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Article: Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method

TitleSimulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method
Authors
Issue Date2006
PublisherCell Press. The Journal's web site is located at http://www.cell.com/biophysj/
Citation
Biophysical Journal, 2006, v. 91 n. 6, p. L57-L59 How to Cite?
AbstractConventional steered molecular dynamics (SMD) simulations do not readily reproduce equilibrium conditions of atomic force microscopy (AFM) stretch and release measurements of polysaccharides undergoing force-induced conformational transitions because of the gap between the timescales of computer simulations (∼1 μs) and AFM measurements (∼1 s). To circumvent this limitation, we propose using the replica exchange method (REM) to enhance sampling during SMD simulations. By applying REM SMD to a small polysaccharide system and comparing the results with those from AFM stretching experiments, we demonstrate that REM SMD reproduces the experimental results not only qualitatively but quantitatively, approaching near equilibrium conditions of AFM measurements. As tested in this work, hysteresis and computational time of REM SMD simulations of short polysaccharide chains are significantly reduced as compared to regular SMD simulations, making REM SMD an attractive tool for studying forced-induced conformational transitions of small biopolymer systems. © 2006 by the Biophysical Society.
Persistent Identifierhttp://hdl.handle.net/10722/168037
ISSN
2015 Impact Factor: 3.632
2015 SCImago Journal Rankings: 2.188
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLu, Zen_US
dc.contributor.authorHu, Hen_US
dc.contributor.authorYang, Wen_US
dc.contributor.authorMarszalek, PEen_US
dc.date.accessioned2012-10-08T03:14:26Z-
dc.date.available2012-10-08T03:14:26Z-
dc.date.issued2006en_US
dc.identifier.citationBiophysical Journal, 2006, v. 91 n. 6, p. L57-L59en_US
dc.identifier.issn0006-3495en_US
dc.identifier.urihttp://hdl.handle.net/10722/168037-
dc.description.abstractConventional steered molecular dynamics (SMD) simulations do not readily reproduce equilibrium conditions of atomic force microscopy (AFM) stretch and release measurements of polysaccharides undergoing force-induced conformational transitions because of the gap between the timescales of computer simulations (∼1 μs) and AFM measurements (∼1 s). To circumvent this limitation, we propose using the replica exchange method (REM) to enhance sampling during SMD simulations. By applying REM SMD to a small polysaccharide system and comparing the results with those from AFM stretching experiments, we demonstrate that REM SMD reproduces the experimental results not only qualitatively but quantitatively, approaching near equilibrium conditions of AFM measurements. As tested in this work, hysteresis and computational time of REM SMD simulations of short polysaccharide chains are significantly reduced as compared to regular SMD simulations, making REM SMD an attractive tool for studying forced-induced conformational transitions of small biopolymer systems. © 2006 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.meshComputer Simulationen_US
dc.subject.meshDextrans - Chemistry - Ultrastructureen_US
dc.subject.meshElasticityen_US
dc.subject.meshMicroscopy, Atomic Forceen_US
dc.subject.meshMolecular Conformationen_US
dc.subject.meshPolysaccharides - Chemistry - Ultrastructureen_US
dc.titleSimulating force-induced conformational transitions in polysaccharides with the SMD replica exchange methoden_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.doi10.1529/biophysj.106.090324en_US
dc.identifier.pmid16829559-
dc.identifier.scopuseid_2-s2.0-33748446467en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33748446467&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume91en_US
dc.identifier.issue6en_US
dc.identifier.spageL57en_US
dc.identifier.epageL59en_US
dc.identifier.isiWOS:000240130500001-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridLu, Z=36708080000en_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridYang, W=7407757509en_US
dc.identifier.scopusauthoridMarszalek, PE=7003447079en_US

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