Towards the MHC-peptide combinatorics

Pandjassarame Kangueane, Meena K. Sakharkar, Prasanna R. Kolatkar, Ee Chee Ren

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

The exponentially increased sequence information on major histocompatibility complex (MHC) alleles points to the existence of a high degree of polymorphism within them. To understand the functional consequences of MHC alleles, 36 nonredundant MHC-peptide complexes in the protein data bank (PDB) were examined. Induced fit molecular recognition patterns such as those in MHC-peptide complexes are governed by numerous rules. The 36 complexes were clustered into 19 subgroups based on allele specificity and peptide length. The subgroups were further analyzed for identifying common features in MHC-peptide binding pattern. The four major observations made during the investigation were: (1) the positional preference of peptide residues defined by percentage burial upon complex formation is shown for all the 19 subgroups and the burial profiles within entries in a given subgroup are found to be similar; (2) in class I specific 8- and 9-mer peptides, the fourth residue is consistently solvent exposed, however this observation is not consistent in class I specific 10-mer peptides; (3) an anchor-shift in positional preference is observed towards the C terminal as the peptide length increases in class II specific peptides; and (4) peptide backbone atoms are proportionately dominant at the MHC-peptide interface.

Original languageEnglish
Pages (from-to)539-556
Number of pages18
JournalHuman Immunology
Volume62
Issue number5
DOIs
Publication statusPublished - 1 May 2001

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Keywords

  • Binding pattern
  • Binding value
  • MHC-peptide interface
  • Residue preference

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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