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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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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 |
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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 |
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