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Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum

Anton Arkhipov ^* , Peter L. Freddolino  , Katsumi Imada  ^¶, Keiichi Namba  ^¶ and Klaus Schulten ^*  

^* Department of Physics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan; and ^¶ Dynamic Nano Machine Project, International Cooperative Research Project, Japan Science and Technology Agency, Tokyo, Japan

Correspondence: Address reprint requests to K. Schulten, E-mail: kschulte{at}ks.uiuc.edu.

Many types of bacteria propel themselves using elongated structures known as flagella. The bacterial flagellar filament is a relatively simple and well-studied macromolecular assembly, which assumes different helical shapes when rotated in different directions. This polymorphism enables a bacterium to switch between running and tumbling modes; however, the mechanism governing the filament polymorphism is not completely understood. Here we report a study of the bacterial flagellar filament using numerical simulations that employ a novel coarse-grained molecular dynamics method. The simulations reveal the dynamics of a half-micrometer-long flagellum segment on a timescale of tens of microseconds. Depending on the rotation direction, specific modes of filament coiling and arrangement of monomers are observed, in qualitative agreement with experimental observations of flagellar polymorphism. We find that solvent-protein interactions are likely to contribute to the polymorphic helical shapes of the filament.