Capturing coevolutionary signals inrepeat proteins

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Background: The 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 f...

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Autores principales:	Espada, R., Parra, R.G., Mora, T., Walczak, A.M., Ferreiro, D.U.
Formato:	JOUR
Materias:	Co-evolution Direct coupling analysis Direct information Repeat proteins Amino acids Statistical mechanics Confidence levels Direct coupling Evolutionary information Pair correlations Translational symmetry Proteins
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p1_Espada
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_14712105_v16_n1_p1_Espada
record_format	dspace
spelling	todo:paper_14712105_v16_n1_p1_Espada2023-10-03T16:17:42Z Capturing coevolutionary signals inrepeat proteins Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. Co-evolution Direct coupling analysis Direct information Repeat proteins Amino acids Statistical mechanics Co-evolution Confidence levels Direct coupling Direct information Evolutionary information Pair correlations Repeat proteins Translational symmetry Proteins Background: The 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. Results: We 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. Conclusions: The 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. © 2015 Espada et al. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p1_Espada
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Co-evolution Direct coupling analysis Direct information Repeat proteins Amino acids Statistical mechanics Co-evolution Confidence levels Direct coupling Direct information Evolutionary information Pair correlations Repeat proteins Translational symmetry Proteins
spellingShingle	Co-evolution Direct coupling analysis Direct information Repeat proteins Amino acids Statistical mechanics Co-evolution Confidence levels Direct coupling Direct information Evolutionary information Pair correlations Repeat proteins Translational symmetry Proteins Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U. Capturing coevolutionary signals inrepeat proteins
topic_facet	Co-evolution Direct coupling analysis Direct information Repeat proteins Amino acids Statistical mechanics Co-evolution Confidence levels Direct coupling Direct information Evolutionary information Pair correlations Repeat proteins Translational symmetry Proteins
description	Background: The 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. Results: We 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. Conclusions: The 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. © 2015 Espada et al.
format	JOUR
author	Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U.
author_facet	Espada, R. Parra, R.G. Mora, T. Walczak, A.M. Ferreiro, D.U.
author_sort	Espada, R.
title	Capturing coevolutionary signals inrepeat proteins
title_short	Capturing coevolutionary signals inrepeat proteins
title_full	Capturing coevolutionary signals inrepeat proteins
title_fullStr	Capturing coevolutionary signals inrepeat proteins
title_full_unstemmed	Capturing coevolutionary signals inrepeat proteins
title_sort	capturing coevolutionary signals inrepeat proteins
url	http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p1_Espada
work_keys_str_mv	AT espadar capturingcoevolutionarysignalsinrepeatproteins AT parrarg capturingcoevolutionarysignalsinrepeatproteins AT morat capturingcoevolutionarysignalsinrepeatproteins AT walczakam capturingcoevolutionarysignalsinrepeatproteins AT ferreirodu capturingcoevolutionarysignalsinrepeatproteins
_version_	1807323483969945600

Capturing coevolutionary signals inrepeat proteins

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