Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.03.29.533758v1?rss=1
Authors: Shcherbinin, D. S., Karnaukhov, V. K., Zvyagin, I. V., Chudakov, D. M., Shugay, M.
Abstract:
T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. A large number of TCR sequences specific to different antigens are known to date, however, the structural data describing the conformation and contacting residues for TCR:antigen:MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of TCR:antigen:MHC complexes using TCR sequences with known specificity. Using the set of 29 complex templates and 732 specificity records, we built a database of 1517 model structures. This database allowed us to analyze features of amino acid contacts in TCR:antigen interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues. Our results provide a methodology for building high-quality TCR:antigen:MHC models for certain antigens that can be utilized to assay TCR specificity.
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