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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Autor principal:	Ferreiro, Diego U.
Publicado:	2015
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 amino acid protein chemistry human molecular evolution molecular model protein folding protein motif protein multimerization Amino Acid Motifs Amino Acids Evolution, Molecular Humans Models, Molecular Protein Folding Protein Multimerization
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712105_v16_n1_p_Espada http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p_Espada
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_14712105_v16_n1_p_Espada
record_format	dspace
spelling	paper:paper_14712105_v16_n1_p_Espada2023-06-08T16:17:10Z Capturing coevolutionary signals inrepeat proteins Ferreiro, Diego 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 amino acid protein chemistry human molecular evolution molecular model protein folding protein motif protein multimerization Amino Acid Motifs Amino Acids Evolution, Molecular Humans Models, Molecular Protein Folding Protein Multimerization 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. 2015 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712105_v16_n1_p_Espada http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p_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 amino acid protein chemistry human molecular evolution molecular model protein folding protein motif protein multimerization Amino Acid Motifs Amino Acids Evolution, Molecular Humans Models, Molecular Protein Folding Protein Multimerization 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 amino acid protein chemistry human molecular evolution molecular model protein folding protein motif protein multimerization Amino Acid Motifs Amino Acids Evolution, Molecular Humans Models, Molecular Protein Folding Protein Multimerization Proteins Ferreiro, Diego 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 amino acid protein chemistry human molecular evolution molecular model protein folding protein motif protein multimerization Amino Acid Motifs Amino Acids Evolution, Molecular Humans Models, Molecular Protein Folding Protein Multimerization 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.
author	Ferreiro, Diego U.
author_facet	Ferreiro, Diego U.
author_sort	Ferreiro, Diego U.
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
publishDate	2015
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712105_v16_n1_p_Espada http://hdl.handle.net/20.500.12110/paper_14712105_v16_n1_p_Espada
work_keys_str_mv	AT ferreirodiegou capturingcoevolutionarysignalsinrepeatproteins
_version_	1768546364691578880

Capturing coevolutionary signals inrepeat proteins

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