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

Publication: Research - peer-reviewJournal article – Annual report year: 2012

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Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign. / Andreatta, Massimo; Nielsen, Morten.

In: Immunology, Vol. 136, No. 3, 2012, p. 306-311.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

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Andreatta, Massimo; Nielsen, Morten / Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign.

In: Immunology, Vol. 136, No. 3, 2012, p. 306-311.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Bibtex

@article{286ad3f59ca94629a3ee6626b9d52b53,
title = "Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign",
publisher = "Wiley-Blackwell Publishing Ltd.",
author = "Massimo Andreatta and Morten Nielsen",
year = "2012",
doi = "10.1111/j.1365-2567.2012.03579.x",
volume = "136",
number = "3",
pages = "306--311",
journal = "Immunology",
issn = "0019-2805",

}

RIS

TY - JOUR

T1 - Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign

A1 - Andreatta,Massimo

A1 - Nielsen,Morten

AU - Andreatta,Massimo

AU - Nielsen,Morten

PB - Wiley-Blackwell Publishing Ltd.

PY - 2012

Y1 - 2012

N2 - 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 more divergent, displaying unconventional anchor positions and in some cases rather unspecific amino acid preferences.

AB - 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 more divergent, displaying unconventional anchor positions and in some cases rather unspecific amino acid preferences.

U2 - 10.1111/j.1365-2567.2012.03579.x

DO - 10.1111/j.1365-2567.2012.03579.x

JO - Immunology

JF - Immunology

SN - 0019-2805

IS - 3

VL - 136

SP - 306

EP - 311

ER -