MHC-binding Motifs Research Articles

DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction.

Computationally predicting major histocompatibility complex class I (MHC-I) peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep learning-based methods for this problem cannot achieve satisfactory performance, especially for non-9-mer peptides. This is because such methods generate the input by simply concatenating the two given sequences: a peptide and (the pseudo sequence of) an MHC class I molecule, which cannot precisely capture the anchor positions of the MHC binding motif for the peptides with variable lengths. We thus developed an anchor position-aware and high-performance deep model, DeepMHCI, with a position-wise gated layer and a residual binding interaction convolution layer. This allows the model to control the information flow in peptides to be aware of anchor positions and model the interactions between peptides and the MHC pseudo (binding) sequence directly with multiple convolutional kernels. The performance of DeepMHCI has been thoroughly validated by extensive experiments on four benchmark datasets under various settings, such as 5-fold cross-validation, validation with the independent testing set, external HPV vaccine identification, and external CD8+ epitope identification. Experimental results with visualization of binding motifs demonstrate that DeepMHCI outperformed all competing methods, especially on non-9-mer peptides binding prediction. DeepMHCI is publicly available at https://github.com/ZhuLab-Fudan/DeepMHCI.

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding.

T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by major histocompatibility complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here, we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high-throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. While the peptide datasets show broad agreement with previously described MHC-binding motifs, they additionally reveal experimentally validated computational false positives and false negatives. We therefore present this approach as able to complement current experimental datasets and computational predictions. Further, our yeast display approach underlines design considerations for epitope identification experiments and serves as a framework for examining relationships between viral conservation and MHC binding, which can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of our approach to determine peptide-MHC binding interactions in a manner that can supplement and potentially enhance current algorithm-based approaches.

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

The set of peptides presented on a cell's surface by MHC molecules is known as the immunopeptidome. Current mass spectrometry technologies allow for identification of large peptidomes, and studies have proven these data to be a rich source of information for learning the rules of MHC-mediated antigen presentation. Immunopeptidomes are usually poly-specific, containing multiple sequence motifs matching the MHC molecules expressed in the system under investigation. Motif deconvolution -the process of associating each ligand to its presenting MHC molecule(s)- is therefore a critical and challenging step in the analysis of MS-eluted MHC ligand data. Here, we describe NNAlign_MA, a computational method designed to address this challenge and fully benefit from large, poly-specific data sets of MS-eluted ligands. NNAlign_MA simultaneously performs the tasks of (1) clustering peptides into individual specificities; (2) automatic annotation of each cluster to an MHC molecule; and (3) training of a prediction model covering all MHCs present in the training set. NNAlign_MA was benchmarked on large and diverse data sets, covering class I and class II data. In all cases, the method was demonstrated to outperform state-of-the-art methods, effectively expanding the coverage of alleles for which accurate predictions can be made, resulting in improved identification of both eluted ligands and T-cell epitopes. Given its high flexibility and ease of use, we expect NNAlign_MA to serve as an effective tool to increase our understanding of the rules of MHC antigen presentation and guide the development of novel T-cell-based therapeutics.

Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.

MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or less flat in the MHC groove, with a fixed distance of nine amino acids between the first and last residue in contact with the MHCII. While confirming that the great majority of peptides bind to the MHC using this canonical mode, we report evidence for an alternative, less common mode of interaction. A fraction of observed ligands were shown to have an unconventional spacing of the anchor residues that directly interact with the MHC, which could only be accommodated to the canonical MHC motif either by imposing a more stretched out peptide backbone (an 8mer core) or by the peptide bulging out of the MHC groove (a 10mer core). We estimated that on average 2% of peptides bind with a core deletion, and 0·45% with a core insertion, but the frequency of such non-canonical cores was as high as 10% for certain MHCII molecules. A mutational analysis and experimental validation of a number of these anomalous ligands demonstrated that they could only fit to their MHC binding motif with a non-canonical binding core of length different from nine. This previously undescribed mode of peptide binding to MHCII molecules gives a more complete picture of peptide presentation by MHCII and allows us to model more accurately this event.

T cell recognition of naturally presented epitopes of self-heat shock protein 70

Self-reactive T cells have shown to have a potential role as regulators of the immune system preventing or even suppressing autoimmunity. One of the most abundant proteins that can be eluted from human HLA molecules is heat shock protein 70 (HSP70). The aims of the current study are to identify HSP70 epitopes based on published HLA elution studies and to investigate whether T cells from healthy individuals may respond to such self-epitopes. A literature search and subsequent in silico binding prediction based on theoretical MHC binding motifs resulted in the identification of seven HSP70 epitopes. PBMCs of healthy controls proliferated after incubation with two of the seven peptides (H167 and H290). Furthermore H161, H290, and H443 induced CD69 expression or production of cytokines IFNγ or TNFα in healthy controls. The identification of these naturally presented epitopes and the response they elicit in the normal immune system make them potential candidates to study during inflammatory conditions as well as in autoimmune diseases.

Proteome wide mapping of Dengue Virus-specific T cell responses in human donors reveals antigenic hot spots and a dominance of HLA B restricted responses (105.52)

Abstract The frequency of dengue virus (DENV) infection has increased dramatically in the recent decades and the lack of a vaccine has led to significant worldwide morbidity and mortality. To improve on the minimal information available regarding HLA-restricted T cell responses resulting from natural infection with DENV, we endeavored to map T cell responses in individuals with resolved DENV infection. To cover a wide range of HLA phenotypes we first performed bioinformatics predictions of MHC binding motifs of all four DENV serotypes to 16 HLA A and 11 HLA B alleles. To validate this approach, we have tested the predicted motifs in an ex vivo ELISPOT assay for their ability to induce an IFNγ response in HLA-matched PBMC of 250 blood donors from Sri Lanka where DENV is hyper-epidemic. This proteome-wide screen has identified a total of 408 epitopes across all 10 DENV proteins (C, M, E, NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Interestingly, the majority of responses were derived from the highly conserved nonstructural proteins: NS3, NS4B and NS5. Additionally, we have observed a striking dominance of HLA B restricted responses in terms of breath as well as magnitude of the DENV specific response detected. Our data provides specific insight and understanding into the nature of HLA-restricted T cell responses, the role of T cells in DENV infection, and future strategies in vaccine design against this globally intensifying viral threat.

A Novel HLA-A2–restricted CTL Epitope of Tumor-associated Antigen L6 can Inhibit Tumor Growth In Vivo

Vaccines utilizing cytotoxic T lymphocyte (CTL) epitopes are promising for the treatment of cancer and chronic infectious diseases. Tumor-associated antigen L6 (TAL6) is overexpressed in some epithelial cancer cells. In this report, we detected TAL6 expression in breast cancer tissue using quantitative reverse-transcriptase-polymerase chain reaction. We found that >80% of breast tumor tissue highly expressed TAL6 compared with adjacent normal breast tissue. To identify CTL epitopes from TAL6, we synthesized 18 peptides for HLA-A2-binding assay based on the MHC-binding motif using 4 computer prediction programs. Positive binders identified by ELISA were immunized in HLA-A2 transgenic (A2 Tg) mice. Two peptides, peptide 2 and peptide 5, induced T-cell responses in A2 Tg mice. To confirm whether these peptides could be processed and presented to induce T-cell responses in vivo, A2 Tg mice were immunized with plasmid DNA encoding TAL6. We found that both peptides 2 and 5 stimulated splenocytes from TAL6-immunized mice to secrete interferon-γ. However, only peptide 5 could induce expression of the cytolytic molecule CD107a on CD8+ T cells after immunization. Furthermore, peptide 5-immunized A2 Tg mice could inhibit the growth of TAL6-positive tumors (EL4/TAL6/HLA-A2) in A2 Tg mice but not in wild-type mice. These results demonstrate that the TAL6-derived CTL epitope could induce HLA-A2-restricted immunity against TAL6-expressing tumor cells.

Efficacy of HLA-DRB1∗03:01 and H2E transgenic mouse strains to correlate pathogenic thyroglobulin epitopes for autoimmune thyroiditis

Thyroglobulin (Tg), a homodimer of 660 kD comprising 2748 amino acids, is the largest autoantigen known. The prevalence of autoimmune thyroid disease, including Hashimoto’s thyroiditis and Graves’ disease, has provided the impetus for identifying pathogenic T cell epitopes from human Tg over two decades. With no known dominant epitopes, the search has long been a challenge for investigators. After identifying HLA-DRB1∗03:01 (HLA-DR3) and H2E b as susceptibility alleles for Tg-induced experimental autoimmune thyroiditis in transgenic mouse strains, we searched for naturally processed T cell epitopes with MHC class II-binding motif anchors and tested the selected peptides for pathogenicity in these mice. The thyroiditogenicity of one peptide, hTg2079, was confirmed in DR3 transgenic mice and corroborated in clinical studies. In H2E b-expressing transgenic mice, we identified three T cell epitopes from mouse Tg, mTg179, mTg409 and mTg2342, based on homology to epitopes hTg179, hTg410 and hTg2344, respectively, which we and others have found stimulatory or pathogenic in both DR3- and H2E-expressing mice. The high homology among these peptides with shared presentation by DR3, H2E b and H2E k molecules led us to examine the binding pocket residues of these class II molecules. Their similar binding characteristics help explain the pathogenic capacity of these T cell epitopes. Our approach of using appropriate human and murine MHC class II transgenic mice, combined with the synthesis and testing of potential pathogenic Tg peptides predicted from computational models of MHC-binding motifs, should continue to provide insights into human autoimmune thyroid disease.

Development and preliminary clinical evaluation of a peptide immunotherapy vaccine for cat allergy

Allergic sensitization to cat allergens is common and represents a major risk factor for asthma. Specific immunotherapy (SIT) is effective but cumbersome and associated with IgE-dependent adverse events. Immunotherapy targeting allergen-specific T cells, with synthetic peptides representing T-cell epitopes, might improve safety and reduce the duration of treatment. We sought to define major T-cell epitopes of Fel d 1 for peptide immunotherapy, generate a peptide vaccine, and evaluate its safety and tolerability in subjects with cat allergy. We determined the binding affinities of Fel d 1 peptides for 10 commonly expressed HLA-DR molecules. Functionally immunodominant peptides were identified by means of proliferation and cytokine secretion. Histamine-releasing activity was assessed, and a peptide vaccine was formulated. Safety and tolerability were evaluated in a dose-ranging phase IIa clinical trial. MHC-binding sequences were identified throughout Fel d 1. Some regions contained multiple overlapping T-cell epitopes that bound multiple MHC molecules. Immunodominant sequences were identified on the basis of proliferative and cytokine (IFN-γ, IL-10, and IL-13) responses. Cat allergen extract, but not peptides, induced histamine release in blood basophils. A single administration of peptide vaccine was safe and well tolerated. The dose of vaccine resulting in the greatest inhibition of the late-phase skin response to intradermal whole allergen challenge was 3 nmol. Fel d 1 contains multiple overlapping MHC-binding motifs. A peptide vaccine comprising the immunodominant regions of the allergen was safe and well tolerated when given to subjects with cat allergy as a single dose. The dose of vaccine resulting in the greatest reduction in late-phase skin response was defined for future clinical development.

Real time detection of peptide–MHC dissociation reveals that improvement of primary MHC-binding residues can have a minimal, or no, effect on stability

The majority of known major histocompatibility complex class I (MHCI)-associated tumor-derived peptide antigens do not contain an optimal motif for MHCI binding. As a result, anchor residue-modified ‘heteroclitic’ peptides have been widely used in therapeutic cancer vaccination trials in order to enhance immune responsiveness. In general, the improved stability of these heteroclitic complexes has been inferred from their improved immunogenicity but has not been formally assessed. Here, we investigated the binding of 4 HLA A*0201-restricted tumor-derived peptides and their commonly used heteroclitic variants. We utilized a cell surface binding assay and a novel robust method for testing the durability of soluble recombinant pMHCI in real time by surface plasmon resonance. Surprisingly, we show that heteroclitic peptides designed with optimal MHC binding motifs do not always form pMHCs that are substantially more stable than their wildtype progenitors. These findings, combined with our recent discovery that TCRs can distinguish between wildtype peptides and those altered at a primary buried MHC anchor residue, suggest that altered TCR binding may account for a large part of the increased immune response that can be generated by anchor residue-modified ligands. Our results further highlight the fact that heteroclitic peptide-based immune interventions require careful evaluation to ensure that wildtype antigen specificity is maintained in vivo.

Epitope Identification and Generation of an Antigen-Specific T-Cell Clone in a Mild Hemophilia A Inhibitor Subject with Missense Genotype R593C.

The development of inhibitory anti-FVIII antibodies is a major clinical problem in hemophilia A. While less common in mild/moderately severe patients, the relative risk of inhibitor formation is elevated in patients with missense mutations in the FVIII A2 domain, especially those with an R593C genotype. In this study, T-cell responses to 14 FVIII A2 domain peptides with predicted DRB1*1101 MHC binding motifs were investigated using MHC class II tetramer reagents. CD4+ T cells were isolated from a hemophilic subject (DRB1*1101, 1302) with FVIII missense genotype R593C and stimulated with pooled peptides. This subject had developed a longstanding low titer inhibitor after receiving multiple FVIII infusions. Staining with fluorescent, peptide-loaded tetramers revealed that the hemophilic subject, but not an HLA-matched healthy control, had a DRB1*1101-restricted response to peptide A2589–608, which contained the wild-type R593 sequence. MHC class II tetramers with bound A2589–608 were used to sort antigen-specific T cells and then generate a T-cell clone recognizing this high avidity DRB1*1101-restricted epitope. FVIII residues 594–602 (FLPNPAGVQ) comprise a predicted high-affinity binding motif. Peptide binding assays confirmed that A2589–608 bound to recombinant, monomeric DRB1*1101 protein with high affinity. A peptide with the corresponding hemophilic sequence (A2589–608, 593C) bound with affinity that was threefold lower, but in a range that should be sufficient for presentation to T cells. The other 12 A2 peptides had a wide spectrum of binding affinities for the DRB1*1101 protein. Interestingly, prediction algorithms suggest that the peptides containing residue 593 occupy the MHC Class II peptide-binding groove in a register that places this residue just outside the p1 anchor position. Thus we anticipate that residue 593 modulates T-cell recognition of peptide A2589–608. This provides a potential explanation for inhibitor development in mild hemophilia A patients with a FVIII R593C genotype who are HLA-DRB1*1101. Immunogenicity of this FVIII region with respect to other HLA types is under investigation.

Defining Peptide Sequences: From Antigenicity to Immunogenicity Through Redundancy

The molecular biology era has allowed the exact definition of the disease-associated-proteins (DAPs). The computational era has analyzed full-length DAPs by antigenicity prediction algorythms based on physico-chemical parameters. Today, proteomics is providing a global comprehensive analysis of defined peptide portions of DAPs. The fine profiling of the disease-associated peptide repertoire is of particular importance in the definition of qualities as antigenicity and immunogenicity, and is a concrete promise of a bench-to-bedside translational research. Identifying the peptide sequences within the DAPs, which may potentially provoke (auto)immune responses, more than ever emerges as the key strategy for effective immunotherapeutical treatments in cancer diseases as well as infectious or autoimmune pathologies. Here I draw a schematic picture of the experimental attempts to define immunogenic peptide portions, describe the principle of sequence uniqueness as a rationale for the subproteomic analysis of DAPs and delineate the possible advantages of a peptide-vaccine approach to the treatment of degenerative, infectious and autoimmune diseases that might be effective and devoid of collateral harmful effects. Keywords: disease-associated proteins (DAPs), vaccine immunobiology, MHC binding motifs, autoimmune diseases, epitopes

Developing an epitope-driven tuberculosis (TB) vaccine

Epitope-driven vaccines are created from selected sub-sequences of proteins, or epitopes, derived by scanning the protein sequences of pathogens for patterns of amino acids that permit binding to human MHC molecules. We developed a prototype tuberculosis (TB) vaccine that contains epitopes derived by (1) EpiMer mapping of previously published secreted proteins derived from Mycobacterium tuberculosis (Mtb), and (2) EpiMatrix mapping of selected Mtb genome open reading frames (ORFs). Each of the epitopes contains at least three distinct class II MHC binding motif matches. These Mtb epitope selections were validated by measuring T cell responses from peripheral blood mononuclear cells (PBMC) obtained from healthy, asymptomatic tuberculin skin test-positive donors. Twenty-four validated Mtb epitopes were selected for inclusion in a DNA plasmid vector. We immunized HLA-DR B*0101 transgenic mice with this vaccine prototype augmented by co-administration of rIL-15. Following administration of three immunizations at 14-day intervals in conjunction with rIL-15, epitope-specific T cell responses were observed to eight of the 24 epitopes contained in the DNA construct, one week following the last injection. The systematic application of bioinformatics tools to whole genomes, in combination with in vitro methods for screening and confirming epitopes, may lead to the development of novel vaccines for infectious diseases like TB.

Analyzing Mycobacterium tuberculosis proteomes for candidate vaccine epitopes

Secreted antigens of Mycobacterium tuberculosis (Mtb) induce strong T cell responses and interferon-gamma (IFN-gamma) secretion, both of which are integral in the defense against Mtb. We used web-based tools (SignaIP and Prosite) to identify putative secreted proteins from Mtb genomes CDC 1551 and H37Rv. We then used EpiMatrix, a proprietary pattern-matching algorithm, to do a preliminary analysis of these proteins for regions that contained a high number of class II MHC binding motif matches. The use of bioinformatics tools reduced the number of potential epitopes to be screened to 5% of the 1.3 million overlapping peptides. Peripheral blood mononuclear cells (PBMC) were obtained from healthy, asymptomatic tuberculin skin test-positive donors. Of the 17 highest-ranking peptide candidates that could be synthesized for this preliminary in vitro evaluation, 15 (88%) stimulated IFN-gamma response, and eight (47%) stimulated lymphocyte proliferation in vitro. IFN-gamma ELISpot assays were therefore a more sensitive test for T cell response to these peptides than were proliferation assays. One highly promiscuous epitope (MT2281-26-J, WRRRPLSSALLSFGLLLGGLPL) induced IFN-gamma secretion in PBMC from 11 of 25 Mtb immune subjects (44%). Overall, 15 epitopes, and MT2281-26-J in particular, are candidates for inclusion in a multi-epitope TB vaccine. These findings support the systematic application of bioinformatics tools to whole genomes when used in combination with in vitro methods for screening and confirming epitopes.

Induction of arthritis in SCID mice by T cells specific for the "shared epitope" sequence in the G3 domain of human cartilage proteoglycan.

To study the immunologic function and determine the fine epitope structure of a synthetic peptide p135H ((2373)TTYKRRLQKRSSRHP) of the G3 domain of human cartilage proteoglycan (aggrecan), which contains a highly homologous sequence motif of the shared epitope (QKRAA), the most common sequence motif in HLA-DR4 alleles, which predispose humans to the development of rheumatoid arthritis (RA). Synthetic p135 peptides with altered sequences were used for (hyper)immunization of arthritis-susceptible BALB/c mice and then challenged with a single dose of cartilage proteoglycan. Human p135 (p135H) and mouse p135 (p135M) synthetic peptides of the G3 domain of aggrecan were used to prime lymphocytes, which were then used for adoptive transfer of arthritis into "presensitized" SCID mice, determining cross-reactivity among p135 peptides and their analogous sequences, and generating T cell hybridomas. T cell hybridomas were also used for arthritis transfer into SCID mice and for characterizing the fine epitope structure of T cell receptor (TCR) and major histo-compatibility complex (MHC) binding sites of the immunogenic/arthritogenic p135H sequence. While p135H peptide-(hyper)immunized mice became sensitized, they developed arthritis only after injection of a single dose of cartilage proteoglycan aggrecan. An altered peptide sequence (p135H-AA) carrying the shared epitope motif (QKRAA) was as effective as the natural peptide p135H sequence for inducing arthritis. Mouse p135M-specific lymphocytes induced arthritis with a lower incidence, but synthetic peptides to Escherichia coli heat-shock protein (DnaJ) or HLA-DR4 allele (both having the shared epitope sequence with different flanking regions) were also positive. Fine epitope sequence recognition of an arthritogenic T cell hybridoma derived from p135H-primed lymphocyte population was determined. Interestingly, in the most central position, a basic amino acid triplet of p135H peptide was found to be the MHC-binding motif, whereas the flanking amino acids bound to the TCR. Peptide p135H, corresponding to the peptide sequence in the G3 domain of human cartilage proteoglycan aggrecan, is immunogenic/arthritogenic in BALB/c mice. Peptide p135H includes a highly homologous motif of the shared epitope, a sequence that is overrepresented in bacterial heat-shock proteins, envelope protein of human JC polyomavirus, and numerous HLA-DR4 alleles. Since the G3 domain of cartilage proteoglycan aggrecan with the p135 sequence is "lost" during the normal metabolic turnover of cartilage proteoglycan or in pathologic conditions, an antigenoriented T cell migration into joints of presensitized (susceptible) individuals may contribute to the organ-specificity of RA.

Differential recognition of a retinal autoantigen peptide and its variants by rat T cells in vitro and in vivo.

Previously we have described the role of two 14mer peptides in autoimmune uveitis, PDSAg from the retinal autoantigen S-antigen (S-Ag) and B27PD from the sequence of disease-associated HLA-B molecules, which show antigenic mimicry. The retinal peptide gave rise to severe uveitis in the Lewis rat model of experimental autoimmune uveitis (EAU) and was effective in inducing oral tolerance, while the HLA peptide B27PD caused only mild disease, but it was at least equally effective in preventing uveitis by oral tolerance. Here, we further defined the major T cell epitopes on both peptides responsible for the different functions. For this purpose we tested C- and N-terminal truncations, and chimeras consisting of amino acid sequences of both peptides in vitro and in vivo. We were able to determine the motif for binding to Lewis rat MHC class II as well as those amino acids important for recognition by T cells specific for the retinal peptide. The minimal MHC-binding nonamer peptide of PDSAg was not recognized by TCR, and we also found striking differences of T cell recognition in vitro and in vivo. The ability to induce oral tolerance was not closely correlated with uveitogenicity or with strong binding to MHC class II molecules. Our data furthermore demonstrate the importance of specific and exact trimming of peptides to be presented on MHC class II, suggesting that the presentation of cryptic epitopes is favored or prevented by existence of multiple MHC-binding motifs within a certain amino acid sequence, which can result in different or altered T cell reactions.

Molecular Mimicry and Antigen-Specific T Cell Responses in Multiple Sclerosis and Chronic CNS Lyme Disease

The concept of molecular mimicry provides and elegant framework as to how cross-reactivity between antigens from a foreign agent with self proteins may trigger autoimmune diseases. While it was previously thought that sequence and structural homology between foreign and self proteins or the sharing of T cell receptor (TCR) and MHC-binding motifs are required for molecular mimicry to occur, we have shown that even completely unrelated peptide sequences may lead to cross-recognition by T cells. The use of synthetic combinatorial peptide libraries in the positional scanning format (PS-SCL) together with novel biometric prediction approaches has allowed us to describe the recognition profiles of individual autoreactive T cell clones (TCC) with unprecedented accuracy. Through studies of myelin-specific TCC as well as clones from the nervous system of patients suffering from chronic central nervous (CNS) Lyme disease it has become clear that at least some T cells are more degenerate than previously anticipated. These data will not only help us to redefine what constitutes specific T cell recognition, but also allow us to study in more detail the biological role of molecular mimicry. A recent clinical trial with an altered peptide ligand (APL) of one of the candidate myelin basic protein (MBP) epitopes in MS (amino acids 83–99) has shown that such a modified MBP peptide may not only have therapeutic efficacy, but also bears the potential to exacerbate disease. Thus, we provide firm evidence that the basic principles of cross-recognition and their pathogenetic significance are relevant in MS.

The role of mass spectrometry in vaccine development

For the most part, vaccine development to date has been empiric. While sometimes successful, such a strategy is ‘hit or miss’, and fails to advance the basic science of vaccine development. Preferable would be tools that allow for a more directed development of vaccines at either the population or sub-population level. Characteristics of useful tools in vaccine development should include the ability to identify and characterize the spectrum of antigenic peptides presented by MHC molecules to which the immune system responds by the development of protective immune responses. In addition, because the explosion in human genomics allows the ability to understand MHC haplotypes at the population level, as well as an enhanced understanding of MHC binding motifs, new tools might further allow for an understanding of which vaccine antigens are capable of being bound and presented to the immune system by MHC molecules. New mass spectrometry technology fulfils these criteria, and may well lead to a revolution in the design of new vaccines. This paper will review the basics of mass spectrometry techniques as applied to the identification and characterization of vaccine peptide antigens, and discusses how these tools can be applied to vaccine development.

Peptide Binding Motifs for MHC Class I and II Molecules

This overview discusses the use of peptide-binding motifs to predict interaction with a specific MHC class I or II allele, and gives examples for the use of MHC binding motifs to predict T-cell recognition.

The MHC Class I-Restricted Immune Response to HIV-gag in BALB/c Mice Selects a Single Epitope That Does Not Have a Predictable MHC-Binding Motif and Binds to Kd Through Interactions Between a Glutamine at P3 and Pocket D

Using a strain of Listeria monocytogenes that stably expresses and secretes HIV gag to deliver this Ag to the MHC class I pathway of Ag processing, we have identified the immunodominant CTL epitope to gag in the BALB/c mouse and shown that it is Kd restricted. The specific motif for the peptides that bind the MHC class I molecule H-2 Kd is believed to be a nonamer with residues tyrosine or phenylalanine in the second amino acid position and leucine or isoleucine in the carboxyl-terminal or ninth amino acid position as dominant anchoring positions. Surprisingly, the identified gag peptide, AMQMLKETI, does not contain an anchoring aromatic residue in position two although competition assays with other Kd-restricted epitopes indicated that it binds to Kd with comparable affinity. Using a theoretical molecular dynamics approach to probe the stability of peptide binding to MHC class I molecules, we show that the absence of an appropriate anchor residue at P2 in AMQMLKETI is compensated by favorable interactions of the glutamine at P3 with pocket D of Kd. These findings were verified experimentally, demonstrating the predictive power of this theoretical approach in analyzing MHC class I/peptide interactions. These studies also indicate that CTL epitope prediction that relies on dominant peptide motifs may not always identify the correct epitope.