Web of Science: 3 citations, Scopus: 4 citations, Google Scholar: citations
Molecular dynamics study of naturally existing cavity couplings in proteins
Barbany, Montserrat (Institut de Recerca Biomèdica)
Meyer, Tim (Max-Planck-Institut für biophysikalische Chemie)
Hospital,Adam (Institut de Recerca Biomèdica)
Faustino, Ignacio (Institut de Recerca Biomèdica)
D'Abramo, Marco (Università degli Studi di Roma "La Sapienza". Dipartimento di Chimica)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
Orozco, Modesto (Institut de Recerca Biomèdica)
de la Cruz, Xavier (Institució Catalana de Recerca i Estudis Avançats)

Date: 2015
Abstract: Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0. 25/0. 5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.
Note: Número d'acord de subvenció EC/FP7/261523
Note: Número d'acord de subvenció MINECO/BIO2012/40133
Note: Número d'acord de subvenció MINECO/BIO2012/32868
Note: Número d'acord de subvenció MICINN/BCV-2009-1-0003
Note: Número d'acord de subvenció MICINN/BFU2009/11527
Note: Número d'acord de subvenció MICINN/BCV-2008-1-0012
Note: Número d'acord de subvenció MICINN/200420E578
Note: Número d'acord de subvenció MSC/CD08/00241
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; publishedVersion
Published in: Plos One, Vol. 10, issue 3 (March 2015) , e0119978, ISSN 1471-2164

DOI: 10.1371/journal.pone.0119978
PMID: 25816327

28 p, 1.7 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (scientific output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles

 Record created 2017-07-03, last modified 2018-10-21

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