Article: Equilibrium sampling for biomolecules under mechanical tension

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TitleEquilibrium sampling for biomolecules under mechanical tension
AuthorsZeng, X1
Hu, H1
Zhou, HX2
Marszalek, PE1
Yang, W1
Issue Date2010
PublisherCell Press. The Journal's web site is located at http://www.cell.com/biophysj/
CitationBiophysical Journal, 2010, v. 98 n. 4, p. 733-740 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.bpj.2009.11.004
AbstractIn the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella sampling (REM-US) was developed to simulate mechanical stretching of biomolecules under equilibrium conditions. Equilibrium properties of conformational transitions can be obtained directly from simulations without further assumptions. To test the performance, we carried out REMUS simulations of atomic force microscope (AFM) stretching and relaxing measurements on the polysaccharide pustulan, a (1→6)-β-D-glucan, which undergoes well-characterized rotameric transitions in the backbone bonds. With significantly enhanced sampling convergence and efficiency, the REM-US approach closely reproduced the equilibrium force-extension curves measured in AFM experiments. Consistent with the reversibility in the AFM measurements, the new approach generated identical force-extension curves in both stretching and relaxing simulations - an outcome not reported in previous studies, proving that equilibrium conditions were achieved in the simulations. REM-US may provide a robust approach to modeling of mechanical stretching on polysaccharides and even nucleic acids. © 2010 by the Biophysical Society.
ISSN0006-3495
2011 Impact Factor: 3.653
2011 SCImago Journal Rankings: 0.583
DOIhttp://dx.doi.org/10.1016/j.bpj.2009.11.004
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorZeng, X
dc.contributor.authorHu, H
dc.contributor.authorZhou, HX
dc.contributor.authorMarszalek, PE
dc.contributor.authorYang, W
dc.date.accessioned2012-10-08T03:18:55Z
dc.date.available2012-10-08T03:18:55Z
dc.date.issued2010
dc.description.abstractIn the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella sampling (REM-US) was developed to simulate mechanical stretching of biomolecules under equilibrium conditions. Equilibrium properties of conformational transitions can be obtained directly from simulations without further assumptions. To test the performance, we carried out REMUS simulations of atomic force microscope (AFM) stretching and relaxing measurements on the polysaccharide pustulan, a (1→6)-β-D-glucan, which undergoes well-characterized rotameric transitions in the backbone bonds. With significantly enhanced sampling convergence and efficiency, the REM-US approach closely reproduced the equilibrium force-extension curves measured in AFM experiments. Consistent with the reversibility in the AFM measurements, the new approach generated identical force-extension curves in both stretching and relaxing simulations - an outcome not reported in previous studies, proving that equilibrium conditions were achieved in the simulations. REM-US may provide a robust approach to modeling of mechanical stretching on polysaccharides and even nucleic acids. © 2010 by the Biophysical Society.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationBiophysical Journal, 2010, v. 98 n. 4, p. 733-740 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.bpj.2009.11.004
dc.identifier.citeulike7660487
dc.identifier.doihttp://dx.doi.org/10.1016/j.bpj.2009.11.004
dc.identifier.epage740
dc.identifier.issn0006-3495
2011 Impact Factor: 3.653
2011 SCImago Journal Rankings: 0.583
dc.identifier.issue4
dc.identifier.pmid20159170
dc.identifier.scopuseid_2-s2.0-77249161667
dc.identifier.spage733
dc.identifier.urihttp://hdl.handle.net/10722/168435
dc.identifier.volume98
dc.languageeng
dc.publisherCell Press. The Journal's web site is located at http://www.cell.com/biophysj/
dc.publisher.placeUnited States
dc.relation.ispartofBiophysical Journal
dc.relation.referencesReferences in Scopus
dc.subject.meshBiomechanics
dc.subject.meshCarbohydrate Conformation
dc.subject.meshComputer Simulation
dc.subject.meshMolecular Dynamics Simulation
dc.subject.meshPolysaccharides - Chemistry - Metabolism
dc.subject.meshStress, Mechanical
dc.titleEquilibrium sampling for biomolecules under mechanical tension
dc.typeArticle
Author Affiliations
  1. Duke University
  2. Florida State University