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Article: Equilibrium sampling for biomolecules under mechanical tension

TitleEquilibrium sampling for biomolecules under mechanical tension
Authors
Issue Date2010
PublisherCell Press. The Journal's web site is located at http://www.cell.com/biophysj/
Citation
Biophysical Journal, 2010, v. 98 n. 4, p. 733-740 How to Cite?
Abstract
In 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.
Persistent Identifierhttp://hdl.handle.net/10722/168435
ISSN
2013 Impact Factor: 3.832
ISI Accession Number ID
References

 

Author Affiliations
  1. Duke University
  2. Florida State University
DC FieldValueLanguage
dc.contributor.authorZeng, Xen_US
dc.contributor.authorHu, Hen_US
dc.contributor.authorZhou, HXen_US
dc.contributor.authorMarszalek, PEen_US
dc.contributor.authorYang, Wen_US
dc.date.accessioned2012-10-08T03:18:55Z-
dc.date.available2012-10-08T03:18:55Z-
dc.date.issued2010en_US
dc.identifier.citationBiophysical Journal, 2010, v. 98 n. 4, p. 733-740en_US
dc.identifier.issn0006-3495en_US
dc.identifier.urihttp://hdl.handle.net/10722/168435-
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.en_US
dc.languageengen_US
dc.publisherCell Press. The Journal's web site is located at http://www.cell.com/biophysj/en_US
dc.relation.ispartofBiophysical Journalen_US
dc.subject.meshBiomechanicsen_US
dc.subject.meshCarbohydrate Conformationen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshMolecular Dynamics Simulationen_US
dc.subject.meshPolysaccharides - Chemistry - Metabolismen_US
dc.subject.meshStress, Mechanicalen_US
dc.titleEquilibrium sampling for biomolecules under mechanical tensionen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1016/j.bpj.2009.11.004en_US
dc.identifier.pmid20159170en_US
dc.identifier.scopuseid_2-s2.0-77249161667en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77249161667&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume98en_US
dc.identifier.issue4en_US
dc.identifier.spage733en_US
dc.identifier.epage740en_US
dc.identifier.isiWOS:000275348200026-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridZeng, X=7403247770en_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridZhou, HX=7404742853en_US
dc.identifier.scopusauthoridMarszalek, PE=7003447079en_US
dc.identifier.scopusauthoridYang, W=7407757509en_US
dc.identifier.citeulike7660487-

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