Molecular dynamics simulation of bacterial flagella
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The bacterial flagellum is a biological nanomachine for the locomotion of bacteria, and is seen in organisms like Salmonella and Escherichia coli. The flagellum consists of tens of thousands of protein molecules and more than 30 different kinds of proteins. The basal body of the flagellum contains a protein export apparatus and a rotary motor that is powered by ion motive force across the cytoplasmic membrane. The filament functions as a propeller whose helicity is controlled by the direction of the torque. The hook that connects the motor and filament acts as a universal joint, transmitting torque generated by the motor to different directions. This report describes the use of molecular dynamics to study the bacterial flagellum. Molecular dynamics simulation is a powerful method that permits the investigation, at atomic resolution, of the molecular mechanisms of biomolecular systems containing many proteins and solvent. When applied to the flagellum, these studies successfully unveiled the polymorphic supercoiling and transportation mechanism of the filament, the universal joint mechanism of the hook, the ion transfer mechanism of the motor stator, the flexible nature of the transport apparatus proteins, and activation of proteins involved in chemotaxis.
KeywordsMolecular dynamics Polymorphic supercoiling Universal joint Protein export Ion transport Chemotaxis
This research was supported by MEXT/JSPS KAKENHI (nos. 25104002 and 15H04357) to A.K. and by MEXT as “Priority Issue on Post-K Computer” (Building Innovative Drug Discovery Infrastructure Through Functional Control of Biomolecular Systems) to A.K. The computations were partly performed using the supercomputers at the RCCS, The National Institute of Natural Science, and ISSP, The University of Tokyo. This research also used computational resources of the K computer provided by the RIKEN Advanced Institute for Computational Science through the HPCI System Research project (project IDs: hp120223, hp140030, hp140031, hp150049, hp150270, hp160207, and hp170254).
Compliance with ethical standards
Conflict of interest
Akio Kitao declares that he has no conflict of interest. Hiroaki Hata declares that he has no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
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