Artículo

Espada, R.; Parra, R.G.; Mora, T.; Walczak, A.M.; Ferreiro, D.U. "Capturing coevolutionary signals inrepeat proteins" (2015) BMC Bioinformatics. 16(1):1
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Abstract:

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.

Registro:

Documento: Artículo
Título:Capturing coevolutionary signals inrepeat proteins
Autor:Espada, R.; Parra, R.G.; Mora, T.; Walczak, A.M.; Ferreiro, D.U.
Filiación:Facultad de Ciencias Exactas y Naturales, Protein Physiology Lab, Dep de Química Biológica, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
Laboratoire de physique statistique, CNRS, UPMC and École normale supérieure, 24 rue Lhomond, Paris, 75005, France
24 rue Lhomond, Paris, 75005, France
Universidad de Buenos Aires, Departamento de Física, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
Palabras clave: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
Año:2015
Volumen:16
Número:1
Página de inicio:1
DOI: http://dx.doi.org/10.1186/s12859-015-0648-3
Título revista:BMC Bioinformatics
Título revista abreviado:BMC Bioinform.
ISSN:14712105
CODEN:BBMIC
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14712105_v16_n1_p1_Espada

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Citas:

---------- APA ----------
Espada, R., Parra, R.G., Mora, T., Walczak, A.M. & Ferreiro, D.U. (2015) . Capturing coevolutionary signals inrepeat proteins. BMC Bioinformatics, 16(1), 1.
http://dx.doi.org/10.1186/s12859-015-0648-3
---------- CHICAGO ----------
Espada, R., Parra, R.G., Mora, T., Walczak, A.M., Ferreiro, D.U. "Capturing coevolutionary signals inrepeat proteins" . BMC Bioinformatics 16, no. 1 (2015) : 1.
http://dx.doi.org/10.1186/s12859-015-0648-3
---------- MLA ----------
Espada, R., Parra, R.G., Mora, T., Walczak, A.M., Ferreiro, D.U. "Capturing coevolutionary signals inrepeat proteins" . BMC Bioinformatics, vol. 16, no. 1, 2015, pp. 1.
http://dx.doi.org/10.1186/s12859-015-0648-3
---------- VANCOUVER ----------
Espada, R., Parra, R.G., Mora, T., Walczak, A.M., Ferreiro, D.U. Capturing coevolutionary signals inrepeat proteins. BMC Bioinform. 2015;16(1):1.
http://dx.doi.org/10.1186/s12859-015-0648-3