Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.

The use of molecular dynamics simulations to provide atomic-level descriptions of biological processes tends to be computationally demanding, and a number of approximations are thus commonly employed to improve computational efficiency. In the past, the effect of these approximations on macromolecul...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Stefano Piana, Kresten Lindorff-Larsen, Robert M Dirks, John K Salmon, Ron O Dror, David E Shaw
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0af276439394470085841599aba15a45
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:0af276439394470085841599aba15a45
record_format	dspace
spelling	oai:doaj.org-article:0af276439394470085841599aba15a452021-11-18T07:13:49ZEvaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.1932-620310.1371/journal.pone.0039918https://doaj.org/article/0af276439394470085841599aba15a452012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22768169/?tool=EBIhttps://doaj.org/toc/1932-6203The use of molecular dynamics simulations to provide atomic-level descriptions of biological processes tends to be computationally demanding, and a number of approximations are thus commonly employed to improve computational efficiency. In the past, the effect of these approximations on macromolecular structure and stability has been evaluated mostly through quantitative studies of small-molecule systems or qualitative observations of short-timescale simulations of biological macromolecules. Here we present a quantitative evaluation of two commonly employed approximations, using a test system that has been the subject of a number of previous protein folding studies--the villin headpiece. In particular, we examined the effect of (i) the use of a cutoff-based force-shifting technique rather than an Ewald summation for the treatment of electrostatic interactions, and (ii) the length of the cutoff used to determine how many pairwise interactions are included in the calculation of both electrostatic and van der Waals forces. Our results show that the free energy of folding is relatively insensitive to the choice of cutoff beyond 9 Å, and to whether an Ewald method is used to account for long-range electrostatic interactions. In contrast, we find that the structural properties of the unfolded state depend more strongly on the two approximations examined here.Stefano PianaKresten Lindorff-LarsenRobert M DirksJohn K SalmonRon O DrorDavid E ShawPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e39918 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stefano Piana Kresten Lindorff-Larsen Robert M Dirks John K Salmon Ron O Dror David E Shaw Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
description	The use of molecular dynamics simulations to provide atomic-level descriptions of biological processes tends to be computationally demanding, and a number of approximations are thus commonly employed to improve computational efficiency. In the past, the effect of these approximations on macromolecular structure and stability has been evaluated mostly through quantitative studies of small-molecule systems or qualitative observations of short-timescale simulations of biological macromolecules. Here we present a quantitative evaluation of two commonly employed approximations, using a test system that has been the subject of a number of previous protein folding studies--the villin headpiece. In particular, we examined the effect of (i) the use of a cutoff-based force-shifting technique rather than an Ewald summation for the treatment of electrostatic interactions, and (ii) the length of the cutoff used to determine how many pairwise interactions are included in the calculation of both electrostatic and van der Waals forces. Our results show that the free energy of folding is relatively insensitive to the choice of cutoff beyond 9 Å, and to whether an Ewald method is used to account for long-range electrostatic interactions. In contrast, we find that the structural properties of the unfolded state depend more strongly on the two approximations examined here.
format	article
author	Stefano Piana Kresten Lindorff-Larsen Robert M Dirks John K Salmon Ron O Dror David E Shaw
author_facet	Stefano Piana Kresten Lindorff-Larsen Robert M Dirks John K Salmon Ron O Dror David E Shaw
author_sort	Stefano Piana
title	Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
title_short	Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
title_full	Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
title_fullStr	Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
title_full_unstemmed	Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
title_sort	evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0af276439394470085841599aba15a45
work_keys_str_mv	AT stefanopiana evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations AT krestenlindorfflarsen evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations AT robertmdirks evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations AT johnksalmon evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations AT ronodror evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations AT davideshaw evaluatingtheeffectsofcutoffsandtreatmentoflongrangeelectrostaticsinproteinfoldingsimulations
_version_	1718423708168617984

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.

Ejemplares similares