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Structure of the MotA/B Proton Channel

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The Bacterial Flagellum

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1593))

Abstract

Flagellar motors utilize the motive force of protons and other ions as an energy source. To elucidate the mechanisms of ion permeation and torque generation, it is essential to investigate the structure of the motor stator complex; however, the atomic structure of the transmembrane region of the stator has not been determined experimentally. We recently constructed an atomic model structure of the transmembrane region of the Escherichia coli MotA/B stator complex based on previously published disulfide cross-linking and tryptophan scanning mutations. Dynamic permeation by hydronium ions, sodium ions, and water molecules was then observed using steered molecular dynamics simulations, and free energy profiles for ion/water permeation were calculated using umbrella sampling. We also examined the possible ratchet motion of the cytoplasmic domain induced by the protonation/deprotonation cycle of the MotB proton binding site, Asp32. In this chapter, we describe the methods used to conduct these analyses, including atomic structure modeling of the transmembrane region of the MotA/B complex; molecular dynamics simulations in equilibrium and in ion permeation processes; and ion permeation-free energy profile calculations.

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Acknowledgements

This research was supported by a Grant-in-Aid for Science Research in Innovative Areas (No. JP25104002) and by Grants-in-Aid for Science Research B (No. JP23370066 and No. JP15H04357) from the Japan Society for The Promotion of Science (JSPS) and Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) to A.K.. This work was also financially supported by Innovative Drug Discovery Infrastructure through Functional Control of Biomolecular Systems, Priority Issue 1 in Post-K Supercomputer Development (Project ID: hp150270) to A.K. The computations were partially performed using the supercomputers at the RCCS, National Institute of Natural Science and ISSP, The University of Tokyo.

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Authors and Affiliations

  1. Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan

    Akio Kitao & Yasutaka Nishihara

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  1. Akio Kitao
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  2. Yasutaka Nishihara
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Correspondence to Akio Kitao .

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Editors and Affiliations

  1. Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan

    Tohru Minamino

  2. Quantitative Biology Center RIKEN, Suita, Osaka, Japan

    Keiichi Namba

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Kitao, A., Nishihara, Y. (2017). Structure of the MotA/B Proton Channel. In: Minamino, T., Namba, K. (eds) The Bacterial Flagellum. Methods in Molecular Biology, vol 1593. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6927-2_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6927-2_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6926-5

  • Online ISBN: 978-1-4939-6927-2

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