title: Structure of the MotA/B Proton Channel.
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.
authors.affiliation: Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan. kitao@iam.u-tokyo.ac.jp.
authors.forename: Akio
authors.initials: A
authors.lastname: Kitao
authors.affiliation: Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan.
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Nishihara
mesh_terms: D001665:Binding Sites; D003593:Cytoplasm / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D005407:Flagella / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D020409:Molecular Motor Proteins / Q000737:chemistry*; D009154:Mutation / Q000235:genetics; D011522:Protons
chemical_list: D029968:Escherichia coli Proteins; D007477:Ions; D008565:Membrane Proteins; D020409:Molecular Motor Proteins; D011522:Protons
keywords: Distance restraint; Molecular dynamics simulation; Proton transfer; Steered molecular dynamics; Structure modeling; Transmembrane prediction; Umbrella sampling