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Mesoscale modeling of molecular machines: Cyclic dynamics and hydrodynamical fluctuations

Andrew Cressman, Yuichi Togashi, Alexander S. Mikhailov, and Raymond Kapral
Phys. Rev. E 77, 050901(R) – Published 7 May 2008
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Abstract

Proteins acting as molecular machines can undergo cyclic internal conformational motions that are coupled to ligand binding and dissociation events. In contrast to their macroscopic counterparts, nanomachines operate in a highly fluctuating environment, which influences their operation. To bridge the gap between detailed microscopic and simple phenomenological descriptions, a mesoscale approach, which combines an elastic network model of a machine with a particle-based mesoscale description of the solvent, is employed. The time scale of the cyclic hinge motions of the machine prototype is strongly affected by hydrodynamical coupling to the solvent.

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  • Received 25 January 2008

DOI:https://doi.org/10.1103/PhysRevE.77.050901

©2008 American Physical Society

Authors & Affiliations

Andrew Cressman1,*, Yuichi Togashi2,†, Alexander S. Mikhailov3,‡, and Raymond Kapral1,§

  • 1Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
  • 2Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
  • 3Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany

  • *andrew.cressman@utoronto.ca
  • togashi@phys1.med.osaka-u.ac.jp
  • mikhailov@fhi-berlin.mpg.de
  • §rkapral@chem.utoronto.ca

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Issue

Vol. 77, Iss. 5 — May 2008

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