Simulating Force-Induced Conformational Transitions in Polysaccharides with the SMD Replica Exchange Method
Zhenyu Lu 1, Hao Hu 2, Weitao Yang 2 and Piotr E Marszalek 2*
1 New York University
2 Duke University
* To whom correspondence should be addressed. E-mail: pemar{at}duke.edu.
Submitted on June 1, 2006
Revised on June 9, 2006
Accepted on 30 June 2006
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Abstract |
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Conventional steered molecular dynamics (SMD) simulations do not readily reproduce equilibrium conditions of AFM stretch and release measurements of polysaccharides undergoing force-induced conformational transitions because of the gap between the time scales of computer simulations (~1 µ s) 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 the current 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.
Key Words:
AFM, Dextran, Molecular Dynamics, Polysaccharides, Replica Exchange, SMD
