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

Journal Article (Journal Article)

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 ( approximately 1 mus) and AFM measurements ( approximately 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.

Full Text

Duke Authors

Cited Authors

  • Lu, Z; Hu, H; Yang, W; Marszalek, PE

Published Date

  • September 2006

Published In

Volume / Issue

  • 91 / 6

Start / End Page

  • L57 - L59

PubMed ID

  • 16829559

Pubmed Central ID

  • PMC1557546

Electronic International Standard Serial Number (EISSN)

  • 1542-0086

International Standard Serial Number (ISSN)

  • 0006-3495

Digital Object Identifier (DOI)

  • 10.1529/biophysj.106.090324


  • eng