Wave function analysis of MHC–peptide interactions

Constanza Cárdenas, Mateo Obregón, Alejandro Balbín, José Luis Villaveces, Manuel E. Patarroyo

Research output: Contribution to journalArticlepeer-review

Abstract

We have carried out an analysis of the wave function data for three MHC–peptide complexes: HLA-DRβ1*0101-HA, HLA-DRβ1*0401-HA and HLA-DRβ1*0401-Col. We used quantum chemistry computer programs to generate wave function coefficients for these complexes, from which we obtained both molecular and atomic orbital data for both pocket and peptide amino acids within each pocket region. From these discriminated data, interaction molecular orbitals (IMOs) were identified as those with large and similar atomic orbital coefficient contributions from both pocket and peptide amino acids. The present results correlate well with our previous research where only electrostatic moments were used to explore molecular component interactions. Furthermore, we show a quantum chemical methodology to produce more fine-grained results concerning amino acid behavior in the MHC–peptide interaction.
Original languageEnglish
Pages (from-to)605 - 615
Number of pages11
JournalJournal of Molecular Graphics and Modelling
Volume25
Issue number5
Early online date28 Apr 2006
DOIs
Publication statusPublished - Jan 2007

Keywords

  • Molecular interactions
  • Molecular orbital coefficients
  • MHC pockets
  • Theoretical study of MHC

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