Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.

Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a network of co-evolving clusters of residues. The goal of this work is two-fold: first, we have combined mutual infor...

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Autores principales:	Daniel Aguilar, Baldo Oliva, Cristina Marino Buslje
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4d3c88af5d6e46cf9c3da22ca133298f
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spelling	oai:doaj.org-article:4d3c88af5d6e46cf9c3da22ca133298f2021-11-18T07:11:08ZMapping the mutual information network of enzymatic families in the protein structure to unveil functional features.1932-620310.1371/journal.pone.0041430https://doaj.org/article/4d3c88af5d6e46cf9c3da22ca133298f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22848494/?tool=EBIhttps://doaj.org/toc/1932-6203Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a network of co-evolving clusters of residues. The goal of this work is two-fold: first, we have combined mutual information and structural data to describe the amino acid networks within a protein and their interactions. Second, we have investigated how this information can be used to improve methods of prediction of functional residues by reducing the search space. As a main result, we found that clusters of co-evolving residues related to the catalytic site of an enzyme have distinguishable topological properties in the network. We also observed that these clusters usually evolve independently, which could be related to a fail-safe mechanism. Finally, we discovered a significant enrichment of functional residues (e.g. metal binding, susceptibility to detrimental mutations) in the clusters, which could be the foundation of new prediction tools.Daniel AguilarBaldo OlivaCristina Marino BusljePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 7, p e41430 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daniel Aguilar Baldo Oliva Cristina Marino Buslje Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
description	Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a network of co-evolving clusters of residues. The goal of this work is two-fold: first, we have combined mutual information and structural data to describe the amino acid networks within a protein and their interactions. Second, we have investigated how this information can be used to improve methods of prediction of functional residues by reducing the search space. As a main result, we found that clusters of co-evolving residues related to the catalytic site of an enzyme have distinguishable topological properties in the network. We also observed that these clusters usually evolve independently, which could be related to a fail-safe mechanism. Finally, we discovered a significant enrichment of functional residues (e.g. metal binding, susceptibility to detrimental mutations) in the clusters, which could be the foundation of new prediction tools.
format	article
author	Daniel Aguilar Baldo Oliva Cristina Marino Buslje
author_facet	Daniel Aguilar Baldo Oliva Cristina Marino Buslje
author_sort	Daniel Aguilar
title	Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
title_short	Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
title_full	Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
title_fullStr	Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
title_full_unstemmed	Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
title_sort	mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/4d3c88af5d6e46cf9c3da22ca133298f
work_keys_str_mv	AT danielaguilar mappingthemutualinformationnetworkofenzymaticfamiliesintheproteinstructuretounveilfunctionalfeatures AT baldooliva mappingthemutualinformationnetworkofenzymaticfamiliesintheproteinstructuretounveilfunctionalfeatures AT cristinamarinobuslje mappingthemutualinformationnetworkofenzymaticfamiliesintheproteinstructuretounveilfunctionalfeatures
_version_	1718423785014558720

Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.

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