dc.contributor.author | Skjaerven, Lars | |
dc.contributor.author | Grant, Barry | |
dc.contributor.author | Muga Villate, Arturo | |
dc.contributor.author | Teigen, Knut | |
dc.contributor.author | McCammon, J. Andrew | |
dc.contributor.author | Reuter, Nathalie | |
dc.contributor.author | Martínez, Aurora | |
dc.date.accessioned | 2011-05-31T17:53:23Z | |
dc.date.available | 2011-05-31T17:53:23Z | |
dc.date.issued | 2011-03-10 | |
dc.identifier.citation | PLoS Comput Biol 7(3) : (2011) // e1002004 | es |
dc.identifier.issn | 1553-734X | |
dc.identifier.uri | http://hdl.handle.net/10810/2691 | |
dc.description | 14 p. | es |
dc.description.abstract | GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total 2.2 mu s long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant "opening" of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition. | es |
dc.description.sponsorship | The Norwegian Research Council is acknowledged for CPU resources granted through the NOTUR supercomputing program (http://www.notur.no/) and Bergen Center for Computational Science for providing powerful computer facilities (http://www.bccs.uni.no/). Work at CSIC/UPV/EHU was financed by MICINN (Grant BUF2007-64452). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | es |
dc.language.iso | eng | es |
dc.publisher | Public Library of Science | es |
dc.rights | info:eu-repo/semantics/openAccess | es |
dc.subject | normal mode analysis | es |
dc.subject | bacterial chaperonin groel | es |
dc.subject | amber force field | es |
dc.subject | crystal structure | es |
dc.subject | allosteric mechanism | es |
dc.subject | escherichia coli | es |
dc.subject | proteins | es |
dc.subject | ATP | es |
dc.subject | cooperativity | es |
dc.subject | binding | es |
dc.title | Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations | es |
dc.type | info:eu-repo/semantics/article | es |
dc.rights.holder | © 2011 Skjaerven et al. 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 credited. | es |
dc.relation.publisherversion | http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002004 | es |
dc.identifier.doi | 10.1371/journal.pcbi.1002004 | |
dc.departamentoes | Bioquímica y biología molecular | es_ES |
dc.departamentoeu | Biokimika eta biologia molekularra | es_ES |
dc.subject.categoria | CELLULAR AND MOLECULAR NEUROSCIENCE | |
dc.subject.categoria | MOLECULAR BIOLOGY | |
dc.subject.categoria | MODELING AND SIMULATION | |
dc.subject.categoria | GENETICS AND HEREDITY | |
dc.subject.categoria | ECOLOGY, EVOLUTION, BEHAVIOR AND SYSTEMATICS | |
dc.subject.categoria | ECOLOGY | |
dc.subject.categoria | COMPUTATIONAL THEORY AND MATHEMATICS | |