An immunological glimpse of human virus peptides: distance from self, MHC class I binding, Proteasome Cleveage, TAP Transport and sequence composition entropy

Virus Res. 2022 May 16:198814. doi: 10.1016/j.virusres.2022.198814. Online ahead of print.ABSTRACTAdaptive immune response is triggered when specific pathogen peptides called epitopes are recognised as exogenous according to the paradigm of self/non-self. To be recognized by immune cells, epitopes have to be exposed (presented) on the surface of the cell. Predicting if a peptide is exposed is important to shed light on the rules that govern immune response, and thus to identify potential targets, and to design vaccine and drugs. We focused on peptides exposed on cell surface and made accessible to immune system through the MHC Class I complex. Before this can happen, three successive selection steps have to take place: a) Proteasome cleveage, b) TAP Transport, and c) binding to MHC-class I. Starting from a set of 211 host human reference viruses, we computed the set of unique peptides occurring in the correspondent proteomes. Then, we obtained the probability values of Proteasome Cleveage, TAP Transport and Binding to MHC Class I associated to those peptides through established prediction software tools. Such values were analysed in conjunction with two other features that could play a major role: the distance from self, strictly linked to the concept of nullomers, and the sequence entropy, measuring the complexity of the peptide amino acid composition. The analysis confirmed and extended previous results on a larger, more significant and consistent data set; we showed that t...
Source: Virus Research - Category: Virology Authors: Source Type: research