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Direct coevolutionary couplings reflect biophysical residue interactions in proteins

Abstract : Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.
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https://hal.archives-ouvertes.fr/hal-01528504
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Submitted on : Monday, May 29, 2017 - 11:25:03 AM
Last modification on : Thursday, December 10, 2020 - 12:36:35 PM

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Alice Coucke, Guido Uguzzoni, Francesco Oteri, Simona Cocco, Rémi Monasson, et al.. Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Journal of Chemical Physics, American Institute of Physics, 2016, 145 (17), pp.174102. ⟨10.1063/1.4966156⟩. ⟨hal-01528504⟩

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