDLEEKAAK	147	9	1	100	0.0002	2721
LSA	EFKPIVQY	1784	8	1	100		2722
LSA	EGRRDIHK	1709	8	1	100		2723
LSA	EGRRDIHKGH	1709	10	1	100	0.0002	2724
LSA	EIIKSNLR	33	8	1	100		2725
LSA	EISIIEKTNR	1692	10	1	100	0.0002	2726
LSA	ELEDLIEK	1805	8	1	100		2727
LSA	ELPSENER	1662	8	1	100		2728
LSA	ELPSENERGY	1662	10	1	100	0.0002	2729
LSA	ELPSENERGYY	1662	11	1	100		2730
LSA	ELSEDDK	1897	8	1	100		2731
LSA	ELSEDITKY	1897	9	1	100	0.0002	2732
LSA	ELSEEKIK	1829	8	1	100		2733
LSA	ELSEEKIKK	1829	9	1	100	0.0002	2734
LSA	ELSEEKIKKGK	1829	11	1	100		2735
LSA	ELTMSNVK	83	8	1	100		2736
LSA	ENERGYYIPH	1666	10	1	100		2737
LSA	ENIFLKENK	108	9	1	100		2738
LSA	ENKLNKEGK	114	9	1	100		2739
LSA	ENNKFFDK	73	8	1	100		2740
LSA	ENNKFFDKDK	73	10	1	100		2741
LSA	ENRQEDLEEK	143	10	1	100		2742
LSA	ESITINVEGR	1702	10	1	100	0.0002	2743
LSA	ESITTNVEGRR	1702	11	1	100		2744
LSA	FILVNLLIFH	11	10	1	100	0.0060	2745
LSA	FLKENKLNK	111	9	1	100	0.0005	2746
LSA	GDVLAEDLY	1645	9	1	100		2747
LSA	GDVLAEDLYGR	1645	11	1	100		2748
LSA	GSIKPEQK	1725	8	1	100		2749
LSA	GSIKPEQKEDK	1725	11	1	100		2750
LSA	GSSNSRNR	42	8	1	100		2751
LSA	GVSENIFLK	105	9	1	100	0.6600	2752
LSA	HGDVLAEDLY	1644	10	1	100	0.0002	2753
LSA	HIINDDDDK	126	9	1	100	0.0002	2754
LSA	HIINDDDDKK	126	10	1	100	0.0002	2755
LSA	HIINDDDDKKK	126	11	1	100		2756
LSA	HIKKYKNDK	1860	9	1	100	0.0002	2757
LSA	HILYISFY	3	8	1	100		2758
LSA	HINGKIIK	20	8	1	100		2759
LSA	HLEEKDGSIK	1718	11	1	100		2760
LSA	HNSYEKTK	63	8	1	100		2761
LSA	HVLSHNSY	59	8	1	100		2762
LSA	HVLSHNSYEK	59	10	1	100	0.0140	2763
LSA	IFHINGKIIK	18	10	1	100	0.0006	2764
LSA	IFLKENIQNK	110	10	1	100	0.0002	2765
LSA	IINDDDDK	127	8	1	100		2766
LSA	IINDDDDKK	127	9	1	100	0.0002	2767
LSA	IINDDDDKKK	127	10	1	100	0.0002	2768
LSA	IINDDDDKKKY	127	11	1	100		2769
LSA	ILVNLLIFH	12	9	1	100	0.0008	2770
LSA	INDDDDKK	128	8	1	100		2771
LSA	INDDDDKKK	128	9	1	100		2772
LSA	INDDDDKKKY	128	10	1	100		2773
LSA	INEEKHSC	50	8	1	100		2774
LSA	INEEKHEKK	50	9	1	100		2775
LSA	INEEKNEKKH	50	10	1	100		2776
LSA	INGKIIKNSEK	21	11	1	100		2777
LSA	ISDVNDFQISK	1749	11	1	100		2778
LSA	ISIIEKTNR	1693	9	1	100	0.0008	2779
LSA	ITTNVEGR	1704	8	1	100		2780
LSA	ITTNVEGRR	1704	9	1	100	0.0007	2781
LSA	IVDELSEDMC	1894	11	1	100		2782
LSA	KADTKKNLER	1631	10	1	100	0.0002	2783
LSA	KADTKKNLERK	1631	11	1	100		2784
LSA	KDEIIKSTILR	31	10	1	100		2785
LSA	KDGSIKPEQK	1723	10	1	100	0.0002	2786
LSA	KDKELIMSNVK	80	11	1	100		2787
LSA	KDNNFKPNDK	1845	10	1	100	0.0002	2788
LSA	KFIKSLFH	1876	8	1	100		2789
LSA	KGHLEEKK	1716	8	1	100		2790
LSA	KGKKYEKIK	1837	9	1	100	0.0002	2791
LSA	KIIKNSEK	24	8	1	100		2792
LSA	KIKKGKKY	1834	8	1	100		2793
LSA	KIKKGKKYEK	1834	10	1	100	0.0007	2794
LSA	KLNKEGKLIEH	116	11	1	100		2795
LSA	KLQEQQSDLER	1177	11	1	100		2796
LSA	KNDKQVNK	1865	8	1	100		2797
LSA	KNDKQVNKEK	1865	10	1	100		2798
LSA	KNLERKKEH	1636	9	1	100		2799
LSA	KNNENNKFFDK	70	11	1	100		2800
LSA	KNSEKDEIIK	27	10	1	100		2801
LSA	KNVSQTNFK	90	9	1	100		2802
LSA	KSADIQNH	1735	8	1	100		2803
LSA	KSLYDEHIIK	1854	9	1	100	0.0340	2804
LSA	KSLYDEHIKK	1854	10	1	100	0.0490	2805
LSA	KSLYDEHIIKKY	1854	11	1	100		2806
LSA	KSSEELSEEK	1825	10	1	100	0.0009	2807
LSA	KTKDNNFK	1843	8	1	100		2808
LSA	KTKNNENNK	68	9	1	100	0.0038	2809
LSA	LAEDLYGR	1648	8	1	100		2810
LSA	LAKEKLQEQQR	1615	11	1	100		2811
LSA	LANEKLQEQQR	1530	11	1	100		2812
LSA	LDDLDEGIEK	1816	10	1	100	0.0002	2813
LSA	LDEFKPIVQY	1782	10	1	100		2814
LSA	LGVSENTIFLK	104	10	1	100	0.0063	2815
LSA	LIFHINGK	17	8	1	100		2816
LSA	LIFHINGKIIK	17	11	1	100		2817
LSA	LLIFHINGK	16	9	1	100	0.0100	2818
LSA	LNKEGKLIEH	117	10	1	100		2819
LSA	LSEDITKY	1898	8	1	100		2820
LSA	LSEDITKYFMK	1898	11	1	100		2821
LSA	LSEEKIKK	1830	8	1	100		2822
LSA	LSEEKIKKGK	1830	10	1	100	0.0002	2823
LSA	LSEEKIKKGKK	1830	11	1	100		2824
LSA	LSHNSYEK	61	8	1	100		2825
LSA	LSHNSYEKTK	61	10	1	100	0.0002	2826
LSA	LVNLLIFH	13	8	1	100		2827
LSA	NDDDDKKK	129	8	1	100		2828
LSA	NDDDDKKKY	129	9	1	100		2829
LSA	NDDDDKKKYIK	129	11	1	100		2830
LSA	NDFQISKY	1753	8	1	100		2831
LSA	NDKQVNKEK	1866	9	1	100	0.0002	2832
LSA	NDKQVNKEKEK	1866	11	1	100		2833
LSA	NDKSLYDEH	1852	9	1	100		2834
LSA	NDKSLYDEHIIK	1852	11	1	100		2835
LSA	NFKPNDKSLY	1848	10	1	100		2836
LSA	NFQDEENIGIY	1793	11	1	100		2837
LSA	NGKIIKNSEK	22	10	1	100	0.0002	2838
LSA	NIFLKENK	109	8	1	100		2839
LSA	NIFLKENKLNK	109	11	1	100		2840
LSA	NLDDLDEGIEK	1815	11	1	100		2841
LSA	NLERKKEH	1637	8	1	100		2842
LSA	NLGVSENIFLK	103	11	1	100		2843
LSA	NLLIFHINGK	15	10	1	100	0.0008	2844
LSA	NLRSGSSNSR	38	10	1	100	0.0002	2845
LSA	NNENNFFDK	71	10	1	100		2846
LSA	NNFKPNDK	1847	8	1	100		2847
LSA	NNFKPNDKSLY	1847	11	1	100		2848
LSA	NNKFFDKDK	74	9	1	100		2849
LSA	NSEKDEIIK	28	9	1	100	0.0002	2850
LSA	NSRNRINEEK	45	10	1	100	0.0002	2851
LSA	NSRNRINEEKH	45	11	1	100		2852
ISA	NVEGRRDIH	1707	9	1	100	0.0002	2853
ISA	NVEGRRDIHK	1707	10	1	100	0.0002	2854
LSA	NVKNVSQTNFK	88	11	1	100		2855
LSA	NVSQTNFK	91	8	1	100		2856
LSA	PAIELPSENER	659	11	1	100		2857
LSA	PNDKSLYDEFI	851	10	1	100		2858
LSA	PSENERGY	664	8	1	100		2859
LSA	PSENERGYY	664	9	1	100	0.0002	2860
LSA	QDEENIGIY	795	9	1	100		2861
LSA	QDEENIGIYK	795	10	1	100	0.0002	2862
LSA	QDNRGNSR	681	8	1	100		2863
LSA	QDNRGNSRDSK	681	11	1	100		2864
LSA	QDRLAKEK	391	8	1	100		2865
LSA	QGQQSDLEQER	128	11	1	100		2866
LSA	QSDLEQDR	386	8	1	100		2867
LSA	QSDLEQDRLAK	386	11	1	100		2868
ISA	QSDSEQER	590	8	1	100		2869
LSA	QSDLEQERLAK	590	11	1	100		2870
LSA	QSDLEQERR	573	9	1	100	0.0002	2871
LSA	QSDLEQERRAK	573	11	1	100		2872
LSA	QSDLERTK	182	8	1	100		2873
LSA	QSDLERTKASK	182	11	1	100		2874
LSA	QSDSEQER	519	8	1	100		2875
LSA	QSDSEQERLAK	519	11	1	100		2876
ISA	QSSLPQDNR	1676	9	1	100	0.0013	2877
ISA	QTNFKSLLR	94	9	1	100	0.0440	2878
LSA	QVNKEKEK	1869	8	1	100		2879
LSA	QVNKEKEKFIK	1869	11	1	100		2880
ISA	RDIHKGHLEEK	1712	11	1	100		2881
ISA	RDLEQERLAK	1608	10	1	100	0.0002	2882
LSA	RDLEQERR	1540	8	1	100		2883
LSA	RDLEQERRAK	1540	10	1	100	0.0002	2884
ISA	RDLEQRKADTK	1625	11	1	100		2885
ISA	RDSKEISIIEK	1688	11	1	100		2886
LSA	RGNSRDSK	1684	8	1	100		2887
LSA	RINEEKHEK	49	9	1	100	0.0370	2888
LSA	RINEEKHEKK	49	10	1	100	0.0018	2889
ISA	RINEEKHEKKH	49	11	1	100		2890
LSA	RNRINEEK	47	8	1	100		2891
LSA	RNRINEEKH	47	9	1	100		2892
LSA	RNRINEEKHEK	47	11	1	100		2893
ISA	RSGSSNSR	40	8	1	100		2894
LSA	RSGSSNSRNR	40	10	1	100	0.0002	2895
LSA	SDLEQDRLAK	387	10	1	100	0.0002	2896
ISA	SDLEQERLAK	591	10	1	100	0.0002	2897
LSA	SDLEQERR	574	8	1	100		2898
LSA	SDLEQERRAK	574	10	1	100	0.0002	2899
LSA	SDLERTKASK	183	10	1	100	0.0002	2900
ISA	SDSEQERLAK	520	10	1	100	0.0002	2901
LSA	SDVNDFQISK	750	10	1	100	0.0002	2902
ISA	SDVNDFQISKY	750	11	1	100		2903
ISA	SGSSNSRNR	41	9	1	100	0.0030	2904
ISA	SIIEKTNR	694	8	1	100		2905
ISA	SIKPEQKEDK	726	10	1	100	0.0002	2906
LSA	SITTNVEGR	703	9	1	100	0.0027	2907
LSA	SITTNVEGRR	703	10	1	100	0.0002	2908
LSA	SLPQDNRGNSR	678	11	1	100		2909
LSA	SLYDEHIK	835	8	1	100		2910
LSA	SLYDEHIKK	855	9	1	100	0.4100	2911
LSA	SLYDEHRKY	855	10	1	100	0.0045	2912
LSA	SLYDEHIKKVK	835	11	1	100		2913
LSA	SNLRSGSSNSR	37	11	1	100		2914
LSA	SNSRNRINEEK	44	11	1	100		2915
LSA	SSEELSEEK	1826	9	1	100	0.0017	2916
ISA	SSEELSEEKIK	1826	11	1	100		2917
LSA	SSLPQDNR	1677	8	1	100		2918
LSA	TNFKSLLR	95	8	1	100		2919
LSA	TNVEGRRDIH	1706	10	1	100		2920
LSA	TNVEGRRDIHK	1706	11	1	100		2921
LSA	TTNVEGRR	1705	8	1	100		2922
LSA	TINVEGRRDIH	1705	11	1	100		2923
LSA	VDELSEDTK	1895	10	1	100	0.0002	2924
LSA	VDELSEDITKY	1895	11	1	100		2925
LSA	VLAEDLYGR	1647	9	1	100	0.0004	2926
LSA	VLSHNSYEK	60	9	1	100	0.0280	2927
LSA	VLSHNSYEKTK	60	11	1	100		2928
LSA	VNDFQISK	1752	8	1	100		2929
LSA	VNDFQISKY	1752	9	1	100		2930
LSA	VNKEKEKFIK	1870	10	1	100		2931
LSA	VNLLIFHINGK	14	11	1	100		2932
LSA	VSENIFLK	106	8	1	100		2933
LSA	VSEMFLKENK	106	11	1	100		2934
LSA	VSQTNFKSLLR	92	11	1	100		2935
LSA	YDEHIKKY	1857	8	1	100		2936
LSA	YDEHIKKYK	1857	9	1	100	0.0002	2937
LSA	YFILVNLLIFH	10	11	1	100		2938
LSA	YIKGQDENR	137	9	1	100	0.0002	2939
SSP2	ACAGLAYK	512	8	10	100		2940
SSP2	ADSAWENVK	216	9	10	100	0.0009	2941
SSP2	AFNRFLVGCH	197	10	10	100		2942
SSP2	ALLACAGLAY	509	10	10	100	0.0110	2943
SSP2	ALIACAGLAYK	509	11	10	100		2944
SSP2	ALLQVRKH	136	8	9	90		2945
SSP2	AVCVEVEK	233	8	10	100		2946
SSP2	CGKGTRSR	257	8	10	100		2947
SSP2	CGKGTRSRK	257	9	10	100	0.0002	2948
SSP2	CCKGIRSRKR	257	10	10	100	0.0002	2949
SSP2	CNDEVDLY	43	8	8	80		2950
SSP2	CSGSIRRH	55	8	10	100		2951
SSP2	CSVTCGKGTR	253	10	10	100	0.0002	2952
SSP2	DALLQVRK	135	8	9	90		2953
SSP2	DALLQVRKH	135	9	9	90	0.0002	2954
SSP2	DASKNIUEK	106	8	10	100		2955
SSP2	DCSGSIRR	54	8	10	100		2956
SSP2	DCSGSIRRH	54	9	10	100		2957
SSP2	DDREENFDIPK	385	11	10	100		2958
SSP2	DIPKKPENK	392	9	10	100	0.0002	2959
SSP2	DIPKKPENKH	392	10	10	100	0.0002	2960
SSP2	DLDEPEQFR	546	9	10	100	0.0002	2961
SSP2	DLFLVNGR	19	8	10	100		2962
SSP2	DNQNNLPNDK	402	10	10	100		2963
SSP2	CGAVIENVK	217	8	10	100		2964
SSP2	DSIQDSLK	166	8	10	100		2965
SSP2	DSIQDSLKESR	166	11	10	100		2966
SSP2	DSLKESRK	170	8	9	90		2967
SSP2	DVPKNPEDDR	378	10	10	100	0.0002	2968
SSP2	DVQNNIVDEIK	27	11	10	100		2969
SSP2	EDDQPRPR	300	8	10	100		2970
SSP2	EDRETRPH	450	8	9	90		2971
SSP2	EDRETRPHGR	450	10	9	90		2972
SSP2	EIIRLHSDASK	99	11	10	100		2973
SSP2	ELQEQCEEER	276	10	8	80	0.0002	2974
SSP2	ENFDIPKK	389	8	10	100		2975
SSP2	ENRSYNRK	462	8	10	100		2976
SSP2	ETLGEEDK	538	8	10	100		2977
SSP2	EVCNDEVDLY	41	10	8	80	0.0002	2978
SSP2	EVPSDVPK	374	8	10	100		2979
SSP2	FDEILGEEDK	536	10	10	100	0.0002	2980
SSP2	FDIPKKPENK	391	10	10	100	0.0002	2981
SSP2	FDIPKKPENKH	391	11	10	100		2982
SSP2	FDLFLVNGR	18	9	10	100		2983
SSP2	FFDLFLVNGR	17	10	10	100		2984
SSP2	FLVGCHPSDGK	201	11	10	100		2985
SSP2	FMKAVCVEVEK	230	11	10	100		2986
SSP2	FNRFLVGCH	198	9	10	100		2987
SSP2	FVVPGAATPY	520	10	8	80	0.0002	2988
SSP2	GCHPSDGK	204	8	10	100		2989
SSP2	GDNFAVEK	308	8	9	90		2990
SSP2	GINVAFNR	193	8	10	100		2991
SSP2	GIPDSIQDSLK	163	11	10	100		2992
SSP2	GNRHVPNSEDR	442	11	10	100		2993
SSP2	GSIRRHNWVNH	57	11	8	80		2994
SSP2	GIRSRKREILH	260	11	10	100		2995
SSP2	HAVPLAMK	67	8	10.	100		2996
SSP2	HDNQNNLPNDK	401	11	10	100		2997
SSP2	HGRNNENR	457	8	10	100		2998
SSP2	HORNNENRSY	457	10	10	100	0.0002	2999
SSP2	HLNDRINR	143	8	10	100		3000
SSP2	HSDASKNK	104	8	10	100		3001
SSP2	HSDASKNKEK	104	10	10	100	0.0002	3002
SSP2	HVPNSEDR	445	8	10	100		3003
SSP2	HVPNSEDRETR	445	11	9	90		3004
SSP2	IFFDLFLVNGR	16	11	10	100		3005
SSP2	IGQGINVAFNR	190	11	10	100		3006
SSP2	IIRLHSDASK	100	10	10	100	0.0002	3007
SSP2	IVDEIKYR	32	8	9	90		3008
SSP2	KAVCVEVEK	232	9	10	100	0.0076	3009
SSP2	KDLDEPEQFR	545	10	10	100		3010
SSP2	KFVVPGAATPY	519	11	8	80		3011
SSP2	KGTRSRKR	259	8	10	100		3012
SSP2	KNVIGPFMK	224	9	10	100		3013
SSP2	KVLDNERK	421	8	8	80		3014
SSP2	LACAGLAY	511	8	10	100		3015
SSP2	LACAGLAYK	511	9	10	100	0.0290	3016
SSP2	LALLACAOLAY	508	11	10	100		3017
SSP2	LDEPEQFR	547	8	10	100		3018
SSP2	LLACAGLAY	510	9	10	100	0.0005	3019
SSP2	LLACAGLAYK	510	10	10	100	0.0870	3020
SSP2	LLMDCSGSIR	51	10	10	100	0.0005	3021
SSP2	LLMDCSGSIRR	51	11	10	100		3022
SSP2	LLQVRKHLNDR	137	11	9	90		3023
SSP2	LLSTNLPY	121	8	9	90		3024
SSP2	LLSTNLPYGR	121	10	8	80	0.0025	3025
SSP2	LMDCSGSIR	52	9	10	100	0.0002	3026
SSP2	LMDCSGSIRR	52	10	10	100	0.0002	3027
SSP2	LMDCSGSIRRH	52	11	10	100		3028
SSP2	LSTNLPYGR	122	9	8	80	0.0100	3029
SSP2	LVGCHPSDGK	202	10	10	100	0.0002	3030
SSP2	MDCSGSIR	53	8	10	100		3031
SSP2	MDCSGSIRR	53	9	10	100		3032
SSP2	MDCSGSIRRH	53	10	10	100		3033
SSP2	MNHLGNVK	1	8	10	100		3034
SSP2	MNHLGNVKY	1	9	10	100		3035
SSP2	NFDIPKKPENK	390	11	10	100		3036
SSP2	NIPEDSEK	366	8	10	100		3037
SSP2	NIVDEIKY	31	8	10	100		3038
SSP2	NIVDEIKYR	31	9	9	90	0.0002	3039
SSP2	NLPNDKSDR	406	9	10	100	0.0002	3040
SSP2	NNENFtSYNR	460	9	10	100		3041
SSP2	NNENRSYNRK	460	10	10	100		3042
SSP2	NNIVDEIK	30	8	10	100		3043
SSP2	NNIVDEIKY	30	9	10	100		3044
SSP2	NNIVDEIKYR	30	10	9	90		3045
SSP2	NNLPNDKSDR	405	10	10	100		3046
SSP2	NSEDRETR	448	8	9	90		3047
SSP2	NSEDRETPPH	448	10	9	90	0.0002	3048
SSP2	NVIGPFMK	225	8	10	100		3049
SSP2	NVKNVIGPFMK	222	11	10	100		3050
SSP2	PCSVTCGK	252	8	10	100		3051
SSP2	PCSVTCGKGTR	252	11	10	100		3052
SSP2	PDSIQDSLK	165	9	10	100	0.0002	3053
SSP2	PFDETLGEEDK	535	11	10	100		3054
SSP2	PNIPEDSEK	365	9	10	100		3055
SSP2	PNSEDRETR	447	9	9	90		3056
SSP2	PNSEDREMPFI	447	11	9	90		3057
SSP2	PSDGKCNLY	207	9	10	100	0.0002	3058
SSP2	PSPNPEEGK	328	9	10	100	0.0002	3059
SSP2	QCEEERCPPK	280	10	8	80	0.0002	3060
SSP2	QDNNGNRH	438	8	10	100		3061
SSP2	QDSLKESR	169	8	10	100		3062
SSP2	QDSLKESRK	169	9	9	90	0.0002	3063
SSP2	QGINVAFNR	192	9	10	100	0.0780	3064
SSP2	QNNIVDEIK	29	9	10	100		3065
SSP2	QNNIVDEIKY	29	10	10	100		3066
SSP2	QNNIVDBKYR	29	11	9	90		3067
SSP2	QNNLPNDK	404	8	10	100		3068
SSP2	QNNLPNDKSDR	404	11	10	100		3069
SSP2	QSQDNNGNR	436	9	10	100	0.0002	3070
SSP2	QSQDNNGNRH	436	10	10	100	0.0002	3071
SSP2	QVRKHLNDR	139	9	9	90	0.0002	3072
SSP2	RGDNFAVEK	307	9	9	90	0.0240	3073
SSP2	FILHSDASK	102	8	10	100		3074
SSP2	RLHSDASKNK	102	10	10	100	0.0002	3075
SSP2	RNNENRSY	459	8	10	100		3076
SSP2	RNNENRSYNR	459	10	10	100		3077
SSP2	RNNENRSYNRK	459	11	10	100		3078
SSP2	RSRKREILH	262	9	10	100	0.0002	3079
SSP2	SDASKNKEK	105	9	10	100	0.0002	3080
SSP2	SDGKCNLY	208	8	10	100		3081
SSP2	SDVPKNPEDDR	377	11	10	100		3082
SSP2	SIQDSLKESR	167	10	10	100	0.0009	3083
SSP2	SIQDSLKESRK	167	11	9	90		3084
SSP2	SIRRHNWVNH	58	10	8	80	0.0002	3085
SSP2	SLLSTNLPY	120	9	9	90	0.0046	3086
SSP2	SLLSTNLPYGR	120	11	8	80		3087
SSP2	STNLPYGR	123	8	8	80		3088
SSP2	SVTCGKOTFt	254	9	10	100	0.0009	3089
SSP2	SVTCGKGTRSR	254	11	10	100		3090
SSP2	TCGKGTRSR	256	9	10	100		3091
SSP2	TCGKGIRSRK	256	10	10	100	0.0002	3092
SSP2	TCGKGTRSRKR	256	11	10	100		3093
SSP2	VAFNRFLVGCH	196	11	10	100		3094
SSP2	VCNDEVDLY	42	9	8	80		3095
SSP2	VGCHPSDGK	203	9	10	100	0.0003	3096
SSP2	VNHAVPLAMK	65	10	8	80		3097
SSP2	VTOGKGIR	255	8	10	100		3098
SSP2	VTCGKGTRSR	255	10	10	100	0.0017	3099
SSP2	VTCGKGIRSRK	255	11	10	100		3100
SSP2	VVPGAATPY	521	9	8	80	0.0002	3101
SSP2	WSPCSVTCGK	250	10	10	100	0.0002	3102
SSP2	WVNHAVPLAMK	64	11	8	80		3103
SSP2	YADSAWENVK	215	10	10	100	0.0002	3104
SSP2	YLLMDCSGSIR	50	11	10	100		3105

TABLE XVIII
Malaria A24 Motif Peptides With Binding Information

			No. of	Sequence	Conservancy
Protein	Sequence	Position	Amino Acids	Frequency	(%)	A*2401	Seq. Id

CSP	CYGSSSNTRVL	25	11	19	100		3106
CSP	DYENDREKKI	398	10	18	95		3107
CSP	EMNYYGKQENW	52	11	19	100		3108
CSP	IMVLSFLF	427	8	19	100		3109
CSP	IMVLSFLFL	427	9	19	100	0.0008	3110
CSP	KMEKCSSVF	409	9	19	100		3111
CSP	MMRKLAIL	1	8	19	100		3112
CSP	NYDNAGINL	39	9	18	100	0.0004	3113
CSP	NYYGKQENW	54	9	19	100		3114
CSP	SFLFVEAL	12	8	19	100		3115
CSP	SFLFVEALF	12	9	19	100		3116
CSP	VFNVVNSSI	416	9	19	100		3117
CSP	VFNVVNSSIGL	416	11	19	100		3118
CSP	WYSLKKNSRSL	62	11	19	100		3119
CSP	YYGKQENW	55	8	19	100		3120
CSP	YYGKQENWYSL	55	11	19	100		3121
EXP	DMIKKEEEL	56	9	1	100		3122
EXP	FFIIFNKESL	12	10	1	100		3123
EXP	FFLALFFI	7	8	1	100		3124
EXP	FFLALFFII	7	9	1	100		3125
EXP	FFLALFFIIF	7	10	1	100		3126
EXP	KYKLATSVL	73	9	1	100	0.0960	3127
EXP	LFFIIFNKESL	11	11	1	100		3128
EXP	LYNTEKGRHPF	100	11	1	100		3129
EXP	VFFLALFF	6	8	1	100		3130
EXP	VFFLALFFI	6	9	1	100		3131
EXP	VFFLALFFII	6	10	1	100		3132
EXP	VFFLALFFIIF	6	11	1	100		3133
LSA	DFQISKYEDEI	1754	11	1	100		3134
LSA	EFKPIVQYDNF	1784	11	1	100		3135
LSA	FFDKDKEL	77	8	1	100		3136
LSA	FYFILVNL	9	8	1	100		3137
LSA	FYFILVNLL	9	9	1	100	7.5000	3138
LSA	FYFILVNLLI	9	10	1	100		3139
LSA	FYFILVNLLIF	9	11	1	100		3140
LSA	GYYIPHQSSL	1670	10	1	100	0.0074	3141
LSA	IFDGDNEI	1884	8	1	100		3142
LSA	IFDGDNEIL	1884	9	1	100		3143
LSA	IFDGDNEILQI	1884	11	1	100		3144
LSA	IFHINGKI	18	8	1	100		3145
LSA	IFHINGKII	18	9	1	100		3146
LSA	IFLKENKL	110	8	1	100		3147
LSA	IYKELEDL	1802	8	1	100		3148
LSA	IYKELEDLI	1802	9	1	100		3149
LSA	KFFDKDKEL	76	9	1	100		3150
LSA	KFIKSLFHI	1876	9	1	100		3151
LSA	KFIKSLFHIF	1876	10	1	100		3152
LSA	KYEKTKDNNF	1840	10	1	100	0.0004	3153
LSA	LFHIFDGDNEI	1881	11	1	100		3154
LSA	LYGRLETPAI	1652	10	1	100		3155
LSA	LYISFYFI	5	8	1	100		3156
LSA	LYISFYFIL	5	9	1	100	0.0088	3157
LSA	NFKPNDKSL	1848	9	1	100		3158
LSA	NFKSLLRNL	96	9	1	100		3159
LSA	NFQCEENI	1793	8	1	100		3160
LSA	NFQDEENIGI	1793	10	1	100		3161
LSA	QYDNFQDEENI	1790	11	1	100		3162
LSA	SFYFILVNL	8	9	1	100		3163
LSA	SFYFILVNLL	8	10	1	100		3164
LSA	SFYFILVNLLI	8	11	1	100		3165
LSA	YFILVNLL	10	8	1	100		3166
LSA	YFILVNLLI	10	9	1	100		3167
LSA	YFILVNLLIF	10	10	1	100		3168
LSA	YYIPHQSSL	1671	9	1	100	4.3000	3169
SSP2	AMKLIQQL	72	8	10	100		3170
SSP2	AMKLIQQLNL	72	10	10	100	0.0006	3171
SSP2	AWENVKNVI	219	9	10	100		3172
SSP2	KYKIAGGI	497	8	9	90		3173
SSP2	KYLVIVFL	8	8	10	100		3174
SSP2	KYLVIVFLI	8	9	10	100	4.6000	3175
SSP2	KYLVIVFLIF	8	10	10	100	0.0003	3176
SSP2	KYLVIVFLIFF	8	1 1	10	100		3177
SSP2	LMDCSGSI	52	8	10	100		3178
SSP2	LYLLMDCSGSI	49	11	9	90		3179
SSP2	NWVNHAVPL	63	9	8	80		3180
SSP2	PYAGEPAPF	528	9	8	80	0.0370	3181
SSP2	QFRLPEENEW	552	1 0	10	100		3182
SSP2	VFGIGQGI	187	8	10	100		3183
SSP2	VFLIFFDL	13	8	10	100		3184
SSP2	VFLIFFDLF	13	9	10	100		3185
SSP2	VFLIFFDLFL	13	10	10	100		3186

TABLE XIXa
		Core		Core
	Core	SeqID	Core	Conservancy	Exemplary
Protein	Sequence	Num	Frequency	(%)	Sequence
CSP	FLFVEALFQ	3187	19	100	VSSFLFVEALFQEYQ
CSP	FNVVNSSIG	3188	19	100	SSVFNVVNSSIGLIM
CSP	FQEYQCYGS	3189	19	100	EALFQEYQCYGSSSN
CSP	IEKKICKME	3190	19	100	ENDIEKKICKMEKCS
CSP	IGLIMVLSF	3191	19	100	NSSIGLIMVLSFLFL
CSP	ILSVSSFLF	3192	19	100	KLAILSVSSFLFVEA
CSP	LAILSVSSF	3193	19	100	MRKLAILSVSSFLFV
CSP	MEKCSSVFN	3194	19	100	ICKMEKCSSVFNVVN
CSP	VVNSSIGLI	3195	19	100	VFNVVNSSIGLIMVL
CSP	YQCYGSSSN	3196	19	100	FQEYQCYGSSSNTRV
CSP	YNELEMNYY	3197	19	100	INLYNELEMNYYGKQ
CSP	YDNAGINLY	3198	18	95	ELNYDNAGINLYNEL
CSP	IQNSLSTEW	3199	15	79	LKKIQNSLSTEWSPC
CSP	WSPCSVTCG	3200	10	100	STEWSPCSVTCGNGI
LSA	FILVNLLIF	3201	1	100	SFYFILVNLLIFHIN
LSA	FYFILVNLL	3202	1	100	YISFYFILVNLLIFH
LSA	IHKGHLEEK	3203	1	100	RRDIHKGHLEEKKDG
LSA	IIKSNLRSG	3204	1	100	KDEIIKSNLRSGSSN
LSA	ILVNLLIFH	3205	1	100	FYFILVNLLIFHING
LSA	INGKIIKNS	3206	1	100	IFHINGKIIKNSEKD
LSA	IPAIELPSE	3207	1	100	RLEIPAIELPSENER
LSA	IPHQSSLPQ	3208	1	100	QYYIPHQSSLPQDNR
LSA	IQNHTLETV	3209	1	100	SADIQNHTLETVNIS
LSA	ISFYFILVN	3210	1	100	ILYISFYFILVNLLI
LSA	LDEFKPIVQ	3211	1	100	DEDLDEFKPIVQYDN
LSA	LEEKAAKET	3212	1	100	QEDLEEKAAKETLQG
LSA	LEEPAIELP	3213	1	100	YGRLEEPAIELPSEN
LSA	LEQRKADTK	3214	1	100	QRDLEQRKADTKKNL
LSA	LERTKASKE	3215	1	100	QSDLERTKASKETLQ
LSA	LETVNISDV	3216	1	100	NHTLETVNISDVNDF
LSA	LIEFIENDD	3217	1	100	EGKLIEHIINDDDDK
LSA	LKENKLNKE	3218	1	100	NIFLKENKLNKEGKL
LSA	LLIFHINGK	3219	1	100	LVNLLIFHINGKIIK
LSA	LQEQQSDLE	3220	1	100	KETLQEQQSDLEQER
LSA	LQEQQSDSE	3221	1	100	KEKLQEQQSDSEQER
LSA	LQGQQSDLE	3222	1	100	KETLQGQQSDLEQER
LSA	LRNLGVSEN	3223	1	100	KSLLRNLGVSENIFL
LSA	LRSGSSNSR	3224	1	100	KSNLRSGSSNSRNRI
LSA	LTMSNVKNV	3225	1	100	DKELTMSNVKNVSQT
LSA	LVNLLXFHI	3226	1	100	YFILVNLLIFHINGK
LSA	VLSHNSYEK	3227	1	100	KKHVLSHNSYEKTKN
LSA	VNDFQISKY	3228	1	100	ISDVNDFQISKYEDE
LSA	VNISDVNDF	3229	1	100	LETVNISDVNDFQIS
LSA	YDDSLIDEE	3230	1	100	SAEYDDSLIDEEEDD
LSA	YGRLEIPAI	3231	1	100	EDLYGRLEIPAIELP
LSA	YIPHQSSLP	3232	1	100	RGYYIPHQSSLPQDN
EXP	FIUGSSDPA	3233	1	100	RHPFKIGSSDPADNA
EXP	IDVHDLISD	3234	1	100	EPLIDVHDLISDMIK
EXP	IFNKESLAE	3235	1	100	FFIIFNKESLAEKTN
EXP	IGSSDPADN	3236	1	100	PFIUGSSDPADNANP
EXP	LALFFIIFN	3237	1	100	VFFLALFFIIFNKES
EXP	LATSVLAGL	3238	1	100	KYKLATSVLAGLLGN
EXP	LGGVGLVLY	3239	1	100	TVLLGGVGLVLYNTE
EXP	LGNVSTVLL	3240	I	100	AGLLGNVSTVLLGGV
EXP	LLGNVSTVL	3241	1	100	LAGLLGNVSTVLLGG
EXP	LSVFFLALF	3242	1	100	MKILSVFFLALFFII
EXP	LVLYNTEKG	3243	1	100	GVOLVLYNTEKGRHP
EXP	VFFLALFFI	3244	1	100	ILSVFFLALFFIIFN
EXP	VHDLISDMI	3245	1	100	LIDVHDLISDMIKKE
EXP	VLAGLLGNV	3246	1	100	ATSVLAGLLGNVSTV
EXP	VLLGGVGLV	3247	1	100	VSTVLLGGVGLVLYN
EXP	VNKRKSKYK	3248	1	100	LVEVNKRKSKYKLAT
EXP	VSTVLLGGV	3249	1	100	LGNVSTVLLGGVGLV
EXP	VTAQDVTPE	3250	1	100	DPQVTAQDVTPEQPQ
EXP	YKLATSVLA	3251	1	100	KSKYKLATSVLAGLL
SSP2	FDLFLVNGR	3252	10	100	LIFFDLFLVNGRDVQ
SSP2	FFDLFLVNG	3253	10	100	FLIFFDLFLVNGRDV
SSP2	FMKAVCVEV	3254	10	100	IGPFMKAVCVEVEKT
SSP2	FNRFLVGCH	3255	10	100	NVAFNRFLVGCHPSD
SSP2	IAGGLALLA	3256	10	100	AGGIAGGLALLACAG
SSP2	IAVFGIGQG	3257	10	100	GVKIAVFGIGQGINV
SSP2	LACAGLAYK	3258	10	100	LALLACAGLAYKFVV
SSP2	LALLACAGL	3259	10	100	AGGLALLACAGLAYK
SSP2	LAMKLIQQL	3260	10	100	AVPLAMKLIQQLNLN
SSP2	LAYKFVVPG	3261	10	100	CAGLAYKFVVPGAAT
SSP2	LIFFDLFLV	3262	10	100	IVFLIFFDLFLVNGR
SSP2	LTDGIPDSI	3263	10	100	VVILTDGIPDSIQDS
SSP2	LVGCHPSDG	3264	10	100	NRFLVGCHPSDGKCN
SSP2	LVIVFLIFF	3265	10	100	VKYLVTVFLIFFDLF
SSP2	LVVILTDGI	3266	10	100	ANQLVVILTDGIPDS
SSP2	MDCSGSIRR	3267	10	100	YLLMDCSGSIRRHNW
SSP2	MKAVCVEVE	3268	10	100	GPFMKAVCVEVEKTA
SSP2	VEKTASCGV	3269	10	100	CVEVEKTASCGVWDE
SSP2	VGCHPSDGK	3270	10	100	RFLVGCHPSDGKCNL
SSP2	VIGPFMKAV	3271	10	100	VKNVIGPFMKAVCVE
SSP2	VIVFLIFFD	3272	10	100	KYLVIVFLIFFDLFL
SSP2	VKYLVIVFL	3273	10	100	LGNVKYLVIVFLIFF
SSP2	VNGRDVQNN	3274	10	100	LFLVNGRDVQNNIVD
SSP2	WDEWSPCSV	3275	10	100	CGVWDEWSPCSVTCG
SSP2	IAGGIAGGL	3276	10	100	KYKIAGGIAGGLALL
SSP2	VQNNIVDEI	3277	10	100	GRDVQNNIVDEIKYR
SSP2	YLLMDCSGS	3278	10	100	VDLYLLMDCSGSIRR
SSP2	FVVPGAATP	3279	10	100	AYKFVVPGAATPYAG
SSP2	YKFVVPGAA	3280	10	100	GLAYKFVVPGAATPY
SSP2	IIRLHSDAS	3281	10	100	AKEIIRLHSDASKNK
SSP2	IIDNNPQEP	3282	10	100	EENIIDNNPQEPSPN
SSP2	VDLYLLMDC	3283	9	90	NDEVDLYLLMDCSGS
SSP2	LLSTNLPYG	3284	9	90	IKSLLSTNLPYGRTN
SSP2	LHEGCTSEL	3285	8	80	REILHEGCTSELQEQ
SSP2	VNHAVPLAM	3286	8	80	HNWVNHAVPLAMKLI
SSP2	VPGAATPYA	3287	8	80	KFVVPGAATPYAGEP
SSP2	VVPGAATPY	3288	8	80	YKFVVPGAATPYAGE
SSP2	WVNHAVPLA	3289	8	80	REINWYNHAVPLAMKL
SSP2	LSTNLPYGR	3290	8	80	KSLLSTNLPYGRTNL

		Position	Exemplary	Exemplary
	Exemplary	In PF	Sequence	Sequence
Protein	SeqID Num	Poly-Protein	Frequency	Conservancy (%)
CSP	3291	10	19	100
CSP	3292	440	19	100
CSP	3293	17	19	100
CSP	3294	426	19	100
CSP	3295	447	19	100
CSP	3296	4	19	100
CSP	3297	2	19	100
CSP	3298	433	19	100
CSP	3299	442	19	100
CSP	3300	20	19	100
CSP	3301	45	18	95
CSP	3302	37	18	95
CSP	3303	385	15	79
CSP	3304	393	19	100
LSA	3305	8	1	100
LSA	3306	6	1	100
LSA	3307	1711	1	100
LSA	3308	31	1	100
LSA	3309	9	1	100
LSA	3310	18	1	100
LSA	3311	1655	1	100
LSA	3312	1670	1	100
LSA	3313	1736	1	100
LSA	3314	4	1	100
LSA	3315	1779	1	100
LSA	3316	146	1	100
LSA	3317	1653	1	100
LSA	3318	1624	1	100
LSA	3319	1182	1	100
LSA	3320	1741	1	100
LSA	3321	120	1	100
LSA	3322	109	1	100
LSA	3323	13	1	100
LSA	3324	1192	1	100
LSA	3325	512	1	100
LSA	3326	155	I	100
LSA	3327	98	1	100
LSA	3328	36	1	100
LSA	3329	81	1	100
LSA	3330	10	1	100
LSA	3331	57	1	100
LSA	3332	1749	1	100
LSA	3333	1744	1	100
LSA	3334	1765	1	100
LSA	3335	1650	1	100
LSA	3336	1669	1	100
EXP	3337	107	1	100
EXP	3338	45	1	100
EXP	3339	12	1	100
EXP	3340	109	1	100
EXP	3341	6	1	100
EXP	3342	73	1	100
EXP	3343	90	1	100
EXP	3344	82	1	100
EXP	3345	81	1	100
EXP	3346	1	1	100
EXP	3347	95	1	100
EXP	3348	3	1	100
EXP	3349	47	1	100
EXP	3350	77	1	100
EXP	3351	88	1	100
EXP	3352	64	1	100
EXP	3353	85	1	100
EXP	3574	136	1	100
EXP	3354	71	1	100
SSP2	3355	15	10	100
SSP2	3356	14	10	100
SSP2	3357	227	10	100
SSP2	3358	195	10	100
SSP2	3359	513	10	100
SSP2	3360	182	10	100
SSP2	3361	520	10	100
SSP2	3362	517	10	100
SSP2	3363	68	10	100
SSP2	3364	525	10	100
SSP2	3365	12	10	100
SSP2	3366	157	10	100
SSP2	3367	199	10	100
SSP2	3368	7	10	100
SSP2	3369	153	10	100
SSP2	3370	50	10	100
SSP2	3371	228	10	100
SSP2	3372	235	10	100
SSP2	3373	200	10	100
SSP2	3374	223	10	100
SSP2	3375	8	10	100
SSP2	3376	4	10	100
SSP2	3377	20	10	100
SSP2	3378	244	10	100
SSP2	3379	509	9	90
SSP2	3380	25	9	90
SSP2	3381	47	9	90
SSP2	3382	529	8	80
SSP2	3383	527	8	80
SSP2	3384	97	6	60
SSP2	3385	317	4	40
SSP2	3386	44	8	80
SSP2	3387	118	5	50
SSP2	3388	266	8	80
SSP2	3389	62	8	80
SSP2	3390	531	8	80
SSP2	3391	530	8	80
SSP2	3392	61	8	80
SSP2	3393	119	5	50

TABLE XIXb
Malaria Super Motif Peptides With Binding Data

	Core
Core	SeqID	Exemplary	Exemplary
Sequence	Num	Sequence	SeqID Num	DR1	DR2w2β1
FLFVEALFQ	3187	VSSFLFVEALFQEYQ	3291
FNVVNSSIG	3188	SSVFNVVNSSIGLIM	3292	0.1200	0.0290
FQEYQCYGS	3189	EQLFQEYQCYGSSSN	3293	0.0001
IEKKICKME	3190	ENDIEKKICKMEKCS	3294
IGLIMVLSF	3191	NSSIGLIMVLSFLFL	3295	0.0040	0.0250
ILSVSSFLF	3192	KLAILSVSSFLFVEA	3296
LAILSVSSF	3193	MRKLAILSVSSFLFV	3297	0.1000	0.5000
MEKCSSVFN	3194	ICKMEKCSSVFNVVN	3298
VVNSSGILI	3195	VFNVVNSSIGLIMVL	3299	0.0310	0.0021
YQCYGSSSN	3196	FQEYQCYGSSSNTRV	3300
YNELEMNYY	3197	INLYNELEMNYYGKQ	3301
YDNAGINLY	3198	ELNYDNAGINLYNEL	3302	0.0003
IQNSLSTEW	3199	LKKIQNSLSTEWSPC	3303
WSPSCSVTCG	3200	STEWSPCSVTCGNGI	3304
FILVNLLIF	3201	SFYFILVNLLIFHIN	3305	0.0009	0.0100
FYFILVNLL	3202	YISFYFILVNLLIGH	3306	0.0029	0.0040
IHKGHLEEK	3203	RRDIHKGHLEEKKDG	3307
IIKSNLRSG	3204	KDEIIKSNLRSGSSN	3308
ILVNLLIFH	3205	FYFILVNLLIFHING	3309
INGKIIKNS	3206	IFHINGKIIKNSEKD	3310	0.0320	0.0220
IPAIELPSE	3207	RLEIPAIELPSENER	3311
IPHQSSLPQ	3208	GYYIPHQSSLPQDNR	3312
IQNHTLETV	3209	SADIQNHTLETVNIS	3313	0.0001
ISFYFILVN	3210	ILYISFYFILVNLLI	3314
LDEFKPIQ	3211	DEDLDEFKPIVQYDN	3315
LEEKAAKET	3212	QEDLEEKAAKETLQG	3316	0.0001
LEIPAIELP	3213	YGRLEIPAIELPSEN	3317
LEQRKADTK	3214	QRDLEQRKADTKKNL	3318
LERTKASKE	3215	QDDLERTKASKETLQ	3319
LETVNISDV	3216	NGTLETVNISDVNDF	3320	0.0001
LIEHIINDD	3217	EGKLIEHIINDDDDK	3321
LKENKLNKE	3218	NIFLKEKLNKEGKL	3322
LLIFHINGK	3219	LVNLLIFHINGKIIK	3323	0.0640	0.7100
LQEQQSDLE	3220	KETLQEQQSDLEQER	3324
LQEQQSESE	3221	KEKLQEQQSDSEQER	3325
LQGQQSDLE	3222	KETLQGQQSDLEQER	3326
LRNTLGVSEN	3223	KSLLRNLGVSENIFL	3327	0.0150	0.0088
LRSGSSNSR	3224	KSNLRSGSSNSRNRI	3328
LTMSNVKNV	3225	DKELTMSNVKNVSQT	3329	0.0018	0.0003
LVNLLIFHI	3226	YFILVNLLIFHINGK	3330	0.0018	0.0004
VLSHNSYEK	3227	KKHVLSHNSYEKTKN	3331
VNDFQISKY	3228	ISDVNDFQISKYEDE	3332	0.0001
VNISKVNDF	3229	LETVNISDVNDFQIS	3333
YDDSLIDEE	3230	SAEYDDSLIDEEEDD	3334
YGRLEIPAI	3231	EDLYGRLEIPAIELP	3335	0.0004
YIPHQSSLP	3232	RGYYIPHQSSLPQDN	3336	0.2900	0.0004
FKIGSSDPA	3233	RHPFKIGSSDPADNA	3337	0.0044	-0.0004
IDVHDLISH	3234	EPLIDVHDLISDMIK	3338
IFNKESLAE	3235	FFIIFNKESLAEKTN	3339
IGSSDPADN	3236	PFKIGSSDPADNANP	3340
LALFFIIFN	3237	VFFALFFIIFNKES	3341	0.0006	0.0180
LATSVLAGL	3238	KYKLATSVLAGLLGN	3342	1.2000	0.0018
LGGVGLVLY	3239	TVLLGGVGLVLYNTE	3343	0.4900
LGNVSTVLL	3240	AGLLGNVSTVLLGGV	3344	0.0430	0.0240
LLGNVSTVL	3241	LAGLLGNVSTVLLGG	3345	0.0420	0.0110
LSVFFLALF	3242	MKILSVFFLALFFII	3346	0.0017	0.0170
LVLYNTEKG	3243	GVGLVLYNTEKGRHP	3347
VFFLALFFI	3244	ILSVFFLALFFIIFN	3348	0.0016	0.0036
VHDLISDMI	3245	LIDVHDLISDMIKKE	3349	0.0130
VLAGLLGNV	3246	ATSVLAGLLGNVSTV	3350	0.2600
VLLGGVGLV	3247	VSTVLLGGVGLVLYN	3351	0.8800	0.0080
VNKRKSKYK	3248	LVEVNKRKSKYKLAT	3352
VSTVLLGGV	3249	LGNVSTVLLGGVGLV	3353	0.0140	0.0001
VTAQDVTPE	3250	DPQVTAQDVTPEQPQ	3574
YKLATSVLA	3251	KSKYKLATSVLAGLL	3354	1.4000	0.0073
FDLFLVNGR	3252	LIFFDLFLVNGRDVQ	3355	0.0042
FFDLFLVNG	3253	FLIFFDLFLVNGRDV	3356
FMKAVCVEV	3254	IGPFMKAVCVEVEKT	3357	0.0072	0.0003
FNRFLVGCH	3255	NVAFNRFLVGCHPSD	3358
IAGGLALLA	3256	AGGIAGGLALLACAG	3359	0.0160
IAVFGIGQG	3257	GVKIAVFGIGQGINV	3360
LACAGLAYK	3258	LALLACAGLAYKFVV	3361
LALLACAGL	3259	AGGLALLACAGLAYK	3362	0.0018
LAMKLIQQL	3260	AVPLAMKLIQQLNTN	3363	0.0015
LAYKFVVPG	3261	CAGLAYKFVVPGAAT	3364
LIFFDLFLV	3262	IVFLIFFDLFLVNGR	3365	0.0006	0.0048
LTDGIPDSI	3263	VVILTDGIPDSIQDS	3366	0.0001
LVGCHPSDG	3264	NRFLVGCHPSDGKCN	3367
LVTVFLIFF	3265	VKYLVTVFLIFFDLF	3368	0.0001
LVVILTDGI	3266	ANQLVVILTDGIPDS	3379	0.0038	0.0008
MDCSGSIRR	3267	YLLMDCSGSIRRHNW	3370
MKAVCVEVE	3268	GPFMKAVCVEVEKTA	3371
VEKTASCGV	3269	CVEVEKTASCGVWDE	3372	0.0004
VGCHPSDGK	3270	RFLVGCHPSDGKCNL	3373
VIGPFMKAV	3271	VKNVIGPFMKAVCVE	3374	0.0900	0.0430
VIVFLIFFD	3272	KYVTVFLIFFDLFL	3375	0.0012	0.0057
VKYLVTVFL	3273	LGNVKYLVTVFLIFF	3376	0.0006	0.0033
VNGRDVQNN	3274	LFLVNGRDVQNNTVD	3377
WDEWSPCSV	3275	CGVWDEWSPCSVTCG	3378	0.0001
IAGGIAGGL	3276	KYKIAGGIAGGLALL	3389	0.0380	0.0001
YQNNIVDEI	3277	GRDVQNNIVDEIKYR	3380	0.0001	0.0001
YLLMDCSGS	3278	VDLYLLMDCSGSIRR	3381	0.0015
FVVPGAATP	3279	AYKFVVPGAATPYAG	3382	0.3600	-0.0009
YKFVVPGAA	3280	GLAYKFVVPGAATPY	3383	1.6000	0.0001
IIRLHSDAS	3281	AKEIIRLHSDASKNK	3384
IIDNNPQEP	3282	EENIIDNNPQEPSPN	3385
VDLYLLMDC	3283	NDEVDLYLLMDCSGS	3386	0.0001
LLSTNLPYG	3284	IKSLSSTNLPYGRTN	3387
LHEGCTSEL	3285	REILHEGCTSELQEQ	3388	0.0001
VNHAVPLAM	3286	HNWVNHAVPLAMKLI	3389	0.3500	0.0250
VPGAATPYA	3287	KFVVPGAATPYAGEP	3390	0.0230	0.0001
VVPGAATPY	3288	YKFVVPGAATPYAGE	3391	0.1100	0.0008
WVNHAVPLA	3289	RHNWVNHAVPLAMKL	3392	0.1900	0.0350
LSTNLPYGR	3290	KSLLSTNLPYGRTNL	3393	0.0012

Core
Sequence	DR2w2β2	DR3	DR4w4	DR4w15	DR5w11	DR5w12
FLFVEALFQ
FNVVNSSIG	0.0050	-0.0043	0.1000	0.230	0.0170	0.0051
FQEYQCYGS	-0.0005		0.0053	-0.0009	-0.0002	0.0001
IEKKICKME
IGLIMVLSF	0.0024	-0.0043	0.0120	0.0035	-0.0005	0.0340
ILSVSSFLF
LAILSVSSF	0.0130	-0.0043	0.0078	0.0270	0.0370	0.1200
MEKCSSVFN
VVNSSGILI	0.0006	0.0021	0.0079	0.0056	0.0002	0.0015
YQCYGSSSN
YNELEMNYY
YDNAGINLY	-0.0005	0.0091	-0.0009	-0.0009	-0.0002	0.0001
IQNSLSTEW
WSPSCSVTCG
FILVNLLIF	-0.0020	-0.0043	0.0250	0.0038	-0.0005	0.0009
FYFILVNLL	0.0044	-0.0008	0.0210	-0.0009	0.0011	0.0006
IHKGHLEEK
IIKSNLRSG
ILVNLLIFH
INGKIIKNS	0.0660	0.0120	-0.0007	0.0038	0.0380	0.0055
IPAIELPSE
IPHQSSLPQ
IQNHTLETV	-0.0005	-0.0041	-0.0007	-0.0014	-0.0002	0.0001
ISFYFILVN
LDEFKPIQ
LEEKAAKET	-0.0005		-0.0009	-0.0009	-0.0002	0.0001
LEIPAIELP
LEQRKADTK
LERTKASKE
LETVNISDV	-0.0005		-0.0007	0.0016	-0.0002	0.0015
LIEHIINDD
LKENKLNKE
LLIFHINGK	0.0070	-0.0043	0.0110	-0.0030	0.2700	0.0410
LQEQQSDLE
LQEQQSESE
LQGQQSDLE
LRNTLGVSEN	0.0006		0.0210	0.0810	0.0033
LRSGSSNSR
LTMSNVKNV	0.0009	0.0058	0.0023	0.0074	0.0030	0.0001
LVNLLIFHI	0.0120	-0.008	0.0160	0.0027	0.0015	0.0006
VLSHNSYEK
VNDFQISKY	-0.0005		-0.0007	-0.0014	-0.0002	0.0001
VNISKVNDF
YDDSLIDEE
YGRLEIPAI	-0.0005		-0.0007	0.0170	-0.0002	0.0002
YIPHQSSLP	0.0029		4.1000	0.2800	0.0064
FKIGSSDPA	-0.0003	-0.0008	0.4700	0.0029	0.0056	0.0001
IDVHDLISH
IFNKESLAE
IGSSDPADN
LALFFIIFN	-0.0021	-0.0043	0.0047	0.0100	-0.0005	0.0002
LATSVLAGL	0.0700	0.0010	3.2000	0.1200	0.0210	0.0073
LGGVGLVLY	-0.005		0.0032	-0.0009	-0.0062	0.0004
LGNVSTVLL	0.0013	0.0059	0.0065	0.0360	0.0005	0.0001
LLGNVSTVL	0.0006	0.0078	0.0160	0.0230	0.0004	0.0003
LSVFFLALF	-0.0021	-0.0043	0.0370	-0.0047	-0.0010	0.0023
LVLYNTEKG
VFFLALFFI	0.0091	-0.0008	0.0130	-0.0009	0.0012	0.0008
VHDLISDMI	0.0061	0.0100	0.0310	0.0075	0.0037	0.0001
VLAGLLGNV	-0.0005		0.0021	-0.0014	0.0008	0.0043
VLLGGVGLV	0.0005	-0.0008	0.0067	-0.0009	0.0003	0.0011
VNKRKSKYK
VSTVLLGGV	-0.0005	-0.0008	0.0016	-0.0014	-0.0002	0.0005
VTAQDVTPE
YKLATSVLA	0.8500	-0.0008	6.3000	0.8100	0.6700	0.0009
FDLFLVNGR			0.0036
FFDLFLVNG
FMKAVCVEV	0.0430	-0.0008	-0.0006	0.0086	-0.0004	0.0038
FNRFLVGCH
IAGGLALLA	0.0013		0.0014	0.0014	-0.0002	0.0007
IAVFGIGQG
LACAGLAYK
LALLACAGL	0.0013		-0.0007	-0.0014	-0.0002	0.0051
LAMKLIQQL	-0.0006		0.0023	0.0013	0.0002	0.1300
LAYKFVVPG
LIFFDLFLV	0.0019	-0.0008	0.0130	-0.0009	0.0019	0.0016
LTDGIPDSI	-0.0006		0.1200	-0.0014	-0.0004	0.0001
LVGCHPSDG
LVTVFLIFF			0.0030
LVVILTDGI	-0.0005	0.0019	0.0460	0.0062	-0.0002	0.0003
MDCSGSIRR
MKAVCVEVE
VEKTASCGV	-0.0009		0.0021	-0.0009	-0.0002	0.0001
VGCHPSDGK
VIGPFMKAV	0.0800	-0.0026	-0.0020	-0.0030	0.3420	0.0920
VIVFLIFFD	-0.0020	-0.0043	0.0680	-0.0030	-0.0009	0.0021
VKYLVTVFL	0.0012	-0.0008	0.0120	0.0045	0.0018	0.0011
VNGRDVQNN
WDEWSPCSV	-0.0006		-0.0007	-0.0014	-0.0002	0.0001
IAGGIAGGL	0.0480	0.0250	0.0120	0.0017	0.2300	0.3600
YQNNIVDEI	-0.0006	0.0026	-0.0006	-0.0014	-0.0004	0.0001
YLLMDCSGS	0.0096		0.0150	-0.0014	-0.0004	0.0001
FVVPGAATP		0.0620	0.1600	0.0036	0.6400	0.1200
YKFVVPGAA	0.7000	-0.0008	1.0000	0.0270	1.9000	0.3500
IIRLHSDAS
IIDNNPQEP
VDLYLLMDC	-0.0005		0.0028	-0.0009	-0.0002	0.0001
LLSTNLPYG
LHEGCTSEL	-0.0005	-0.0041	-0.0009	-0.0014	-0.0002	0.0001
VNHAVPLAM	0.1400	0.2300	3.900	0.0400	0.0074	0.6000
VPGAATPYA	0.0010	0.0620	0.1200	0.0067	0.0010	0.0860
VVPGAATPY	0.0053	-0.0008	0.0057	-0.0014	0.0036	0.0061
WVNHAVPLA	0.1600	0.4000	5.0000	0.0360	0.0079	0.0240
LSTNLPYGR			0.0120

Core	Seq	Exemplary	Exemplary
Sequence	Id.	Sequence	SeqID Num	DR6w19	DR7	DR8w2	DR9	DRw53
FLFVEALFQ	3187	VSSFLFVEALFQEYQ	3291
FNVVNSSIG	3188	SSVFNVVNSSIGLIM	3292	0.3600	0.7600	0.0550	1.2000

FQEYQCYGS	3189	EQLFQEYQCYGSSSN	3293		-0.0003	0.0005
IEKKICKME	3190	ENDIEKKICKMEKCS	3294
IGLIMVLSF	3191	NSSIGLIMVLSFLFL	3295	0.0009	0.0690	-0.0010	0.0042
ILSVSSFLF	3192	KLAILSVSSFLFVEA	3296
LAILSVSSF	3193	MRKLAILSVSSFLFV	3297	0.0930	0.0500	0.0013	0.1100
MEKCSSVFN	3194	ICKMEKCSSVFNVVN	3298
VVNSSGILI	3195	VFNVVNSSIGLIMVL	3299	0.2600	0.1800	0.0012	0.5000
YQCYGSSSN	3196	FQEYQCYGSSSNTRV	3300
YNELEMNYY	3197	INLYNELEMNYYGKQ	3301
YDNAGINLY	3198	ELNYDNAGINLYNEL	3302		-0.0003	-0.0003
IQNSLSTEW	3199	LKKIQNSLSTEWSPC	3303
WSPSCSVTCG	3200	STEWSPCSVTCGNGI	3304
FILVNLLIF	3201	SFYFILVNLLIFHIN	3305	0.0004	0.0084	-0.0007	-0.0018
FYFILVNLL	3202	YISFYFILVNLLIGH	3306	0.0003	0.0020	0.0010	-0.0003
IHKGHLEEK	3203	RRDIHKGHLEEKKDG	3307
IIKSNLRSG	3204	KDEIIKSNLRSGSSN	3308
ILVNLLIFH	3205	FYFILVNLLIFHING	3309
INGKIIKNS	3206	IFHINGKIIKNSEKD	3310	0.0120	0.0150	0.0400	0.0093	0.0020
IPAIELPSE	3207	RLEIPAIELPSENER	3311
IPHQSSLPQ	3208	GYYIPHQSSLPQDNR	3312
IQNHTLETV	3209	SADIQNHTLETVNIS	3313		-0.0003	-0.0003		0.0012
ISFYFILVN	3210	ILYISFYFILVNLLI	3314
LDEFKPIQ	3211	DEDLDEFKPIVQYDN	3315
LEEKAAKET	3212	QEDLEEKAAKETLQG	3316		-0.0003	-0.0002
LEIPAIELP	3213	YGRLEIPAIELPSEN	3317
LEQRKADTK	3214	QRDLEQRKADTKKNL	3318
LERTKASKE	3215	QDDLERTKASKETLQ	3319		0.0010	-0.0003		-0.0005
LETVNISDV	3216	NGTLETVNISDVNDF	3320
LIEHIINDD	3217	EGKLIEHIINDDDDK	3321
LKENKLNKE	3218	NIFLKEKLNKEGKL	3322	0.0530	0.1200	0.0290	0.1800
LLIFHINGK	3219	LVNLLIFHINGKIIK	3323
LQEQQSDLE	3220	KETLQEQQSDLEQER	3324
LQEQQSESE	3221	KEKLQEQQSDSEQER	3325
LQGQQSDLE	3222	KETLQGQQSDLEQER	3326
LRNTLGVSEN	3223	KSLLRNLGVSENIFL	3327	0.5700	0.0770	0.0021	1.6000
LRSGSSNSR	3224	KSNLRSGSSNSRNRI	3328
LTMSNVKNV	3225	DKELTMSNVKNVSQT	3329	0.0430	0.0410	0.0110	0.0710	0.0024
LVNLLIFHI	3226	YFILVNLLIFHINGK	3330	0.0013	0.0059	0.0005	0.0040	0.0290
VLSHNSYEK	3227	KKHVLSHNSYEKTKN	3331
VNDFQISKY	3228	ISDVNDFQISKYEDE	3332		-0.0003	-0.0003		-0.0005
VNISKVNDF	3229	LETVNISDVNDFQIS	3333
YDDSLIDEE	3230	SAEYDDSLIDEEEDD	3334
YGRLEIPAI	3231	EDLYGRLEIPAIELP	3335		-0.0003	0.0021		-0.0005
YIPHQSSLP	3232	RGYYIPHQSSLPQDN	3336	0.0004	0.1700	0.0150	0.1500
FKIGSSDPA	3233	RHPFKIGSSDPADNA	3337	0.0003	-0.0003	0.0380	0.0950
IDVHDLISH	3234	EPLIDVHDLISDMIK	3338
IFNKESLAE	3235	FFIIFNKESLAEKTN	3339
IGSSDPADN	3236	PFKIGSSDPADNANP	3340
LALFFIIFN	3237	VFFALFFIIFNKES	3341	-0.0002	0.0056	-0.0007	-0.0018
LATSVLAGL	3238	KYKLATSVLAGLLGN	3342	0.0072	0.6500	0.1300	2.6000
LGGVGLVLY	3239	TVLLGGVGLVLYNTE	3343		0.0007	-0.0002
LGNVSTVLL	3240	AGLLGNVSTVLLGGV	3344	4.6000	0.4300	0.0012	0.5300	0.0012
LLGNVSTVL	3241	LAGLLGNVSTVLLGG	3345	0.6400	0.3800	0.0006	0.5500
LSVFFLALF	3242	MKILSVFFLALFFII	3346	0.0019	0.0360	0.0023	0.0060
LVLYNTEKG	3243	GVGLVLYNTEKGRHP	3347
VFFLALFFI	3244	ILSVFFLALFFIIFN	3348	0.0005	0.0110	0.0031	-0.0003
VHDLISDMI	3245	LIDVHDLISDMIKKE	3349	0.0004	0.0100	0.0096	0.0430	0.0940
VLAGLLGNV	3246	ATSVLAGLLGNVSTV	3350		-0.0003	0.0005		0.0039
VLLGGVGLV	3247	VSTVLLGGVGLVLYN	3351	0.0002	0.0020	-0.0002	0.0120
VNKRKSKYK	3248	LVEVNKRKSKYKLAT	3352
VSTVLLGGV	3249	LGNVSTVLLGGVGLV	3353	0.0006	-0.0003	-0.0003	-0.0005	-0.0005
VTAQDVTPE	3250	DPQVTAQDVTPEQPQ	3574
YKLATSVLA	3251	KSKYKLATSVLAGLL	3354	0.0082	1.9000	1.1000	2.7000	0.0150
FDLFLVNGR	3252	LIFFDLFLVNGRDVQ	3355		0.0470
FFDLFLVNG	3253	FLIFFDLFLVNGRDV	3356
FMKAVCVEV	3254	IGPFMKAVCVEVEKT	3357	0.0003	0.0019	-0.0003	0.0820	0.0700
FNRFLVGCH	3255	NVAFNRFLVGCHPSD	3358
IAGGLALLA	3256	AGGIAGGLALLACAG	3359		-0.0003	0.0004		-0.0005
IAVFGIGQG	3257	GVKIAVFGIGQGINV	3360
LACAGLAYK	3258	LALLACAGLAYKFVV	3361
LALLACAGL	3259	AGGLALLACAGLAYK	3362		0.0009	0.0003		-0.0005
LAMKLIQQL	3260	AVPLAMKLIQQLNTN	3363		0.0770	0.0400		0.0350
LAYKFVVPG	3261	CAGLAYKFVVPGAAT	3364
LIFFDLFLV	3262	IVFLIFFDLFLVNGR	3365	0.0006	0.0028	0.0007	-0.0003
LTDGIPDSI	3263	VVILTDGIPDSIQDS	3366		-0.0003	-0.0003		0.0114
LVGCHPSDG	3264	NRFLVGCHPSDGKCN	3367
LVTVFLIFF	3265	VKYLVTVFLIFFDLF	3368		0.0010
LVVILTDGI	3266	ANQLVVILTDGIPDS	3379	0.0070	0.0054	-0.0002	0.0420
MDCSGSIRR	3267	YLLMDCSGSIRRHNW	3370
MKAVCVEVE	3268	GPFMKAVCVEVEKTA	3371
VEKTASCGV	3269	CVEVEKTASCGVWDE	3372		0.0095	0.0005
VGCHPSDGK	3270	RFLVGCHPSDGKCNL	3373
VIGPFMKAV	3271	VKNVIGPFMKAVCVE	3374	0.1100	0.0590	0.0230	0.0870
VIVFLIFFD	3272	KYVTVFLIFFDLFL	3375	0.0034	0.0130	0.0065	-0.0018
VKYLVTVFL	3273	LGNVKYLVTVFLIFF	3376	0.0016	0.0040	0.0050	0.0012
VNGRDVQNN	3274	LFLVNGRDVQNNTVD	3377
WDEWSPCSV	3275	CGVWDEWSPCSVTCG	3378		-0.0003	-0.0003		-0.0006
IAGGIAGGL	3276	KYKIAGGIAGGLALL	3389	0.2400	0.0063	1.6000	0.2600	-0.0010
YQNNIVDEI	3277	GRDVQNNIVDEIKYR	3380	0.0810	-0.0003	-0.0003	-0.0005	0.0850
YLLMDCSGS	3278	VDLYLLMDCSGSIRR	3381		0.0046	0.0007		-0.0010
FVVPGAATP	3279	AYKFVVPGAATPYAG	3382	0.1700	0.1800	0.9200	0.1300
YKFVVPGAA	3280	GLAYKFVVPGAATPY	3383	0.4900	0.1500	2.5000	0.6000	0.0190
IIRLHSDAS	3281	AKEIIRLHSDASKNK	3384
IIDNNPQEP	3282	EENIIDNNPQEPSPN	3385
VDLYLLMDC	3283	NDEVDLYLLMDCSGS	3386		-0.0003	-0.0003
LLSTNLPYG	3284	IKSLSSTNLPYGRTN	3387
LHEGCTSEL	3285	REILHEGCTSELQEQ	3388		-0.0003	-0.0003
VNHAVPLAM	3286	HNWVNHAVPLAMKLI	3389	0.9400	0.3800	0.200	4.000	0.0250
VPGAATPYA	3287	KFVVPGAATPYAGEP	3390	0.0460	0.0017	0.0064	0.2500
VVPGAATPY	3288	YKFVVPGAATPYAGE	3391	0.0017	0.0160	0.0026	0.0200
WVNHAVPLA	3289	RHNWVNHAVPLAMKL	3392	0.8900	0.4400	1.8000	4.6000	0.0430
LSTNLPYGR	3290	KSLLSTNLPYGRTNL	3393		0.0005

TABLE XXa
Malaria DR3a Motif Peptides

				Core		Ex-	Position
		Core	Core	Sequence		emplary	in Pf	Exemplary	Exemplary
	Core	SeqID	Sequence	Conser-	Exemplary	SeqID	Poly-	Sequence	Conser-
Protein	Sequence	Num	Frequency	vancy (%)	Sequence	Num	Protein	Frequency	vancy (%)
CSP	LFQEYQCYG	3394	19	100	VEALFQEYQCYGSSS	3449	16	19	100
CSP	LFVEALFQE	3395	19	100	SSFLFVEALFQEYQC	3450	11	19	100
CSP	MPNDPNRNV	3396	19	100	GHNMPNDPNRNVDEN	3451	347	19	100
CSP	LYNELEMNY	3397	19	100	GINLYNELEMNYYGK	3452	44	18	95
CSP	VLNELNYDN	3398	19	100	NTRVLNELNYDNAGI	3453	31	18	95
CSP	YENDIEKKI	3399	19	100	ELDYENDIEKKICKM	3454	422	12	63
CSP	LNYDNAGIN	3400	18	95	LNELNYDNAGINLYN	3455	35	18	95
CSP	LSTEWSPCS	3401	18	95	QNSLSTEWSPCSVTC	3456	389	15	79
CSP	LDYENDIEK	3402	18	95	KDELDYENDIEKKIC	3457	420	12	63
LSA	FDGDNEILQ	3403	1	100	FHIFDGDNEILQIVD	3458	1882	1	100
LSA	FDKDKELTM	3404	1	100	NKFFDKDKELTMSNV	3459	75	1	100
LSA	FQDEENIGI	3405	1	100	YDNFQDEENIGIYKE	3460	1791	1	100
LSA	IDEEEDDED	3406	1	100	DSLIDEEEDDEDLDE	3461	1770	1	100
LSA	IINDDDDKK	3407	1	100	IEHIINDDDDKKKYI	3462	124	1	100
LSA	INDDDDKKK	3408	1	100	EHIINDDDDKKKYIK	3463	125	1	100
LSA	ISAEYDDSL	3409	1	100	EDEISAEYDDSLIDE	3464	1761	1	100
LSA	IVDELSEDI	3410	1	100	ILQIVDELSEDITKY	3465	1891	1	100
LSA	IYKELEDLI	3411	1	100	NIGIYKELEDLIEKN	3466	1799	1	100
LSA	LAEDLYGRL	3412	1	100	GDVLAEDLYGRLEIP	3467	1645	1	100
LSA	LAKEKLQEQ	3413	1	100	QERLAKEKLQEQQSD	3468	1357	1	100
LSA	LAKEKLQGQ	3414	1	100	QERLAKEKLQGQQSD	3469	1119	1	100
LSA	LANEKLQEQ	3415	1	100	QERLANEKLQEQQRD	3470	1527	1	100
LSA	LEQDRLAKE	3416	1	100	QSDLEQDRLAKEKLQ	3471	1386	1	100
LSA	LEQERLAKE	3417	1	100	QSDLEQERLAKEKLQ	3472	1590	1	100
LSA	LEQERLANE	3418	1	100	QSDLEQERLANEKLQ	3473	1522	1	100
LSA	LIDEEEDDE	3419	1	100	DDSLIDEEEDDEDLD	3474	1769	1	100
LSA	LPSENERGY	3420	1	100	AIELPSENERGYYIP	3475	1660	1	100
LSA	LSEDITKYF	3421	1	100	VDELSEDITKYFMKL	3476	1895	1	100
LSA	LSEEKIKKG	3422	1	100	SEELSEEKIKKGKKY	3477	1827	1	100
LSA	LYDEHIKKY	3423	1	100	DKSLYDEHIKKYKND	3478	1853	1	100
LSA	VLAEDLYGR	3424	1	100	HGDVLAEDLYGRLEI	3479	1644	1	100
LSA	VNKEKEKFI	3425	1	100	DKQVNKEKEKFIKSL	3480	1867	1	100
LSA	VQYDNFQDE	3426	1	100	KPIVQYDNFQDEENI	3481	1786	1	100
LSA	YEDEISAEY	3427	1	100	ISKYEDEISAEYDDS	3482	1757	1	100
LSA	YKNDKQVNK	3428	1	100	IKKYKNDKQVNKEKE	3483	1861	1	100
PfEXP	FNKESLAEK	3429	1	100	FIIFNKESLAEKTNK	3484	13	1	100
PfEXP	IKKEEELVE	3430	1	100	SDMIKKEEELVEVNK	3485	55	1	100
PfEXP	LISDMIKKE	3431	1	100	VHDLISDMIKKEEEL	3486	50	1	100
PfEXP	VTPEQPQGD	3432	1	100	AQDVTPEQPQGDDNN	3487	141	1	100
PfEXP	YNTEKGRHP	3433	1	100	LVLYNTEKGRHPFKI	3488	98	1	100
SSP2	IFFDLFLVN	3434	10	100	VFLIFFDLFLVNGRD	3489	13	10	100
SSP2	ILTDGIPDS	3435	10	100	LVVILTDGIPDSIQD	3490	156	10	100
SSP2	INRENANQL	3436	10	100	NDRINRENANQLVVI	3491	145	10	100
SSP2	LHSDASKNK	3437	10	100	IIRLHSDASKNKEKA	3492	100	10	100
SSP2	LYADSAWEN	3438	10	100	KCNLYADSAWENVKN	3493	211	10	100
SSP2	VCVEVEKTA	3439	10	100	MKAVCVEVEKTASCG	3494	231	10	100
SSP2	VEVEKTASC	3440	10	100	AVCVEVEKTASCGVW	3495	233	10	100
SSP2	VPSDVPKNP	3441	10	100	EKEVPSDVPKNPEDD	3496	384	10	100
SSP2	VWDEWSPCS	3442	10	100	SCGVWDEWSPCSVTC	3497	243	10	100
SSP2	LLMDCSGSI	3443	10	90	DLYLLMDCSGSIRRH	3498	48	9	90
SSP2	ILHEGCTSE	3444	10	80	KREILHEGCTSELQE	3499	265	8	80
SSP2	IPEDSEKEV	3445	10	80	EPNIPEDSEKEVPSD	3500	376	8	80
SSP2	YREEVCNDE	3446	9	80	EIKYREEVCNDEVDL	3501	35	8	80
SSP2	VCNDEVDLY	3447	8	80	REEVCNDEVDLYLLM	3502	39	8	80
SSP2	YAGEPAPFD	3448	8	80	ATPYAGEPAPFDETL	3503	538	8	80

TABLE XXb
DR3a Motif Peptides With Binding Information

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR1	DR2w2β1	DR2w2β2
LFQEYQCYG	3394	VEALFQEYQCYGSSS	3449
LFVEALFQE	3395	SSFLFVEALFQEYQC	3450
MPNDPNRNV	3396	GHNMPNDPNRNVDEN	3451
LYNELEMNY	3397	GINLYNELEMNYYGK	3452
VLNELNYDN	3398	NTRVLNELNYDNAGI	3453
YENDIEKKI	3399	ELDYENDIEKKICKM	3454
LNYDNAGIN	3400	LNELNYDNAGINLYN	3455
LSTEWSPCS	3401	QNSLSTEWSPCSVTC	3456
LDYENDIEK	3402	KDELDYENDIEKKIC	3457
FDGDNEILQ	3403	FHIFDGDNEILQIVD	3458
FDKDKELTM	3404	NKFFDKDKELTMSNV	3459
FQDEENIGI	3405	YDNFQDEENIGIYKE	3460
IDEEEDDED	3406	DSLIDEEEDDEDLDE	3461
IINDDDDKK	3407	IEHIINDDDDKKKYI	3462
INDDDDKKK	3408	EHIINDDDDKKKYIK	3463
ISAEYDDSL	3409	EDEISAEYDDSLIDE	3464
IVDELSEDI	3410	ILQIVDELSEDITKY	3465	0.0001		-0.0005
IYKELEDLI	3411	NIGIYKELEDLIEKN	3466
LAEDLYGRL	3412	GDVLAEDLYGRLEIP	3467
LAKEKLQEQ	3413	QERLAKEKLOEQQSD	3468
LAKEKLQGQ	3414	QERLAKEKLOGQQSD	3469
LANEKLQEQ	3415	QERLANEKLOEQQRD	3470
LEQDRLAKE	3416	QSDLEQDRLAKEKLQ	3471
LEQERLAKE	3417	QSDLEQERLAKEKLQ	3472
LEQERLANE	3418	QSDLEQERLANEKLQ	3473
LIDEEEDDE	3419	DDSLIDEEEDDEDLD	3474
LPSENERGY	3420	AIELPSENERGYYIP	3475
LSEDITKYF	3421	VDELSEDITKYFMKL	3476
LSEEKIKKG	3422	SEELSEEKIKKGKKY	3477
LYDEHIKKY	3423	DKSLYDEHIKKYKND	3478	0.0001		-0.0005
VLAEDLYGR	3424	HGDVLAEDLYGRLEI	3479
VNKEKEKFI	3425	DKOVNKEKEKFIKSL	3480
VQYDNFQDE	3426	KPIVQYDNFQDEENI	3481
YEDEISAEY	3427	ISKYEDEISAEYDDS	3482	0.0001		-0.0005
YKNDKQVNK	3428	IKKYKNDKQVNKEKE	3483
FNKESLAEK	3429	FIIFNKESLAEKTNK	3484
IKKEEELVE	3430	SDMIKKEEELVEVNK	3485
LISDMIKKE	3431	VHDLISDMIKKEEEL	3486
VTPEQPQGD	3432	AQDVTPEQPQGDDNN	3487
YNTEKGRHP	3433	LVLYNTEKGRHPFKI	3488
IFFDLFLVN	3434	VFLIFFDLFLVNGRD	3489
ILTDGIPDS	3435	LVVILTDGIPDSIQD	3490	0.0002	0.0001	-0.0006
INRENANQL	3436	NDRINRENANOLVVI	3491	0.0770		0.0015
LHSDASKNK	3437	IIRLHSDASKNKEKA	3492
LYADSAWEN	3438	KCNLYADSAWENVKN	3493	0.0002	0.0005	-0.0010
VCVEVEKTA	3439	MKAVCVEVEKTASCG	3494
VEVEKTASC	3440	AVCVEVEKTASCGVW	3495	0.0001		-0.0006
VPSDVPKNP	3441	EKEVPSDVPKNPEDD	3496
VWDEWSPCS	3442	SCGVWDEWSPCSVTC	3497	0.0001		-0.0005
LLMDCSGSI	3443	DLYLLMDCSGSIRRH	3498	0.0041		0.0250

Core
Sequence	DR3	DR4w4	DR4w15	DR5w11	DR5w12
LFQEYQCYG	0.0082
LFVEALFQE	0.0051
MPNDPNRNV	-0.0033
LYNELEMNY	0.0270
VLNELNYDN	-0.0033
YENDIEKKI
LNYDNAGIN
LSTEWSPCS	-0.0033
LDYENDIEK
FDGDNEILQ	0.0640
FDKDKELTM
FQDEENIGI	-0.0033
IDEEEDDED
IINDDDDKK
INDDDDKKK
ISAEYDDSL	-0.0033
IVDELSEDI	-0.0041	0.0027	0.0017	-0.0002	0.0001
IYKELEDLI	-0.0033
LAEDLYGRL
LAKEKLQEQ
LAKEKLQGQ
LANEKLQEQ	-0.0033
LEQDRLAKE	0.0038
LEQERLAKE	-0.0033
LEQERLANE
LIDEEEDDE
LPSENERGY	-0.0033
LSEDITKYF
LSEEKIKKG	-0.0033
LYDEHIKKY	-0.0041	-0.0007	-0.0014	-0.0002	0.0001
VLAEDLYGR
VNKEKEKFI	-0.0033
VQYDNFQDE	-0.0033
YEDEISAEY	-0.0041	0.0008	-0.0014	-0.0002	0.0001
YKNDKQVNK	-0.0033
FNKESLAEK	0.0040
IKKEEELVE	-0.0033
LISDMIKKE
VTPEQPQGD	-0.0033
YNTEKGRHP
IFFDLFLVN
ILTDGIPDS	0.1400	0.3600	-0.0014	-0.0004	0.0002
INRENANQL	0.0092	0.0011	0.0010	-0.0004	0.0001
LHSDASKNK	-0.0033
LYADSAWEN	0.3500	-0.0055		-0.0006
VCVEVEKTA
VEVEKTASC	-0.0041	0.0030	-0.0014	0.0003	0.0001
VPSDVPKNP		-0.0130
VWDEWSPCS	-0.0041	-0.0009	-0.0009	-0.0002	0.0001
LLMDCSGSI	0.0300	0.0340	0.0028	-0.0002	0.0001

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR6w19	DR7	DR8w2	DR9	DRw53
LFQEYQCYG	3394	VEALFQEYQCYQSSS	3449
LFVEALFQE	3395	SSFLFVEALFQEYQC	3450
MPNDPNRNV	3396	GHNMPNDPNRNVDEN	3451
LYNELEMNY	3397	GINLYNELEMNYYGK	3452
VLNELNYDN	3398	NTRVLNELNYDNAGI	3453
YENDIEKKI	3399	ELDYENDIEKKICKM	3454
LNYDNAGIN	3400	LNELNYDNAGINLYN	3455
LSTEWSPCS	3401	QNSLSTEWSPCSVTC	3456
LDYENDIEK	3402	KDELDYENDIEKKIC	3457
FDGDNEILQ	3403	FHIFDGDNEILQIVD	3458
FDKDKELTM	3404	NKFFDKDKELTMSNV	3459
FQDEENIGI	3405	YDNFQDEENIGIYKE	3460
IDEEEDDED	3406	DSLIDEEEDDEDLDE	3461
IINDDDDKK	3407	IEHIINDDDDKKKYI	3462
INDDDDKKK	3408	EHIINDDDDKKKYIK	3463
ISAEYDDSL	3409	EDEISAEYDDSLIDE	3464
IVDELSEDI	3410	ILQIVDELSEDITKY	3465		-0.0003	-0.0003		0.0290
IYKELEDLI	3411	NIGIYKELEDLIEKN	3466
LAEDLYGRL	3412	GDVLAEDLYGRLEIP	3467
LAKEKLQEQ	3413	QERLAKEKLQEQQSD	3468
LAKEKLQGQ	3414	QERLAKEKLQGQQSD	3469
LANEKLQEQ	3415	QERLANEKLQEQQRD	3470
LEQDRLAKE	3416	QSDLEQDRLAKEKLQ	3471
LEQERLAKE	3417	QSDLEQERLAKEKLQ	3472
LEQERLANE	3418	QSDLEQERLANEKLQ	3473
LIDEEEDDE	3419	DDSLIDEEEDDEDLD	3474
LPSENERGY	3420	AIELPSENERGYYIP	3475
LSEDITKYF	3421	VDELSEDITKYFMKL	3476
LSEEKIKKG	3422	SEELSEEKIKKGKKY	3477
LYDEHIKKY	3423	DKSLYDEHIKKYKND	3478		-0.0003	-0.0003		0.0006
VLAEDLYGR	3424	HGDVLAEDLYGRLEI	3479
VNKEKEKFI	3425	DKQVNKEKEKFIKSL	3480
VQYDNFQDE	3426	KPIVQYDNFQDEENI	3481
YEDEISAEY	3427	ISKYEDEISAEYDDS	3482		-0.0003	-0.0003		-0.0005
YKNDKQVNK	3428	IKKYKNDKQVNKEKE	3483
FNKESLAEK	3429	FIIFNKESLAEKTNK	3484
IKKEEELVE	3430	SDMIKKEEELVEVNK	3485
LISDMIKKE	3431	VHDLISDMIKKEEEL	3486
VTPEQPQGD	3432	AQDVTPEQPQGDDNN	3487
YNTEKGRHP	3433	LVLYNTEKGRHPFKI	3488
IFFDLFLVN	3434	VFLIFFDLFLVNGRD	3489
ILTDGIPDS	3435	LVVILTDGIPDSIQD	3490	0.0002	0.0046	-0.0003	0.0014	0.0480
INRENANQL	3436	NDRINRENANQLVVI	3491		-0.0003	-0.0003		0.0096
LHSDASKNK	3437	IIRLHSDASKNKEKA	3492
LYADSAWEN	3438	KCNLYADSAWENVKN	3493	0.0003	-0.0014	-0.0009
VCVEVEKTA	3439	MKAVCVEVEKTASCG	3494
VEVEKTASC	3440	AVCVEVEKTASCGVW	3495		0.0073	0.0006		0.0022
VPSDVPKNP	3441	EKEVPSDVPKNPEDD	3496
VWDEWSPCS	3442	SCGVWDEWSPCSVTC	3497		-0.0003	-0.0003
LLMDCSGSI	3443	DLYLLMDCSGSIRRH	3498		0.0072	0.0014		0.0057

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR1	DR2w2β1	DR2w2β2
ILHEGCTSE	3444	KREILHEGCTSELQE	3499
IPEDSEKEV	3445	EPNIPEDSEKEVPSD	3500
YREEVCNDE	3446	EIKYREEVCNDEVDL	3501
VCNDEVDLY	3447	REEVCNDEVDLYLLM	3502	0.0003	-0.0006	0.1300
YAGEPAPFD	3448	ATPYAGEPAPFDETL	3503

Core
Sequence	DR3	DR4w4	DR4w15	DR5w11	DR5w12
ILHEGCTSE
IPEDSEKEV	-0.0130
YREEVCNDE	-0.0033
VCNDEVDLY	-0.0006	-0.0014	-0.0004	0.0001
YAGEPAPFD	-0.0130

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR6w19	DR7	DR8w2	DR9	DRw53
ILHEGCTSE	3444	KREILHEGCTSELQE	3499
IPEDSEKEV	3445	EPNIPEDSEKEVPSD	3500
YREEVCNDE	3446	EIKYREEVCNDEVDL	3501
VCNDEVDLY	3447	REEVCNDEVDLYLLM	3502		-0.0003	-0.0003		-0.0010
YAGEPAPFD	3448	ATPYAGEPAPFDETL	3503

TABLE XXc
		Core		Core
	Core	SeqID	Core	Conservancy	Exemplary
Protein	Sequence	Num	Frequency	(%)	Sequence
CSP	LKKNSRSLG	3504	19	100	WYSLKKNSRSLGEND
CSP	ANNDVKNNN	3505	3	16	NANANNDVKNNNNEE
LSA	ADIQNHTLE	3506	1	100	DKSADIQNHTLETVN
LSA	FHINGKIIK	3507	1	100	LLIFHINGKIIKNSE
LSA	FKPNDKSLY	3508	1	100	DNNFKPNDKSLYDEH
LSA	FLKENKLNK	3509	1	100	ENIFLKENKLNKEGK
LSA	IEKTNRESI	3510	1	100	ISIIEKTNRESITTN
LSA	IKNSEKDEI	3511	1	100	GKIIKNSEKDEIIKS
LSA	IKPEQKEDK	3512	1	100	DGSIKPEQKEDKSAD
LSA	IKSNLRSGS	3513	1	100	DEIIKSNLRSGSSNS
LSA	INEEKHEKK	3514	1	100	RNRINEEKHEKKHVL
LSA	LEQERRAKE	3515	1	100	QSDLEQERRAKEKLQ
LSA	LNKEGKLIE	3516	1	100	ENKLNKEGKLIEHII
LSA	LPQDNRGNS	3517	1	100	QSSLPQDNRGNSRDS
LSA	LQEQQRDLE	3518	1	100	NEKLQEQQRDLEQER
PfEXP	AEKTNKGTG	3519	1	100	ESLAEKTNKGTGSGV
PfEXP	LYNTEKGRH	3520	1	100	GLVLYNTEKGRHPFK
PfEXP	VEVNKRKSK	3521	1	100	EELVEVNKRKSKYKL
SSP2	AWENVKNVI	3522	10	100	ADSAWENVKNVIGPF
SSP2	FLVNGRDVQ	3523	10	100	FDLFLVNGRDVQNNI
SSP2	LGEEDKDLD	3524	10	100	DETLGEEDKDLDEPE
SSP2	LDNERKQSD	3525	10	80	PKVLDNERKQSDPQS
SSP2	VLDNERKQS	3526	10	70	PPKVLDNERKQSDPQ
SSP2	IQDSLKESR	3527	10	60	PDSIQDSLKESRKLN
SSP2	IVDEIKYSE	3528	9	90	QNNIVDEIKYREEVC
SSP2	ALLQVRKHL	3529	9	60	LTDALLQVRKHLNDR
SSP2	LKESRKLND	3530	6	50	QDSLKESRKLSDRGV
SSP2	FSNNAKEII	3531	6	40	VNVFSNNAKEIIRLH
SSP2	YNDTPKHPE	3532	5	50	NRKYNDTPKHPEREE
SSP2	FSNNAREII	3533	4	20	LNIFSNNAREIIRLH
SSP2	LKESRKLSD	3534	3	30	QDSLKESRKLSDRGV
SSP2	YNDTPKYPE	3535	2	20	NRKYNDTPKYPEREE
SSP2	AGSDNKYKI	3536	1	10	KKKAGSDNKYKIAGG
SSP2	ALLEVRKHL	3537	1	10	LTDALLEVRKHLNDR
SSP2	IVDEIKYSE	3538	1	10	QNNIVDEIKYSEEVC

	Exemplary	Position	Exemplary	Exemplary
	SeqID	In PF	Sequence	Sequence
Protein	Num	Poly-Protein	Frequency	Conservancy (%)
CSP	3539	62	19	100
CSP	3540	361	3	16
LSA	3541	1734	1	100
LSA	3542	16	1	100
LSA	3543	1846	1	100
LSA	3544	108	1	100
LSA	3545	1693	1	100
LSA	3546	23	1	100
LSA	3547	1724	1	100
LSA	3548	32	1	100
LSA	3549	47	1	100
LSA	3550	1573	1	100
LSA	3551	114	1	100
LSA	3552	1676	1	100
LSA	3553	1532	1	100
PfEXP	3554	19	1	100
PfEXP	3555	97	1	100
PfEXP	3556	62	1	100
SSP2	3557	216	10	100
SSP2	3558	18	10	100
SSP2	3559	549	10	100
SSP2	3560	435	8	80
SSP2	3561	434	7	70
SSP2	3562	165	6	60
SSP2	3563	29	9	90
SSP2	3564	133	6	60
SSP2	3565	169	5	50
SSP2	3566	90	4	40
SSP2	3567	479	5	50
SSP2	3568	90	2	20
SSP2	3569	169	3	30
SSP2	3570	479	2	20
SSP2	3571	501	1	10
SSP2	3572	133	1	10
SSP2	3573	29	1	10

TABLE XXd
Malaria DR3b Motif Peptides With Binding Information

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR1	DR2w2β1	DR2w2β2
LKKNSRSLG	3504	WYSLKKNSRSLGEND	3539
ANNDVKNNN	3505	NANANNDVKNNNNEE	3540
ADIQNHTLE	3506	DKSADIQNHTLETVN	3541
FHINGKIIK	3507	LLIFHINGKIIKNSE	3542	0.5700	0.2900	0.2500
FKPNDKSLY	3508	DNNFKPNDKSLYDEH	3543
FLKENKLNK	3509	ENIFLKENKLNKEGK	3544
IEKTNRESI	3510	ISIIEKTNRESITIN	3545
IKNSEKDEI	3511	GKIIKNSEKDEIIKS	3546	0.0002	-0.0021	-0.0160
IKPEQKEDK	3512	DGSIKPEQKEDKSAD	3547
IKSNLRSGS	3513	DEIIKSNLRSGSSNS	3548
INEEKHEKK	3514	RNRINEEKHEKKHVL	3549
LEQERRAKE	3515	QSDLEQERRAKEKLQ	3550
LNKEGKLIE	3516	ENKLNKEGKLIEHII	3551	0.0001		-0.0021
LPQDNRGNS	3517	QSSLPQDNRGNSRDS	3552
LQEQQRDLE	3518	NEKLQEQQRDLEQER	3553
AEKTNKGTG	3519	ESLAEKTNKGTGSGV	3554
LYNTEKGRH	3520	GLVLYNTEKGRHPFK	3555
VEVNKRKSK	3521	EELVEVNKRKSKYKL	3556
AWENVKNVI	3522	ADSAWENVKNVIGPF	3557
FLVNGRDVQ	3523	FDLFLVNGRDVQNNI	3558
LGEEDKDLD	3524	DETLGEEDKDLDEPE	3559
LDNERKQSD	3525	PKVLDNERKQSDPQS	3560
VLDNERKQS	3526	PPKVLDNERKQSDPQ	3561
IQDSLKESR	3527	PDSIQDSLKESRKLN	3562	-0.0001	0.0040	-0.0018
IVDEIKYRE	3528	QNNIVDEIKYREEVC	3563
ALLQVRKHL	3529	LTDALLQVRKHLNDR	3564
LKESRKLND	3530	QDSLKESRKLNDRGV	3565
FSNNAKEll	3531	VNVFSNNAKEIIRLH	3566
YNDTPKHPE	3532	NRKYNDTPKHPEREE	3567
FSNNAREII	3533	LNIFSNNAREIIRLH	3568
LKESRKLSD	3534	QDSLKESRKLSDRGV	3569
YNDTPKYPE	3535	NRKYNDTPKYPEREE	3570
AGSDNKYKI	3536	KKKAGSDNKYKIAGG	3571
ALLEVRKHL	3537	LTDALLEVRKHLNDR	3572
IVDEIKYSE	3538	QNNIVDEIKYREEVC	3573

Core
Sequence	DR3	DR4w4	DR4w15	DR5w11	DR5w12
LKKNSRSLG
ANNDVKNNN
ADIQNHTLE
FHINGKIIK	0.5300	0.0060	-0.0030	0.3600	0.0230
FKPNDKSLY	0.1700
FLKENKLNK	0.0950
IEKTNRESI	0.1300
IKNSEKDEI	-0.0017	0.0030	-0.0010	-0.0003
IKPEQKEDK	-0.0033
IKSNLRSGS	0.0050
INEEKHEKK	0.0420
LEQERRAKE
LNKEGKLIE	-0.0140	-0.0017	-0.0047	-0.0005	-0.0003
LPQDNRGNS	-0.0033
LQEQQRDLE
AEKTNKGTG	-0.0033
LYNTEKGRH
VEVNKRKSK	0.0880
AWENVKNVI	-0.0130
FLVNGRDVQ	-0.0033
LGEEDKDLD	-0.0130
LDNERKQSD	-0.0130
VLDNERKQS	-0.0130
IQDSLKESR	0.8400	-0.0055		-0.0006
IVDEIKYRE
ALLQVRKHL	-0.0033
LKESRKLND
FSNNAKEll
YNDTPKHPE
FSNNAREII
LKESRKLSD
YNDTPKYPE
AGSDNKYKI
ALLEVRKHL
IVDEIKYSE

	Core		Exemplary
Core	SeqID	Exemplary	SeqID
Sequence	Num	Sequence	Num	DR6w19	DR7	DR8w2	DR9	DRw53
LKKNSRSLG	3504	WYSLKKNSRSLGEND	3539
ANNDVKNNN	3505	NANANNDVKNNNNEE	3540
ADIQNHTLE	3506	DKSADIQNHTLETVN	3541
FHINGKIIK	3507	LLIFHINGKIIKNSE	3542	0.0330	0.1300	0.1400	0.1500
FKPNDKSLY	3508	DNNFKPNDKSLYDEH	3543
FLKENKLNK	3509	ENIFLKENKLNKEGK	3544
IEKTNRESI	3510	ISIIEKTNRESITTN	3545
IKNSEKDEI	3511	GKIIKNSEKDEIIKS	3546		-0.0011	-0.0007
IKPEQKEDK	3512	DGSIKPEQKEDKSAD	3547
IKSNLRSGS	3513	DEIIKSNLRSGSSNS	3548
INEEKHEKK	3514	RNRINEEKHEKKHVL	3549
LEQERRAKE	3515	QSDLEQERRAKEKLQ	3550
LNKEGKLIE	3516	ENKLNKEGKLIEHII	3551		-0.0009	-0.0007
LPQDNRGNS	3517	QSSLPQDNRGNSRDS	3552
LQEQQRDLE	3518	NEKLQEQQRDLEQER	3553
AEKTNKGTG	3519	ESLAEKTNKGTGSGV	3554
LYNTEKGRH	3520	GLVLYNTEKGRHPFK	3555
VEVNKRKSK	3521	EELVEVNKRKSKYKL	3556
AWENVKNVI	3522	ADSAWENVKNVIGPF	3557
FLVNGRDVQ	3523	FDLFLVNGRDVQNNI	3558
LGEEDKDLD	3524	DETLGEEDKDLDEPE	3559
LDNERKQSD	3525	PKVLDNERKQSDPQS	3560
VLDNERKQS	3526	PPKVLDNERKQSDPQ	3561
IQDSLKESR	3527	PDSIQDSLKESRKLN	3562	-0.0002	-0.0014	0.0012
IVDEIKYRE	3528	QNNIVDEIKYREEVC	3563
ALLQVRKHL	3529	LTDALLQVRKHLNDR	3564
LKESRKLND	3530	QDSLKESRKLNDRGV	3565
FSNNAKEII	3531	VNVFSNNAKEIIRLH	3566
YNDTPKHPE	3532	NRKYNDTPKHPEREE	3567
FSNNAREII	3533	LNIFSNNAREIIRLH	3568
LKESRKLND	3534	QDSLKESRKLNDRGV	3569
YNDTPKYPE	3535	NRKYNDTPKYPEREE	3570
AGSDNKYKI	3536	KKKAGSDNKYKIAGG	3571
ALLEVRKHL	3537	LTDALLEVRKHLNDR	3572
IVDEIKYSE	3538	QNNIVDEIKYREEVC	3573

TABLE XXI
Population coverage with combined HLA Supertypes

PHENOTYPIC FREQUENCY

		North
		American
HLA-SUPERTYPES	Caucasian	Black	Japanese	Chinese	Hispanic	Average

a. Individual Supertypes
A2	45.8	39.0	42.4	45.9	43.0	43.2
A3	37.5	42.1	45.8	52.7	43.1	44.2
B7	38.6	52.7	48.8	35.5	47.1	44.7
A1	47.1	16.1	21.8	14.7	26.3	25.2
A24	23.9	38.9	58.6	40.1	38.3	40.0
B44	43.0	21.2	42.9	39.1	39.0	37.0
B27	28.4	26.1	13.3	13.9	35.3	23.4
B62	12.6	4.8	36.5	25.4	11.1	18.1
B58	10.0	25.1	1.6	9.0	5.9	10.3
b. Combined Supertypes
A2, A3, B7	83.0	86.1	87.5	88.4	86.3	86.2
A2, A3, B7, A24, B44, A1	99.5	98.1	100.0	99.5	99.4	99.3
A2, A3, B7, A24, B44, A1,	99.9	99.6	100.0	99.8	99.9	99.8
B27, B62, B58

TABLE XXII
Fixed analogs of P. falciparum CTL epitopes

			SEQ					SEQ
Supertype			ID		Alleles	Fixing	Fixed	ID
(or allele)	Peptide	Sequence	NO:	Source	bounda	strategy	sequence	NO:

A2	1167.21	FLIFFDLFLV	3610	Pf SSP2 14	5	V2	FLIFFDLFLV	3803
supertype	1167.16	FMKAVCVEV	3611	Pf SSP2 230	5	V2	FVKAVCVEV	3804
	1167.08	GLIMVLSFL	3612	Pf CSP 425	4	Vc	GLIMVLSFV	3805
						V2	GVIMVLSFL	3806
						V2Nc	GVIMVLSFV	3807
	1167.12	VLAGLLGNV	3613	Pf EXP1 80	4	V2	VLAGLLGNV	3808
	1167.13	KILSVFFLA	3614	Pf EXP1 2	3	L2	KLLSVFFLA	3809
						V2	KVLSVFFLA	3810
						Vc	KILSVFFLV	3811
						L2/Vc	KLLSVFFLV	3812
						V2/Vc	KVLSVFFLV	3813
	1167.10	GLLGNVSTV	3615	Pf EXP1 83	3	V2	GVLGNVSTV	3814
	1167.18	ILSVSSFLFV	3616	Pf CSP 7	2	V2	IVSVSSFLFV	3815
	1167.19	VLLGGVGLVL	3617	Pf EXP1 91	2	Vc	VLLGGVGLVV	3816
						V2	VVLGGVGLVL	3817
						V2/Vc	VVLGGVGLVV	3818
A3-	1167.36	LACAGLAYK	3718	Pf SSP2 511	4	V2	LVCAGLAYK	3819
supertype	1167.32	QTNFKSLLR	3619	Pf LSA1 94	4	V2	QVNFKSLLR	3820
	1167.43	VTCGNGIQVR	3620	Pf CSP 375	4	V2	VVCGNGIQVR	3821
	1167.24	ALFFIIFNK	3621	Pf EXP1 10	3	V2	AVFFIIFNK	3822
	1167.28	GVSENIFLK	3622	Pf LSA1 105	3	—
	1167.47	HVLSHNSYEK	3623	Pf LSA1 59	3	—
	1167.51	LLACAGLAYK	3624	Pf SSP2 510	3	V2	LVACAGLAYK	3823
	1167.46	FILVNLLIFH	3625	Pf LSA1 11	2	V2	FVLVNLLIFH	3824
						Rc	FILVNLLIFR	3825
						Kc	FILVNLLIFK	3826
						V2/Rc	FVLVNLL1FR	3827
						V2/Kc	FVLVNLLIFK	3828
B7-	1167.61	TPYAGEPAPF	3626	Pf SSP2 539	4	Ic	TPYAGEPAPI	3829
supertype
	19.0051	LPYGRTNL	3627	Pf SSP2 126	3	Ic	LPYGRTNI	3830
A1	16.0245	FQDEENIGIY	3628	Pf LSA1 1794	1	T2	FTDEENIGIY	3831
	16.0040	FVEALFQEY	3629	Pf CSP 15	1	D3	FVEALFQEY	3832
						T2	FTEALFQEY	3833
	15.0184	LPSENERGY	3630	Pf LSA1 1663	1	D3	LPDENERGY	3834
						T2	LTSENERGY	3835
	16.0130	PSDGKCNLY	3631	Pf SSP2 207	1	T2	PTDGKCNLY	3836
A24	1167.54	FYFILVNLL	3632	Pf LSA1 9	1	Fc	FYFILVNLF	3837
	1167.53	KYKLATSVL	3633	Pf EXP1 73	1	Fc	KYKLATSVF	3838
	1167.56	KYLVIVFLI	3634	Pf SSP2 8	1	Fc	KYLVIVFLF	3839
	1167.55	YYIPHQSSL	3635	Pf LSA1 1671	1	Fc	YYIPHQSSF	3840
aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding ato A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101, and A*2402, respectively.

TABLE XXIII
Plasmodium falciparum CTL-inducing epitopes

	SEQ
	ID			HLA-
Epitope	NO:	Antigen	Residues	restriction
GLIMVLSFL	3636	CSP	386-394	A2-supertype
ILSVSSFLFV	3637	CSP	7-16	A2-supertype
VLAGLLGNV	3638	Exp-1	80-88	A2-supertype
KILSVFFLA	3639	Exp-1	2-10	A2-supertype
GLLGNVSTV	3640	Exp-1	83-91	A2-supertype
VLLGGVGLVL	3641	Exp-1	91-100	A2-supertype
FLIFFDLFLV	3642	SSP2	14-23	A2-supertype
VTCGNGIQVR	3643	CSP	336-345	A3-supertype
ALFFIIFNK	3644	Exp-1	10-18	A3-supertype
QTNFKSLLR	3645	LSA-1	94-102	A3-supertype
GVSENIFLK	3646	LSA-1	105-113	A3-supertype
HVLSHNSYEK	3647	LSA-1	59-68	A3-supertype
FILVNLLIFH	3648	LSA-1	11-20	A3-supertype
TPYAGELPAPF	3649	SSP2	539-548	B7-supertype
MPLETQLAI	3650	s16	77-85	B7-supertype
MRKLAILSVSSFLVF	3651	CSP	2-16	DR-supermotif
MNYYGKQENWYSLICK	3652	CSP	53-67	DR-supermotif
RHNWVNHAVPLAMKLI	3653	SSP2	61-76	DR-supermotif
VKNVIGPFMKAVCVE	3654	SSP2	223-237	DR-supermotif
SSVFNVVNSSIGLIM	3655	CSP	410-424	DR-supermotif
AGLLGNVSTVSTVLLGGV	3656	EXP1	82-96	DR-supermotif
KSKYKLATSVLAGLL	3657	EXP1	71-85	DR-supermotif
GLAYKFVVPGAATPY	3658	SSP2	512-526	DR-supermotif
KYKIAGGIAGGLALL	3659	SSP2	494-508	DR-supermotif

TABLE XXIV
MHC-peptide binding assays: cell lines and radiolabeled ligands.
A. Class I binding assays

Radiolabeled peptide

Species	Antigen	Allele	Cell line	Source	Sequence	SEQ ID NO:
Human	A1	A*0101	Steinlin	Hu. J chain 102-110	YTAVVPLVY	3660
	A2	A*0201	JY	HBVc 18-27 F6->Y	FLPSDYFPSV	3661
	A2	A*0202	P815	HBVc 18-27 F6->Y	FLPSDYFPSV	3662
			(transfected)
	A2	A*0203	FUN	HBVc 18-27 F6->Y	FLPSDYFPSV	3663
	A2	A*0206	CLA	HBVc 18-27 F6->Y	FLPSDYFPSV	3664
	A2	A*0207	721.221	HBVc 18-27 F6->Y	FLPSDYFPSV	3665
			(transfected)
	A3		GM3107	non-natural (A3CON1)	KVFPYALINK	3666
	A11		BVR	non-natural (A3CON1)	KVFPYALINK	3667
	A24	A*2402	KAS116	non-natural (A24CON1)	AYIDNYNKF	3668
	A31	A*3101	SPACH	non-natural (A3CON1)	KVFPYALINK	3669
	A33	A*3301	LWAGS	non-natural (A3CON1)	KVFPYALINK	3670
	A28/68	A*6801	C1R	HBVc 141-151 T7->Y	STLPETYVVRR	3671
	A28/68	A*6802	AMAI	HBV pol 646-654 C4->A	FTQAGYPAL	3672
	B7	B*0702	GM3107	A2 sigal seq. 5-13	APRTLVYLL	3673
				(L7->Y)
	B8	B*0801	Steinlin	HIVgp 586-593 Y1->F,	FLKDYQLL	3674
				Q5->Y
	B27	B*2705	LG2	R 60s	FRYNGLIHR	3675
	B35	B*3501	C1R, BVR	non-natural (B35CON2)	FPFKYAAAF	3676
	B35	B*3502	TISI	non-natural (B35CON2)	FPFKYAAAF	3677
	B35	B*3503	EHM	non-natural (B35CON2)	FPFKYAAAF	3678
	B44	B*4403	PITOUT	EF-1 G6->Y	AEMGKYSFY	3679
	B51		KAS116	non-natural (B35CON2)	FPFKYAAAF	3680
	B53	B*5301	AMAI	non-natural (B35CON2)	FPFKYAAAF	3681
	B54	B*5401	KT3	non-natural (B35CON2)	FPFKYAAAF	3682
	Cw4	Cw*0401	CIR	non-natural (C4CON1)	QYDDAVYKL	3683
	Cw6	Cw*0602	721.221	non-natural (C6CON1)	YRHDGGNVL	3684
			transfected
	Cw7	Cw*0702	721.221	non-natural (C6CON1)	YRHDGGNVL	3685
			transfected
Mouse	Db		EL4	Adenovirus ElA P7->Y	SGPSNTYPEI	3686
	Kb		EL4	VSV NP 52-59	RGYVFQGL	3687
	Dd		P815	HIV-IIIB ENV 04->Y	RGPYRAFVTI	3688
	Kd		P815	non-natural (KdCON1)	KFNPMKTYI	3689
	Ld		P815	HBVs 28-39	IPQSLDSYWTSL	3690

B. Class II binding assays

Radiolabeled peptide

Species	Antigen	Allele	Cell line	Source	Sequence	SEQ ID NO:
Human	DR1	DRB1*0101	LG2	HA Y307-319	YPKYVKQNTLKLAT	3691
	DR2	DRB1*1501	L466.1	MBP 88-102Y	VVHFFKNIVTPRTPPY	3692
	DR2	DRB1*1601	L242.5	non-natural (760.16)	YAAFAAAKTAAAFA	3693
	DR3	DRB1*0301	MAT	MT 65kD Y3-13	YKTIAFDEEARR	3694
	DR4w4	DRB1*0401	Preiss	non-natural (717.01)	YARFQSQTTLKQKT	3695
	DR4w10	DRB1*0402	YAR	non-natural (717.10)	YARFQRQTTLKAAA	3696
	DR4w14	DRB1*0404	BIN 40	non-natural (717.01)	YARFQSQTTLKQKT	3697
	DR4w15	DRB1*0405	KT3	non-natural (717.01)	YARFQSQTTLKQKT	3698
	DR7	DRB1*0701	Pitout	Tet. tox. 830-843	QYIKANSKFIGITE	3699
	DR8	DRB1*0802	OLL	Tet. tox. 830-843	QYIKANSKFIGITE	3700
	DR8	DRB1*0803	LUY	Tet. tox. 830-843	QYIKANSKFIGITE	3701
	DR9	DRB1*0901	HID	Tet. tox. 830-843	QYIKANSKFIGITE	3702
	DR11	DRB1*1101	Sweig	Tet. tox. 830-843	QYIKANSKFIGITE	3703
	DR12	DRB1*1201	Herluf	unknown eluted peptide	EALIHQLKINPYVLS	3704
	DR13	DRB1*1302	H0301	Tet. tox. 830-843 S->A	QYIKANAKFIGITE	3705
	DR51	DRB5*0101	GM3107	Tet. tox. 830-843	QYIKANAKFIGITE	3706
			or
			L416.3
	DR51	DRB5*0201	L255.1	HA 307-319	PKYVKQNTLKLAT	3707
	DR52	DRB3*0101	MAT	Tet. tox. 830-843	NGQIGNDPNRDIL	3708
	DR53	DRB4*0101	L257.6	non-natural (717.01)	YARFQSQTTLKQKT	3709
	DQ3.1	QA1*0301/	PF	non-natural (ROIV)	YAHAAHAAHAAHAAHAA	3710
		DQB1*03(
Mouse	IAb		DB27.4	non-natural (ROIV)	YAHAAHAAHAAHAAHAA	3711
	IAd		A20	non-natural (ROIV)	YAHAAHAAHAAHAAHAA	3712
	IAk		CH-12	HEL 46-61	YNTDGSTDYGILQINSR	3713
	IAs		LS102.9	non-natural (ROIV)	YAHAAHAAHAAHAAHAA	3714
	IAu		91.7	non-natural (ROIV)	YAHAAHAAHAAHAAHAA	3715
	IEd		A20	Lambda repressor 12-26	YLEDARRKKAIYEKKK	3716
	lEk		CH-12	Lambda repressor 12-26	YLEDARRKKAIYEKKK	3717

TABLE XXV
Monoclonal antibodies used
in MHC purification.

	Monoclonal antibody	Specificity
	W6/32	HLA-class I
	B123.2	HLA-B and C
	IVD12	HLA-DQ
	LB3.1	HLA-DR
	M1/42	H-2 class I
	28-14-8S	H-2 Db and Ld
	34-5-8S	H-2 Dd
	B8-24-3	H-2 Kb
	SF1-1.1.1	H-2 Kd
	Y-3	H-2 Kb
	10.3.6	H-2 IAk
	14.4.4	H-2 IEd, IEK
	MKD6	H-2 IAd
	Y3JP	H-2 IAb, IAs, IAu

TABLE XXVI
P. falciparum A2-supermotif CTL epitopes

SEQ ID

A2-supertype binding capacity (IC50 nM)

Alleles

Peptide	AA	Sequence	NO:	Source	A*0201	A*0202	A*0203	A*0206	A*6802	bounda

1167.21	10	FLIFFDLFLV	3718	Pf SSP2 14	12	10	5.9	11	333	5
1167.16	9	FMKAVCVEV	3719	Pf SSP2 230	63	307	2.9	389	143	5
1167.12	9	VLAGLLGNV	3720	Pf EXP1 80	19	24	0.67	31	606	4
1167.08	9	GLIMVLSFL	3721	Pf CSP 425	22	20	3.6	74	4396	4
1167.13	9	KILSVFFLA	3722	Pf EXP1 2	5.0	172	3448	8.0	9524	3
1167.10	9	GLLGNVSTV	3723	Pf EXP1 83	24	1194	1.2	25	21053	3
1167.19	10	VLLGGVGLVL	3724	Pf EXP1 91	94	—	2500	420	16000	2
1167.18	10	ILSVSSFLFV	3725	Pf CSP 7	208	3583	19	587	2105	2
* A dash indicates IC50 nM > 30000.

TABLE XXVII
P. falciparum A3-supermotif CTL epitopes

A3-supertype binding capacity (IC50 nm)

			SEQ ID							Alleles
Peptide	AA	Sequence	NO:	Source	A*301	A-1101	A*3101	A*3301	A*6801	bounda

1167.32	9	QTNFKSLLR	3726	Pf LSA1 94	50	14	180	617	4	4
1167.36	9	LACAGLAYK	3727	Pf SSP2 511	423	143	5294	64	32	4
1167.43	10	VTCGNGIQVR	3728	Pf CSP 375	6875	11	15	64	444	4
1167.24	9	ALFFIIFNK	3729	Pf EXP1 10	9.2	2.2	720	1261	73	3
1167.51	10	LLACAGLAYK	3730	Pf SSP2 510	22	73	692	1526	24	3
1167.28	9	GVSENIFLK	3731	Pf LSA1 105	151	5.0	2250	8286	10	3
1167.47	10	HVLSHNSYEK	3732	Pf LSA1 59	407	200	—	—	114	3
1167.46	10	FILVNLLIFH	3733.	Pf LSA1 11	733	1333	1957	397	154	2
* A dash indicates IC50 nM > 30000.

TABLE XXVIII
P. falciparum B7-supermotif CTL epitopes

SEQ ID

B7-supertype binding capacity (IC50 nM)

Alleles

Peptide	AA	Sequence	NO:	Source	B*0702	B*3501	B*5101	B*5301	B*5401	bounda

1167.61	10	TPYAGEPAPF	3734	Pf SSP2 539	31	14	15	158	25000	4
19.0051	8	LPYGRTNL	3735	Pf SSP2 126	50	—	32	15500	417	3
* A dash indicates 1050 nM > 30000.

TABLE XXIX
P. falciparum HLA-A*0101 and A*2402 binding peptides

	Binding capacity
	(IC50 nM)

Motif	Peptide	AA	Sequence	SEQ ID NO:	Source	A*0101	A*2401

A1	16.0040	9	FVEALFQEY	3736	Pf CSP 15	7.4
	16.0245	10	FQDEENIGIY	3737	Pf LSA1 1794	23
	15.0184	9	LPSENERGY	3738		37
	16.0130	9	PSDGKCNLY	3739	Pf SSP2 207	46
A24	1167.55	9	YYPHQSSL	3740	Pf LSA1 1671		2.4
	1167.54	9	FYFILVNLL	3741	Pf LSA1 9		25
	1167.56	9	KYLVIVFLI	3742	Pf SSP2 8		34
	1167.53	9	KYKLATSVL	3743	Pf EXP1 73		75

TABLE XXX
HLA-DR screening panels

Screening

Representative Assay

Phenotypic Frequencies

Panel	Antigen	Alleles	Allele	Alias	Cauc.	Blk.	Jpn.	Chn.	Hisp.	Avg.

Primary	DR1	DRB1*0101-03	DRB1*0101	(DR1)	18.5	8.4	10.7	4.5	10.1	10.4
	DR4	DRB1*0401-12	DRB1*0401	(DR4w4)	23.6	6.1	40.4	21.9	29.8	24.4
	DR7	DRB1*0701-02	DRB1*0701	(DR7)	26.2	11.1	1.0	15.0	16.6	14.0
	Panel total				59.6	24.5	49.3	38.7	51.1	44.6
Secondary	DR2	DRB1*1501-03	DRB1*1501	(DR2w2 β1)	19.9	14.8	30.9	22.0	15.0	20.5
	DR2	DRB5*0101	DRB5*0101	(DR2w2 β2)	—	—	—	—	—	—
	DR9	DRB1*09011, 09012	DRB1*0901	(DR9)	3.6	4.7	24.5	19.9	6.7	11.9
	DR13	DRB1*1301-06	DRB1*1302	(DR6w19)	21.7	16.5	14.6	12.2	10.5	15.1
	Panel total				42.0	33.9	61.0	48.9	30.5	43.2
Tertiary	DR4	DRB1*0405	DRB1*0405	(DR4w15)	—	—	—	—	—	—
	DR8	DRB1*0801-5	DRB1*0802	(DR8w2)	5.5	10.9	25.0	10.7	23.3	15.1
	DR11	DRB1*1101-05	DRB1*1101	(DR5w11)	17.0	18.0	4.9	19.4	18.1	15.5
	Panel total				22.0	27.8	29.2	29.0	39.0	29.4
Quartemary	DR3	DRB1*0301-2	DRB1*0301	(DR3w17)	17.7	19.5	0.4	7.3	14.4	11.9
	DR12	DRB1*1201-02	DRB1*1201	(DR5w12)	2.8	5.5	13.1	17.6	5.7	8.9
	Panel total				20.2	24.4	13.5	24.2	19.7	20.4

TABLE XXXI
P. falciparum derived HTL candidate epitopes

SEQ ID

Binding capacity (IC50 nM)

Peptide	Sequence	NO:	Source	DR1	DR2w2β1	DR2w2β2	DR4w4	DR4w15
F125.04	RHNWVNHAVPLAMKLI	3744	Pf SSP2 61	26	260	83	14	317
1188.34	HNWVNHAVPLAMKLI	3745	Pf SSP2 62	14	364	143	12	950
1188.16	KSKYKLATSVLAGLL	3746	Pf EXP1 71	3.6	1247	24	7.1	47
	LVNLLIFHINGKIIKNSE	3747	Pf LSA1 13
F125.02	LVNLLIFHINGKIIKNS	3748	Pf LSA1 13	78	13	426	—	1810
27.0402	LLIFHINGKIIKNSE	3749	Pf LSA1 16	8.8		80	7500
1188.32	GLAYKFVVPGAATPY	3750	Pf SSP2 512	3.1	-	29	45	1407
27.0392	SSVFNVVNSSIGLIM	3751	Pf CSP 410	42	314	2500	450	1652
27.0417	VKNVIGPFMKAVCVE	3752	Pf SSP2 223	56	212	250	—	—
27.0388	MRKLAILSVSSFLFV	3753	Pf CSP 2	50	18	1538	5769	1407
27.0387	MNYYGKQENWYSLKK	3754	Pf CSP 53	6.4	9100	435	21	292
1188.38	KYKIAGGIAGGLALL	3755	Pf SSP2 494	132	-	417	3750	22353
1188.13	AGLLGNVSTVLLGGV	3756	Pf EXP1 82	116	379	15,385	6923	1056
27.0408	QTNFKSLLRNLGVSE	3757	Pf LSA1 94	91	8273	5405	2500	1900
35.0171	PDSIQDSLKESRKLN	3758	Pf SSP2 165	-	2285	-	-
35.0172	KCNLYADSAWENVKN	3759	Pf SSP2 211	23425	18200	-	-

Binding capacity (IC50 nM)

Alleles

Peptide	DR5w11	DR6w19	DR7	DR8w2	DR9	DR3	DR5w12	bound2
F125.04	282	3.9	23	41	33	8751	441	11
1188.34	2703	3.7	66	68	19	1304	497	10
1188.16	30	427	13	45	28	—	—	9
F125.02	408	66	260	766	625	19722	11610	8
27.0402	56	106	192	350	500	566	12957	8
1188.32	11	7.1	167	20	125	—	851	9
27.0392	1176	9.7	33	891	63	—	—	7
27.0417	476	32	424	2130	862	—	3239	7
27.0388	541	38	500	—	682			6
27.0387	351	3182	3788	538	22059			6
1188.38	87	15	3968	31	288			6
1188.13	—	0.76	58	—	142			5
27.0408	51	47	7813	69	—			4
35.0171	—	—	—	—	—	357		1
35.0172	—	11061	—	—	—	857		1
A dash (—) indicates IC50 > 20 μM.

TABLE XXXII
PBMC responses of individuals from the Irian Java
endemic malaria region.

Percent individuals yielding positive responses (n)

Peptide	IFNγ	TNFα	Proliferation
CSP.2	11% (7)	59% (39)	9% (11)
LSA1.13	16% (9)	30% (21)	8% (10)
CSP.53	7% (4)	53% (40)	3% (4)
SSP2.61	7% (4)	45% (36)	7% (9)
SSP2.223	15% (9)	42% (31)	5% (6)
CSP.410	16% (9)	47% (33)	12% (14)
EXP1.82	29% (17)	43% (32)	6% (7)
EXP1.71	9% (5)	49% (36)	12% (14)
SSP2.512	14% (8)	41% (30)	3% (4)
SSP2.62	11% (6)	42% (31)	12% (14)
SSP2.494	7% (4)	36% (26)	2% (3)

TABLE XXXIII
P. falciparum CTL epitopes

Supertype				SEQ ID		Alleles
(or allele)	Peptide	AA	Sequence	NO:	Source	bounda

A2-	1167.08	9	GLIMVLSFL	3760	Pf CSP 425	4
supertype	1167.10	9	GLLGNVSTV	3761	Pf EXP1 83	3
	1167.12	9	VLAGLLGNV	3762	Pf EXP1 80	4
	1167.13	9	KILSVFFLA	3763	Pf EXP1 2	3
	1167.16	9	FMKAVCVEV	3764	Pf SSP2 230	5
	1167.18	10	ILSVSSFLFV	3765	Pf CSP 7	2
	1167.19	10	VLLGGVGLVL	3766	Pf EXP1 91	2
	1167.21	10	FLIFFDLFLV	3767	Pf SSP2 14	5
A3-	1167.24	9	ALFFIIFNK	3768	PF EXP1 10	3
supertype	1167.28	9	GVSENIFLK	3769	Pf LSA1 105	3
	1167.32	9	QTNFKSLLR	3770	Pf LSA1 94	4
	1167.36	9	LACAGLAYK	3771	Pf SSP2 511	4
	1167.43	10	VTCGNGIQVR	3772	Pf CSP 375	4
	1167.46	10	FILVNLLIFH	3773	Pf LSA1 11	2
	1167.47	10	HVLSHNSYEK	3774	Pf LSA1 59	3
	1167.51	10	LLACAGLAYK	3775	Pf SSP2 510	3
B7-	19.0051	8	LPYGRTNL	3776	Pf SSP2 126	3
supertype	1167.61	10	TPYAGEPAPF	3777	Pf SSP2 539	4
A1	15.0184	9	LPSENERGY	3778	Pf LSA1 1663	1
	16.0040	9	FVEALFQEY	3779	Pf CSP 15	1
	16.0130	9	PSDGKCNLY	3780	Pf SSP2 207	1
	16.0245	10	FQDEENIGIY	3781	Pf LSA1 1794	1
A24	1167.53	9	KYKLATSVL	3782	Pf EXP1 73	1
	1167.54	9	FYFILVNLL	3783	Pf LSA1 9	1
	1167.55	9	YYIPHQSSL	3784	Pf LSA1 1671	1
	1167.56	9	KYLVIVFLI	3785	Pf SSP2 8	1
aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding to A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101 and A*2402, respectively.

TABLE XXXIV
P. falciparum HTL epitopes

			SEQ ID		Alleles
Motif	Peptide	Sequence	NO:	Source	bounda
DR-	F125.04	RHNWVNHAVPLAMKLI	3786	Pf SSP2 61	11
supermotif	1188.16	KSKYKLATSVLAGLL	3787	Pf EXP1 71	9
	27.0402	LLIFHINGKIIKNSE	3788	Pf LSA1 16	9(DR3)
	1188.32	GLAYKFVVPGAATPY	3789	Pf SSP2 512	9
	27.0392	SSVFNVVNSSIGLIM	3790	Pf CSP 410	7
	27.0417	VKNVIGPFMKAVCVE	3791	Pf SSP2 223	7
	27.0388	MRKLAILSVSSFLFV	3792	Pf CSP 2	6
	27.0387	MNYYGKQENWYSLKK	3793	PF CSP53	6
	1188.38	KYKIAGGIAGGLALL	3794	Pf SSP2 494	6
	1188.13	AGLLGNVSTVLLGGV	3795	Pf EXP1 82	5
	27.0408	QTNFKSLLRNLGVSE	3796	Pf LSA1 94	4
DR3	35.0171	PDSIQDSLKESRKLN	3797	Pf SSP2 165	DR3
	35.0172	KCNLYADSAWENVKN	3798	Pf SSP2 211	DR3
aHLA-DR supermotif peptides are screened for binding to a panel alleles representing the 10 most common HLA antigens, including DR1, DR2w2 β1, DR2w2 β2, DR4w4, DR4w15, DR5w11, DR6w19, DR7, DR8w2, and DR9. Additional alleles that are tested include DR3, DR5w12, DR52a, and DR53. DR3-motif peptides are tested for binding to DR3.

TABLE XXXV
Estimated population coverage by a panel of P. falciparum derived HTL epitopes

Representative

No. of

Population coverage (phenotypic frequency)

Antigen	Alleles	assay	epitopes2	Cauc.	Blk.	Jpn.	Chn.	Hisp.	Avg.

DR1	DRB1*0101-03	DR1	11	18.5	8.4	10.7	4.5	10.1	10.4
DR2	DRB1*1501-03	DR2w2 β1	6	19.9	14.8	30.9	22.0	15.0	20.5
DR2	DRB5*0101	DR2w2 β2	7	—	—	—	—	—	—
DR3	DRB1*0301-2	DR3	3	17.7	19.5	0.40	7.3	14.4	11.9
DR4	DRB1*0401-12	DR4w4	5	23.6	6.1	40.4	21.9	29.8	24.4
DR4	DRB1*0401-12	DR4w15	3	—	—	—	—	—	—
DR7	DRB1*0701-02	DR7	8	26.2	11.1	1.0	15.0	16.6	14.0
DR8	DRB1*0801-5	DR8w2	8	5.5	10.9	25.0	10.7	23.3	15.1
DR9	DRB1*09011, 09012	DR9	9	3.6	4.7	24.5	19.9	6.7	11.9
DR11	DRB1*1101-05	DR5w11	9	17.0	18.0	4.9	19.4	18.1	15.5
DR12	DRB1*1201-2	DR5w12	2	2.8	5.5	13.1	17.6	5.7	8.9
DR13	DRB1*1301-06	DR6w19	10	21.7	16.5	14.6	12.2	10.5	15.1
Total				97.0	83.9	98.8	95.5	95.6	94.7