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A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins.

Zavala-Ruiz Z, Strug I, Anderson MW, Gorski J, Stern LJ
Chem Biol 11 1395-402 (2004)
Cited: 43 times
EuropePMC logo PMID: 15489166

Abstract

Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.

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Reviews citing this publication (2)

  1. Conformational variation in structures of classical and non-classical MHCII proteins and functional implications. Painter CA, Stern LJ. Immunol Rev 250 144-157 (2012)
  2. HLA-DR: molecular insights and vaccine design. Stern LJ, Calvo-Calle JM. Curr Pharm Des 15 3249-3261 (2009)

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  17. Computational Identification and Characterization of a Promiscuous T-Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide-Based Subunit Vaccine Design. Hossain MS, Azad AK, Chowdhury PA, Wakayama M. Biomed Res Int 2017 4826030 (2017)
  18. A Newly Recognized Pairing Mechanism of the α- and β-Chains of the Chicken Peptide-MHC Class II Complex. Zhang L, Li X, Ma L, Zhang B, Meng G, Xia C. J Immunol 204 1630-1640 (2020)
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