title: Mesoscale modeling of molecular machines: cyclic dynamics and hydrodynamical fluctuations.
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.
authors.affiliation: Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6. andrew.cressman@utoronto.ca
authors.forename: Andrew
authors.initials: A
authors.lastname: Cressman
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Togashi
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mikhailov
authors.forename: Raymond
authors.initials: R
authors.lastname: Kapral
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D009038:Motion; D011487:Protein Conformation
chemical_list: D020409:Molecular Motor Proteins