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Convergent evolution in structural elements of proteins investigated using cross profile analysis

BACKGROUND: Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequenc...

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Autores principales: Tomii, Kentaro, Sawada, Yoshito, Honda, Shinya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398312/
https://www.ncbi.nlm.nih.gov/pubmed/22244085
http://dx.doi.org/10.1186/1471-2105-13-11
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author Tomii, Kentaro
Sawada, Yoshito
Honda, Shinya
author_facet Tomii, Kentaro
Sawada, Yoshito
Honda, Shinya
author_sort Tomii, Kentaro
collection PubMed
description BACKGROUND: Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments. RESULTS: This report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors. CONCLUSIONS: Cross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments.
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spelling pubmed-33983122012-07-18 Convergent evolution in structural elements of proteins investigated using cross profile analysis Tomii, Kentaro Sawada, Yoshito Honda, Shinya BMC Bioinformatics Research Article BACKGROUND: Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments. RESULTS: This report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors. CONCLUSIONS: Cross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments. BioMed Central 2012-01-16 /pmc/articles/PMC3398312/ /pubmed/22244085 http://dx.doi.org/10.1186/1471-2105-13-11 Text en Copyright ©2012 Tomii et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Tomii, Kentaro
Sawada, Yoshito
Honda, Shinya
Convergent evolution in structural elements of proteins investigated using cross profile analysis
title Convergent evolution in structural elements of proteins investigated using cross profile analysis
title_full Convergent evolution in structural elements of proteins investigated using cross profile analysis
title_fullStr Convergent evolution in structural elements of proteins investigated using cross profile analysis
title_full_unstemmed Convergent evolution in structural elements of proteins investigated using cross profile analysis
title_short Convergent evolution in structural elements of proteins investigated using cross profile analysis
title_sort convergent evolution in structural elements of proteins investigated using cross profile analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398312/
https://www.ncbi.nlm.nih.gov/pubmed/22244085
http://dx.doi.org/10.1186/1471-2105-13-11
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