Publish with Bio Med Central and every scientist can read your work free of charge  Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire BACKGROUND: Cytotoxic T cell (CTL) cross-reactivity is believed to play a pivotal role in generating immune responses but the extent and mechanisms of CTL cross-reactivity remain largely unknown. Several studies suggest that CTL clones can recognize highly diverse peptides, some sharing no obvious sequence identity. The emerging realization in the field is that T cell receptors (TcR) recognize multiple distinct ligands. PRINCIPAL FINDINGS: First, we analyzed peptide scans of the HIV epitope SLFNTVATL (SFL9) and found that TCR specificity is position dependent and that biochemically similar amino acid substitutions do not drastically affect recognition. Inspired by this, we developed a general model of TCR peptide recognition using amino acid similarity matrices and found that such a model was able to predict the cross-reactivity of a diverse set of CTL epitopes. With this model, we were able to demonstrate that seemingly distinct T cell epitopes, i.e., ones with low sequence identity, are in fact more biochemically similar than expected. Additionally, an analysis of HIV immunogenicity data with our model showed that CTLs have the tendency to respond mostly to peptides that do not resemble self-antigens. CONCLUSIONS: T cell cross-reactivity can thus, to an extent greater than earlier appreciated, be explained by amino acid similarity. The results presented in this paper will help resolving some of the long-lasting discussions in the field of T cell cross-reactivity. Each T cell expresses thousands of T cell receptors (TCR) of a single specificity that allows inspection of peptide fragments bound by major histocompatibility complex molecules (MHC) on the surface of other cells. Peptides originate as the product of intracellular protein turnover, and both foreign and self-peptides are able to form peptide:MHC complexes (pMHC). Presentation of peptides for which the inspecting CTLs have not been tolerized, triggers a cytotoxic response. Although much has been learned about peptide processing and MHC presentation [1, 2] it is still largely unknown why roughly half of all natural foreign pMHC are ignored [3, 4] . The processing and MHC binding of naturally processed foreign peptides is a primary requirement for the initiation of a cellular immune response. However, the availability of a suitable TCR further determines if a peptide is immunogenic. The structural mechanism of T cell recognition is a highly debated subject in the immunological literature and a consensus view of the promiscuous peptide recognition has not yet been reached (see e.g., [5] ). The core problem is that T cells seem to combine high specificity with the ability to recognize a surprisingly large number of dissimilar antigens. Two terms are often used to describe this nature of T cell recognition. Poly-specificity is used to emphasize TCR's ability to recognize multiple distinct/unrelated pMHC ligands with high specificity (with little or no tolerance to substitutions of the ligands) [6, 7] . Cross-reactivity is a term that was originally used to indicate unexpected reactivity to targets that differed from those used to initially define the T cell clone [8] . Several studies suggest that T cells can recognize seemingly dissimilar epitopes (for a summary see [6] ), while other studies have established that substitutions affect peptide recognition in a predictable and additive manner [9] suggesting that the majority of cross-reactive pMHC complexes share structural similarities. One outstanding question in T cell biology is therefore whether T cell cross-reactivity is mostly a stochastic phenomenon induced by unpredictable structural constraints or, whether we can predict which peptides should be cross-reactive. Previous studies of crossreactivity have focused on limited data covering a single or a few T cell clones. Here, we investigate a simple model of T cell crossreactivity and perform a large-scale analysis spanning both a broad set of experimental settings, heterogeneous pathogens, MHC molecules and T cell clones. We use this benchmark to investigate whether cross-reactivity is either generally predictable or mostly random. Finally, we test whether the degree of host mimicry is negatively correlated with immunogenicity. By analyzing a large set of known HLA-A2 restricted HIV epitopes, we investigate if potential HIV epitopes with high similarity to self are able to trigger detectable immune responses. Our results suggest that amino acid similarity, rather than identity, is a predictive measure of cross-reactivity.