scholarly journals Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase

2002 ◽  
Author(s):  
Rainer A. Böckmann ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Energy Transfer ◽  
Molecular Dynamics Simulation ◽  
Atp Synthase ◽  
Mechanical Energy ◽  
Dynamics Simulation

Elucidating Microscopic Events Driven by GTP Hydrolysis Reaction in Ras-GAP System with Semi-reactive Molecular Dynamics Simulation: Alternative Role of Phosphate Binding Loop as Mechanical Energy Storage

2021 ◽  
Author(s):  
Ikuo Kurisaki ◽  
Shigenori Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Energy Storage ◽  
Molecular Dynamics Simulation ◽  
Mechanical Energy ◽  
Dynamics Simulation ◽  
Phosphate Binding ◽  
Gtp Hydrolysis ◽  
Reactive Molecular Dynamics ◽  
Binding Loop

ATPase and GTPase have been widely found as chemical energy-mechanical work transducers, whereas the physicochemical mechanisms are not satisfactorily understood. We addressed the problem by examining John Ross’ conjecture that...

The mechanism of energy transfer in H2O–H2O collisions – a molecular dynamics simulation

1998 ◽  
Vol 236 (1-3) ◽  
pp. 189-205 ◽  
Author(s):  
Harald Svedung ◽  
L.E.B. Börjesson ◽  
Nikola Marković ◽  
Sture Nordholm
Keyword(s):  
Molecular Dynamics ◽  
Energy Transfer ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

scholarly journals Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

2019 ◽  
Author(s):  
Shintaroh Kubo ◽  
Toru Niina ◽  
Shoji Takada
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Proton Transfer ◽  
Atp Synthase ◽  
Atp Hydrolysis ◽  
Atp Synthesis ◽  
Simulation Method ◽  
Proton Pumping ◽  
Dynamics Simulation ◽  
Transduction Efficiency

AbstractThe FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, developing a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reaches ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments.

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