dc.contributor.author |
Barbany, Montserrat |
dc.contributor.author |
Meyer, Tim |
dc.contributor.author |
Hospital, Adam |
dc.contributor.author |
Faustino, Ignacio |
dc.contributor.author |
D'Abramo, Marco |
dc.contributor.author |
Morata, Jordi |
dc.contributor.author |
Orozco, Modesto |
dc.contributor.author |
de la Cruz, Xavier |
dc.date |
2015 |
dc.identifier |
https://ddd.uab.cat/record/176418 |
dc.identifier |
urn:10.1371/journal.pone.0119978 |
dc.identifier |
urn:oai:ddd.uab.cat:176418 |
dc.identifier |
urn:pmid:25816327 |
dc.identifier |
urn:articleid:14712164v10n3e0119978 |
dc.identifier |
urn:scopus_id:84928910472 |
dc.identifier |
urn:wos_id:000352133600023 |
dc.identifier |
urn:pmc-uid:4376744 |
dc.identifier |
urn:pmcid:PMC4376744 |
dc.identifier |
urn:oai:pubmedcentral.nih.gov:4376744 |
dc.format |
application/pdf |
dc.language |
eng |
dc.publisher |
|
dc.relation |
European Commission 261523 |
dc.relation |
Ministerio de Economía y Competitividad BIO2012/40133 |
dc.relation |
Ministerio de Economía y Competitividad BIO2012/32868 |
dc.relation |
Ministerio de Ciencia e Innovación BCV-2009-1-0003 |
dc.relation |
Ministerio de Ciencia e Innovación BFU2009/11527 |
dc.relation |
Ministerio de Ciencia e Innovación BCV-2008-1-0012 |
dc.relation |
Ministerio de Ciencia e Innovación 200420E578 |
dc.relation |
BMC genomics ; Vol. 10, issue 3 (March 2015), e0119978 |
dc.rights |
open access |
dc.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. |
dc.rights |
https://creativecommons.org/licenses/by/4.0/ |
dc.title |
Molecular dynamics study of naturally existing cavity couplings in proteins |
dc.type |
Article |
dc.description.abstract |
Altres ajuts: MSC/CD08/00241 |
dc.description.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. |