We also developed a bioinformatics method to predict pMHC-I stability, which suggested that 30% of the nonimmunogenic binders hitherto classified as “holes in the T-cell repertoire” can be explained as being unstably

bound to MHC-I. Finally, we suggest that nonoptimal anchor residues in position 2 of the peptide are particularly prone to cause unstable interactions BGB324 mouse with MHC-I. We conclude that the availability of accurate predictors of pMHC-I stability might be helpful in the elucidation of MHC-I restricted antigen presentation, and might be instrumental in future search strategies for MHC-I epitopes. Major histocompatibility complex class I (MHC-I) plays a pivotal role in the generation of specific immune responses mediated

by cytotoxic T lymphocytes (CTLs). MHC-I molecules sample peptides derived from intracellular proteins, translocate them to the cell surface, and display them to CTLs, allowing immune scrutiny of the ongoing intracellular metabolism leading to the detection of the presence of any intracellular pathogens. To fulfill this crucial antigen presenting function, MHC-I molecules must be endowed with the ability to retain bound peptides at the cell surface while waiting for the arrival of rare circulating CTL clones of the appropriate specificity. Sustained presentation at the cell surface and induction of specific immune T-cell responses therefore requires

some LY294002 mouse degree of pMHC-I stability. Indeed, it has been claimed that stability, rather than affinity, of pMHC-I complexes is the better correlate of immunogenicity and immunodominance [[1-5]]. Experimentally, however, affinity remains the most frequently DNA ligase established correlate of immunogenicity. Thus, when Assarsson et al. [[6]] recently conducted a quantitative analysis of the variables affecting the repertoire of T-cell specificities recognized after vaccinia virus infection, they found that the vast majority of epitopes (85%) bound their restricting allele with an affinity of 500 nM or better, and most (75%) bound with an affinity of 100 nM or better. Investigating the stability of pMHC-I complexes for a small sample of immunogenic and nonimmunogenic peptides, they found a suggestive, but not statistically significant, trend for off-rates and immunodominance being correlated. The authors concluded that “in our hands, peptide stability did not correlate significantly better with immunodominance than did equilibrium binding measurements”. One reason why pMHC stability has not been addressed more extensively undoubtedly relates to the cumbersome and/or low-throughput nature of current biochemical methods used to measure the dissociation of pMHC complexes [[6-12]]. A particularly interesting dissociation assay developed by Parker et al.