Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recu...

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Autores principales:	Ulf Hensen, Tim Meyer, Jürgen Haas, René Rex, Gert Vriend, Helmut Grubmüller
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2c79a227766d4d6bbab45a660db53b0c
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spelling	oai:doaj.org-article:2c79a227766d4d6bbab45a660db53b0c2021-11-18T07:19:01ZExploring protein dynamics space: the dynasome as the missing link between protein structure and function.1932-620310.1371/journal.pone.0033931https://doaj.org/article/2c79a227766d4d6bbab45a660db53b0c2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22606222/?tool=EBIhttps://doaj.org/toc/1932-6203Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.Ulf HensenTim MeyerJürgen HaasRené RexGert VriendHelmut GrubmüllerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 5, p e33931 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ulf Hensen Tim Meyer Jürgen Haas René Rex Gert Vriend Helmut Grubmüller Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
description	Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.
format	article
author	Ulf Hensen Tim Meyer Jürgen Haas René Rex Gert Vriend Helmut Grubmüller
author_facet	Ulf Hensen Tim Meyer Jürgen Haas René Rex Gert Vriend Helmut Grubmüller
author_sort	Ulf Hensen
title	Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
title_short	Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
title_full	Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
title_fullStr	Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
title_full_unstemmed	Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
title_sort	exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2c79a227766d4d6bbab45a660db53b0c
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Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

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