1t5x Citations

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

Chem. Biol. 11 1395-402 (2004)

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.

Articles - 1t5x mentioned but not cited (2)



Reviews citing this publication (4)

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

Articles citing this publication (13)

  1. Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells. Venkatraman P, Nguyen TT, Sainlos M, Bilsel O, Chitta S, Imperiali B, Stern LJ. Nat. Chem. Biol. 3 222-228 (2007)
  2. Model for the peptide-free conformation of class II MHC proteins. Painter CA, Cruz A, López GE, Stern LJ, Zavala-Ruiz Z. PLoS ONE 3 e2403 (2008)
  3. Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. Salomon J, Flower DR. BMC Bioinformatics 7 501 (2006)
  4. Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity. Sidney J, Steen A, Moore C, Ngo S, Chung J, Peters B, Sette A. J. Immunol. 184 2492-2503 (2010)
  5. Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection. Calvo-Calle JM, Strug I, Nastke MD, Baker SP, Stern LJ. PLoS Pathog. 3 1511-1529 (2007)
  6. Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. Sidney J, Steen A, Moore C, Ngo S, Chung J, Peters B, Sette A. J. Immunol. 185 4189-4198 (2010)
  7. Peptide-MHC class II complex stability governs CD4 T cell clonal selection. Baumgartner CK, Ferrante A, Nagaoka M, Gorski J, Malherbe LP. J. Immunol. 184 573-581 (2010)
  8. Structural basis for the presentation of tumor-associated MHC class II-restricted phosphopeptides to CD4+ T cells. Li Y, Depontieu FR, Sidney J, Salay TM, Engelhard VH, Hunt DF, Sette A, Topalian SL, Mariuzza RA. J. Mol. Biol. 399 596-603 (2010)
  9. Identification of the rheumatoid arthritis shared epitope binding site on calreticulin. Ling S, Cheng A, Pumpens P, Michalak M, Holoshitz J. PLoS ONE 5 e11703 (2010)
  10. Gauche(+) side-chain orientation as a key factor in the search for an immunogenic peptide mixture leading to a complete fully protective vaccine. Bermúdez A, Calderon D, Moreno-Vranich A, Almonacid H, Patarroyo MA, Poloche A, Patarroyo ME. Vaccine 32 2117-2126 (2014)
  11. Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets. Parry CS. BMC Struct. Biol. 8 44 (2008)
  12. Amino acid signatures in the Ovar-DRB1 peptide-binding pockets are associated with Ovine Pulmonary Adenocarcinoma susceptibility/resistance. Larruskain A, Minguijón E, Garcia-Etxebarria K, Arostegui I, Moreno B, Juste RA, Jugo BM. Biochem. Biophys. Res. Commun. 428 463-468 (2012)
  13. 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)