Semi-empirical quantum evaluation of peptide – MHC class II binding

Ronald González, Carlos F. Suárez, Hugo J. Bohórquez, Manuel A. Patarroyo, Manuel E. Patarroyo

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions.

Original languageEnglish (US)
Pages (from-to)29-34
Number of pages6
JournalChemical Physics Letters
Volume668
DOIs
StatePublished - Jan 16 2017

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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