Coupling in silico and in vitro analysis of peptide-MHC binding:a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes

The ability to define and manipulate the interaction of peptides with MHC molecules has immense immunological utility, with applications in epitope identification, vaccine design, and immunomodulation. However, the methods currently available for prediction of peptide-MHC binding are far from ideal. We recently described the application of a bioinformatic prediction method based on quantitative structure-affinity relationship methods to peptide-MHC binding. In this study we demonstrate the predictivity and utility of this approach. We determined the binding affinities of a set of 90 nonamer peptides for the MHC class I allele HLA-A*0201 using an in-house, FACS-based, MHC stabilization assay, and from these data we derived an additive quantitative structure-affinity relationship model for peptide interaction with the HLA-A*0201 molecule. Using this model we then designed a series of high affinity HLA-A2-binding peptides. Experimental analysis revealed that all these peptides showed high binding affinities to the HLA-A*0201 molecule, significantly higher than the highest previously recorded. In addition, by the use of systematic substitution at principal anchor positions 2 and 9, we showed that high binding peptides are tolerant to a wide range of nonpreferred amino acids. Our results support a model in which the affinity of peptide binding to MHC is determined by the interactions of amino acids at multiple positions with the MHC molecule and may be enhanced by enthalpic cooperativity between these component interactions.

Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection

Virus-specific CD8+ T cells are known to play an important role in the control of HIV infection. In this study we investigated whether there may be qualitative differences in the CD8+ T cell response in HIV-1- and HIV-2-infected individuals that contribute to the relatively efficient control of the latter infection. A molecular comparison of global TCR heterogeneity showed a more oligoclonal pattern of CD8 cells in HIV-1- than HIV-2-infected patients. This was reflected in restricted and conserved TCR usage by CD8+ T cells recognizing individual HLA-A2- and HLA-B57-restricted viral epitopes in HIV-1, with limited plasticity in their response to amino acid substitutions within these epitopes. The more diverse TCR usage observed for HIV-2-specific CD8 T cells was associated with an enhanced potential for CD8+ expansion and IFN- production on cross-recognition of variant epitopes. Our data suggest a mechanism that could account for any possible cross-protection that may be mediated by HIV-2-specific CD8+ T cells against HIV-1 infection. Furthermore, they have implications for HIV vaccine development, demonstrating an association between a polyclonal, virus-specific CD8+ T cell response and an enhanced capacity to tolerate substitutions within T cell epitopes.

Designing immunogenic peptides

Peptides fulfill many roles in immunology, yet none are more important than their role as immunogenic epitopes driving the adaptive immune response, our ultimate bulwark against infectious disease. Peptide epitopes are mediated primarily by their interaction with major histocompatibility complexes (T-cell epitopes) and antibodies (B-cell epitopes). As pathogen genomes continue to be revealed, both experimental and computational epitope mapping are becoming crucial tools in vaccine discovery1,2. Immunoinformatics offers many tools, techniques and approaches for in silico epitope characterization, which is capable of greatly accelerating epitope design. © 2013 Nature America, Inc. All rights reserved.

Lymphocyte peroxiredoxin-2 levels are depleted one week after ultra-endurance exercise

Peroxiredoxin-2 (PRDX-2) belongs to a family of thiol containing proteins and is important for antioxidant defense, redox signaling and cell function. This study examined whether lymphocyte PRDX-2 levels are altered over one month following ultra-endurance exercise. Nine middle-aged men participated in a 145 mile ultra-endurance running race event. Blood drawing was undertaken immediately before, upon completion/retirement, and at one, seven and twenty eight-days following the race. PRDX-2 levels were examined at each time-point, for all participants (n=9) by reducing SDS-PAGE and western blotting. Further analysis using non-reducing SDS-PAGE and western blotting was undertaken in a sub-group of men who completed the race (n = 4) to investigate PRDX-2 oligomeric state (indicative of oxidation state). Ultra-endurance exercise caused a significant alteration in lymphocyte PRDX-2 levels (F(4,32) 3.409, p=0.020, η2 =0.299): seven-days after the race PRDX-2 levels fell by 70% (p=0.013) and at twenty eight-days after the race returned to near-normal levels. PRDX-2 dimers (intracellular reduced PRDX-2 monomers) in three of the four participants, who finished the race, were increased upon race completion. Furthermore, PRDX-2 monomers (intracellular over-oxidized PRDX-2 monomers) in two of these four participants were present upon race completion, but absent seven-days after the race. This study found that PRDX-2 levels in lymphocytes were reduced below normal levels seven-days after an ultra-endurance running race. We suggest that excessive reactive oxygen species production, induced by ultra-endurance exercise may, in part, explain the depletion of lymphocyte PRDX-2 by triggering its turnover after oxidation.

EPIPOX:immunoinformatic characterization of the shared T-cell epitome between variola virus and related pathogenic orthopoxviruses

Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes.

Investigating the ability of antibodies to recognize specific oxidized protein epitopes

There is a growing awareness that inflammatory diseases have an oxidative pathology, which can result in specific oxidation of amino acids within proteins. Antibody-based techniques for detecting oxidative posttranslational modifications (oxPTMs) are often used to identify the level of protein oxidation. There are many commercially available antibodies but some uncertainty to the potential level of cross reactivity they exhibit; moreover little information regarding the specific target epitopes is available. The aim of this work was to investigate the potential of antibodies to distinguish between select peptides with and without oxPTMs. Two peptides, one containing chlorotyrosine (DY-Cl-EDQQKQLC) and the other an unmodified tyrosine (DYEDQQKQLC) were synthesized and complementary anti-sera were produced in sheep using standard procedures. The anti-sera were tested using a half-sandwich ELISA and the anti-serum raised against the chloro-tyrosine containing peptide showed increased binding to the chlorinated peptide, whereas the control anti-serum bound similarly to both peptides. This suggested that antibodies can discriminate between similar peptide sequences with and without an oxidative modification. A peptide (STSYGTGC) and its variants with chlorotyrosine or nitrotyrosine were produced. The anti-sera showed substantially less binding to these alternative peptides than to the original peptides the anti-sera were produced against. Work is ongoing to test commercially available antibodies against the synthetic peptides as a comparison to the anti-sera produced in sheep. In conclusion, the antisera were able to distinguish between oxidatively modified and unmodified peptides, and two different sequences around the modification site.