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- Publisher Website: 10.1016/j.bpj.2009.11.004
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- PMID: 20159170
- WOS: WOS:000275348200026
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Article: Equilibrium sampling for biomolecules under mechanical tension
Title | Equilibrium sampling for biomolecules under mechanical tension |
---|---|
Authors | |
Issue Date | 2010 |
Publisher | Cell 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 Identifier | http://hdl.handle.net/10722/168435 |
ISSN | 2023 Impact Factor: 3.2 2023 SCImago Journal Rankings: 1.188 |
ISI Accession Number ID | |
References |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Zeng, X | en_US |
dc.contributor.author | Hu, H | en_US |
dc.contributor.author | Zhou, HX | en_US |
dc.contributor.author | Marszalek, PE | en_US |
dc.contributor.author | Yang, W | en_US |
dc.date.accessioned | 2012-10-08T03:18:55Z | - |
dc.date.available | 2012-10-08T03:18:55Z | - |
dc.date.issued | 2010 | en_US |
dc.identifier.citation | Biophysical Journal, 2010, v. 98 n. 4, p. 733-740 | en_US |
dc.identifier.issn | 0006-3495 | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/168435 | - |
dc.description.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. | en_US |
dc.language | eng | en_US |
dc.publisher | Cell Press. The Journal's web site is located at http://www.cell.com/biophysj/ | en_US |
dc.relation.ispartof | Biophysical Journal | en_US |
dc.subject.mesh | Biomechanics | en_US |
dc.subject.mesh | Carbohydrate Conformation | en_US |
dc.subject.mesh | Computer Simulation | en_US |
dc.subject.mesh | Molecular Dynamics Simulation | en_US |
dc.subject.mesh | Polysaccharides - Chemistry - Metabolism | en_US |
dc.subject.mesh | Stress, Mechanical | en_US |
dc.title | Equilibrium sampling for biomolecules under mechanical tension | en_US |
dc.type | Article | en_US |
dc.identifier.email | Hu, H:haohu@hku.hk | en_US |
dc.identifier.authority | Hu, H=rp00707 | en_US |
dc.description.nature | link_to_subscribed_fulltext | en_US |
dc.identifier.doi | 10.1016/j.bpj.2009.11.004 | en_US |
dc.identifier.pmid | 20159170 | - |
dc.identifier.scopus | eid_2-s2.0-77249161667 | en_US |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-77249161667&selection=ref&src=s&origin=recordpage | en_US |
dc.identifier.volume | 98 | en_US |
dc.identifier.issue | 4 | en_US |
dc.identifier.spage | 733 | en_US |
dc.identifier.epage | 740 | en_US |
dc.identifier.isi | WOS:000275348200026 | - |
dc.publisher.place | United States | en_US |
dc.identifier.scopusauthorid | Zeng, X=7403247770 | en_US |
dc.identifier.scopusauthorid | Hu, H=7404097564 | en_US |
dc.identifier.scopusauthorid | Zhou, HX=7404742853 | en_US |
dc.identifier.scopusauthorid | Marszalek, PE=7003447079 | en_US |
dc.identifier.scopusauthorid | Yang, W=7407757509 | en_US |
dc.identifier.citeulike | 7660487 | - |
dc.identifier.issnl | 0006-3495 | - |