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Edited* by Gerhard Ertl, Fritz Haber Institute, Berlin, Germany, and approved October 20, 2010 (received for review September 29, 2010)
Abstract
Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated.
- molecular machines
- elastic-network models
- conformational relaxation
- mechanochemical motions
- nonequilibrium dynamics
Footnotes
Author contributions: A.S.M. designed research; H.F. performed research; H.F. and A.S.M. analyzed data; and H.F. and A.S.M. wrote the paper.
The authors declare no conflict of interest.
*This Direct Submission article had a prearranged editor.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1014631107/-/DCSupplemental.
Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations
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- Biological Sciences
- Biophysics and Computational Biology
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