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Title: Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses

Abstract

V1-ATPase exemplifies the ubiquitous rotary motor, in which a central shaft DF complex rotates inside a hexagonally arranged catalytic A3B3 complex, powered by the energy from ATP hydrolysis. We have recently reported a number of crystal structures of the Enterococcus hirae A3B3DF (V1) complex corresponding to its nucleotide-bound intermediate states, namely the forms waiting for ATP hydrolysis (denoted as catalytic dwell), ATP binding (ATP-binding dwell), and ADP release (ADP-release dwell) along the rotatory catalytic cycle of ATPase. Furthermore, we have performed microsecond-scale molecular dynamics simulations and free-energy calculations to investigate the conformational transitions between these intermediate states and to probe the long-time dynamics of the molecular motor. Finally in this article, the molecular structure and dynamics of the V1-ATPase are reviewed to bring forth a unified model of the motor’s remarkable rotational mechanism.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7]
+ Show Author Affiliations
  1. Arizona State Univ., Tempe, AZ (United States)
  2. Université de Lorraine, Nancy (France); Univ. of Illinois at Urbana-Champaign, IL (United States)
  3. Yokohama City University (Japan)
  4. Chiba University (Japan)
  5. Yokohama City University (Japan); RIKEN Medical Sciences Innovation Hub Program, Yokohama (Japan)
  6. Chiba University (Japan); Tokyo University of Science (Japan)
  7. Chiba University (Japan); Japan Science and Technology Agency (JST), Chiba (Japan)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH); Ministry of Education, Culture, Sports, Science and Technology (MEXT); Japan Agency for Medical Research and Development (AMED)
OSTI Identifier:
1565788
Grant/Contract Number:  
AC05-00OR22725; 17H03638; 18H05425; 18H05426
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Physiology
Additional Journal Information:
Journal Volume: 10; Journal ID: ISSN 1664-042X
Publisher:
Frontiers Media S.A.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; physiology; rotary motor; V-ATPase; X-ray structure; molecular dynamics; free energy

Citation Formats

Singharoy, Abhishek, Chipot, Chris, Ekimoto, Toru, Suzuki, Kano, Ikeguchi, Mitsunori, Yamato, Ichiro, and Murata, Takeshi. Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses. United States: N. p., 2019. Web. doi:10.3389/fphys.2019.00046.
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Singharoy, Abhishek, Chipot, Chris, Ekimoto, Toru, Suzuki, Kano, Ikeguchi, Mitsunori, Yamato, Ichiro, & Murata, Takeshi. Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses. United States. https://doi.org/10.3389/fphys.2019.00046
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Singharoy, Abhishek, Chipot, Chris, Ekimoto, Toru, Suzuki, Kano, Ikeguchi, Mitsunori, Yamato, Ichiro, and Murata, Takeshi. Tue . "Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses". United States. https://doi.org/10.3389/fphys.2019.00046. https://www.osti.gov/servlets/purl/1565788.
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@article{osti_1565788,
title = {Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses},
author = {Singharoy, Abhishek and Chipot, Chris and Ekimoto, Toru and Suzuki, Kano and Ikeguchi, Mitsunori and Yamato, Ichiro and Murata, Takeshi},
abstractNote = {V1-ATPase exemplifies the ubiquitous rotary motor, in which a central shaft DF complex rotates inside a hexagonally arranged catalytic A3B3 complex, powered by the energy from ATP hydrolysis. We have recently reported a number of crystal structures of the Enterococcus hirae A3B3DF (V1) complex corresponding to its nucleotide-bound intermediate states, namely the forms waiting for ATP hydrolysis (denoted as catalytic dwell), ATP binding (ATP-binding dwell), and ADP release (ADP-release dwell) along the rotatory catalytic cycle of ATPase. Furthermore, we have performed microsecond-scale molecular dynamics simulations and free-energy calculations to investigate the conformational transitions between these intermediate states and to probe the long-time dynamics of the molecular motor. Finally in this article, the molecular structure and dynamics of the V1-ATPase are reviewed to bring forth a unified model of the motor’s remarkable rotational mechanism.},
doi = {10.3389/fphys.2019.00046},
journal = {Frontiers in Physiology},
number = ,
volume = 10,
place = {United States},
year = {Tue Feb 05 00:00:00 EST 2019},
month = {Tue Feb 05 00:00:00 EST 2019}
}
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https://doi.org/10.3389/fphys.2019.00046
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