Capturing coevolutionary signals inrepeat proteins

BMC Bioinformatics

Research Article

Aleksandra M Walczak¹  Thierry Mora²  R Gonzalo Parra³  Rocío Espada⁴ 

[1] 24 rue Lhomond, 75005, Paris, France;Laboratoire de physique statistique, CNRS, UPMC and École normale supérieure, 24 rue Lhomond, 75005, Paris, France;Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina;Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina;Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina;

关键词: Direct coupling analysis;    Repeat proteins;    Direct information;    Co-evolution;   

DOI  :  10.1186/s12859-015-0648-3

 received in 2015-03-17, accepted in 2015-06-16,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe analysis of correlations of amino acid occurrences in globular domains has led to the development of statistical tools that can identify native contacts – portions of the chains that come to close distance in folded structural ensembles. Here we introduce a direct coupling analysis for repeat proteins – natural systems for which the identification of folding domains remains challenging.ResultsWe show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. Equalizing for this bias in an objective way reveals true co-evolutionary signals from which local native contacts can be identified. Importantly, parameter values obtained for all other interactions are not significantly affected by the equalization. We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families.ConclusionsThe overall procedure can be used to reconstruct the interactions at distances larger than repeat-pairs, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric.

【 授权许可】

Unknown   
© Espada et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.