TY - JOUR
T1 - Chemomechanical coupling in hexameric protein-protein interfaces harnesses energy within V-type ATPases
AU - Singharoy, Abhishek
AU - Chipot, Christophe
AU - Moradi, Mahmoud
AU - Schulten, Klaus
N1 - Funding Information:
The present contribution is dedicated to Klaus Schulten (1947-2016), who, in the course of his scientific career, pursued the dream of deciphering by means of large-scale simulations the molecular mechanisms that underlie energy transduction in molecular motors of living organisms. The research reported has been supported by the National Institute of Health through Grants 9P41GM104601 and RO1-GM067887-11 and the National Science Foundation through Grants MCB1616590 and PHY1430124. The authors also acknowledge supercomputer time on Stampede provided by the Texas Advanced Computing Center (TACC) at the University of Texas at Austin through Extreme Science and Engineering Discovery Environment (XSEDE) Grants XSEDE MCA93S028. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-000R22725. AS. is grateful for financial support from the Beckman Foundation and NSF through the Center for Physics of Living Cells.
Publisher Copyright:
© 2016 American Chemical Society.
PY - 2017/1/11
Y1 - 2017/1/11
N2 - ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein-protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.
AB - ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein-protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.
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U2 - 10.1021/jacs.6b10744
DO - 10.1021/jacs.6b10744
M3 - Article
C2 - 27936329
AN - SCOPUS:85016153728
SN - 0002-7863
VL - 139
SP - 293
EP - 310
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
IS - 1
ER -