Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign.

Immunology
Massimo Andreatta, Morten Nielsen

Abstract

Compared with HLA-DR molecules, the specificities of HLA-DP and HLA-DQ molecules have only been studied to a limited extent. The description of the binding motifs has been mostly anecdotal and does not provide a quantitative measure of the importance of each position in the binding core and the relative weight of different amino acids at a given position. The recent publication of larger data sets of peptide-binding to DP and DQ molecules opens the possibility of using data-driven bioinformatics methods to accurately define the binding motifs of these molecules. Using the neural network-based method NNAlign, we characterized the binding specificities of five HLA-DP and six HLA-DQ among the most frequent in the human population. The identified binding motifs showed an overall concurrence with earlier studies but revealed subtle differences. The DP molecules revealed a large overlap in the pattern of amino acid preferences at core positions, with conserved hydrophobic/aromatic anchors at P1 and P6, and an additional hydrophobic anchor at P9 in some variants. These results confirm the existence of a previously hypothesized supertype encompassing the most common DP alleles. Conversely, the binding motifs for DQ molecules appear mor...Continue Reading

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Citations

May 11, 2013·Protein Engineering, Design & Selection : PEDS·Mariyana AtanasovaIrini Doytchinova
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Stefan IvanovIrini Doytchinova
Jun 1, 2015·Molecular Informatics·Ivan Dimitrov, Irini Doytchinova
Jul 21, 2016·Proceedings of the National Academy of Sciences of the United States of America·Isabel LeungSachdev S Sidhu
Sep 24, 2016·Respiratory Research·Fatemeh MoheimaniDarryl A Knight
Sep 3, 2013·Transplantation·Anat R TamburJohn J Friedewald
May 1, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Peter van BalenJ H Frederik Falkenburg
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Aug 21, 2018·World Journal of Gastroenterology : WJG·Izzet Mehmet AkcayLevent Doganay
Nov 14, 2015·Cancer Immunology Research·Stefanie GrossEckhart Kaempgen
Nov 20, 2020·Molecular Therapy : the Journal of the American Society of Gene Therapy·Pierre DillardElse Marit Inderberg
Jul 19, 2017·Journal of Chemical Information and Modeling·Ventsislav YordanovIrini Doytchinova

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