Cargando…

Protein Fragments: Functional and Structural Roles of Their Coevolution Networks

Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be m...

Descripción completa

Detalles Bibliográficos
Autores principales: Dib, Linda, Carbone, Alessandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489791/
https://www.ncbi.nlm.nih.gov/pubmed/23139761
http://dx.doi.org/10.1371/journal.pone.0048124
_version_ 1782248784108978176
author Dib, Linda
Carbone, Alessandra
author_facet Dib, Linda
Carbone, Alessandra
author_sort Dib, Linda
collection PubMed
description Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Indeed, coevolving fragments are indicators of important information explaining folding intermediates, peptide assembly, key mutations with known roles in genetic diseases, distinguished subfamily-dependent motifs and differentiated evolutionary pressures on protein regions. Coevolution analysis detects networks of fragments interaction and highlights a high order organization of fragments demonstrating the importance of studying at a deeper level this structure. We demonstrate that it can be applied to protein families that are highly conserved or represented by few sequences, enlarging in this manner, the class of proteins where coevolution analysis can be performed and making large-scale coevolution studies a feasible goal.
format Online
Article
Text
id pubmed-3489791
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-34897912012-11-08 Protein Fragments: Functional and Structural Roles of Their Coevolution Networks Dib, Linda Carbone, Alessandra PLoS One Research Article Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Indeed, coevolving fragments are indicators of important information explaining folding intermediates, peptide assembly, key mutations with known roles in genetic diseases, distinguished subfamily-dependent motifs and differentiated evolutionary pressures on protein regions. Coevolution analysis detects networks of fragments interaction and highlights a high order organization of fragments demonstrating the importance of studying at a deeper level this structure. We demonstrate that it can be applied to protein families that are highly conserved or represented by few sequences, enlarging in this manner, the class of proteins where coevolution analysis can be performed and making large-scale coevolution studies a feasible goal. Public Library of Science 2012-11-05 /pmc/articles/PMC3489791/ /pubmed/23139761 http://dx.doi.org/10.1371/journal.pone.0048124 Text en © 2012 Dib, Carbone http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Dib, Linda
Carbone, Alessandra
Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title_full Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title_fullStr Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title_full_unstemmed Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title_short Protein Fragments: Functional and Structural Roles of Their Coevolution Networks
title_sort protein fragments: functional and structural roles of their coevolution networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489791/
https://www.ncbi.nlm.nih.gov/pubmed/23139761
http://dx.doi.org/10.1371/journal.pone.0048124
work_keys_str_mv AT diblinda proteinfragmentsfunctionalandstructuralrolesoftheircoevolutionnetworks
AT carbonealessandra proteinfragmentsfunctionalandstructuralrolesoftheircoevolutionnetworks