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Simulating Force-Induced Conformational Transitions in Polysaccharides with the SMD Replica Exchange Method

Zhenyu Lu ^*, Hao Hu ^*, Weitao Yang ^* and Piotr E. Marszalek 

^* Department of Chemistry, and Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials, Duke University, Durham, North Carolina 27708

Correspondence: Address reprint requests and inquiries to Piotr E. Marszalek, E-mail: pemar{at}duke.edu; or Weitao Yang, E-mail: weitao.yang{at}duke.edu.

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.