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- Publisher Website: 10.1529/biophysj.106.090324
- Scopus: eid_2-s2.0-33748446467
- PMID: 16829559
- WOS: WOS:000240130500001
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Article: Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method
Title | Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method |
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Authors | |
Issue Date | 2006 |
Publisher | Cell 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? |
Abstract | Conventional 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 Identifier | http://hdl.handle.net/10722/168037 |
ISSN | 2023 Impact Factor: 3.2 2023 SCImago Journal Rankings: 1.188 |
ISI Accession Number ID | |
References |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Lu, Z | en_US |
dc.contributor.author | Hu, H | en_US |
dc.contributor.author | Yang, W | en_US |
dc.contributor.author | Marszalek, PE | en_US |
dc.date.accessioned | 2012-10-08T03:14:26Z | - |
dc.date.available | 2012-10-08T03:14:26Z | - |
dc.date.issued | 2006 | en_US |
dc.identifier.citation | Biophysical Journal, 2006, v. 91 n. 6, p. L57-L59 | en_US |
dc.identifier.issn | 0006-3495 | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/168037 | - |
dc.description.abstract | Conventional 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.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 | Computer Simulation | en_US |
dc.subject.mesh | Dextrans - Chemistry - Ultrastructure | en_US |
dc.subject.mesh | Elasticity | en_US |
dc.subject.mesh | Microscopy, Atomic Force | en_US |
dc.subject.mesh | Molecular Conformation | en_US |
dc.subject.mesh | Polysaccharides - Chemistry - Ultrastructure | en_US |
dc.title | Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method | 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 | 10.1529/biophysj.106.090324 | en_US |
dc.identifier.pmid | 16829559 | - |
dc.identifier.scopus | eid_2-s2.0-33748446467 | en_US |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-33748446467&selection=ref&src=s&origin=recordpage | en_US |
dc.identifier.volume | 91 | en_US |
dc.identifier.issue | 6 | en_US |
dc.identifier.spage | L57 | en_US |
dc.identifier.epage | L59 | en_US |
dc.identifier.isi | WOS:000240130500001 | - |
dc.publisher.place | United States | en_US |
dc.identifier.scopusauthorid | Lu, Z=36708080000 | en_US |
dc.identifier.scopusauthorid | Hu, H=7404097564 | en_US |
dc.identifier.scopusauthorid | Yang, W=7407757509 | en_US |
dc.identifier.scopusauthorid | Marszalek, PE=7003447079 | en_US |
dc.identifier.issnl | 0006-3495 | - |