Equilibrium sampling for biomolecules under mechanical tension.
Journal Article (Journal Article)
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 REM-US simulations of atomic force microscope (AFM) stretching and relaxing measurements on the polysaccharide pustulan, a (1-->6)-beta-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.
Full Text
Duke Authors
Cited Authors
- Zeng, X; Hu, H; Zhou, H-X; Marszalek, PE; Yang, W
Published Date
- February 2010
Published In
Volume / Issue
- 98 / 4
Start / End Page
- 733 - 740
PubMed ID
- 20159170
Pubmed Central ID
- PMC2820644
Electronic International Standard Serial Number (EISSN)
- 1542-0086
International Standard Serial Number (ISSN)
- 0006-3495
Digital Object Identifier (DOI)
- 10.1016/j.bpj.2009.11.004
Language
- eng