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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
2012 Impact Factor: 3.668
2012 SCImago Journal Rankings: 1.923
 
DOIhttp://dx.doi.org/10.1016/j.bpj.2009.11.004
 
ReferencesReferences in Scopus
 
DC FieldValue
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
2012 Impact Factor: 3.668
2012 SCImago Journal Rankings: 1.923
 
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
 
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Author Affiliations
  1. Duke University
  2. Florida State University