scholarly journals Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase

2015 ◽  
Vol 112 (34) ◽  
pp. 10720-10725 ◽  
Author(s):  
Kei-ichi Okazaki ◽  
Gerhard Hummer
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Viscoelastic Model ◽  
Thermodynamic Efficiency ◽  
Γ Subunit ◽  
Frictional Dissipation ◽  
Rotary Motors ◽  
Subunit Rotation ◽  
Dynamics Simulations ◽  
Rotary Motor

We combine molecular simulations and mechanical modeling to explore the mechanism of energy conversion in the coupled rotary motors of FoF1-ATP synthase. A torsional viscoelastic model with frictional dissipation quantitatively reproduces the dynamics and energetics seen in atomistic molecular dynamics simulations of torque-driven γ-subunit rotation in the F1-ATPase rotary motor. The torsional elastic coefficients determined from the simulations agree with results from independent single-molecule experiments probing different segments of the γ-subunit, which resolves a long-lasting controversy. At steady rotational speeds of ∼1 kHz corresponding to experimental turnover, the calculated frictional dissipation of less than kBT per rotation is consistent with the high thermodynamic efficiency of the fully reversible motor. Without load, the maximum rotational speed during transitions between dwells is reached at ∼1 MHz. Energetic constraints dictate a unique pathway for the coupled rotations of the Fo and F1 rotary motors in ATP synthase, and explain the need for the finer stepping of the F1 motor in the mammalian system, as seen in recent experiments. Compensating for incommensurate eightfold and threefold rotational symmetries in Fo and F1, respectively, a significant fraction of the external mechanical work is transiently stored as elastic energy in the γ-subunit. The general framework developed here should be applicable to other molecular machines.

PROTEIN MOTOR F1 AS A MODEL SYSTEM FOR FLUCTUATION THEORIES OF NON-EQUILIBRIUM STATISTICAL MECHANICS

2012 ◽  
Vol 11 (03) ◽  
pp. 1241001 ◽  
Author(s):  
KUMIKO HAYASHI ◽  
RYUNOSUKE HAYASHI
Keyword(s):  
Statistical Mechanics ◽  
Single Molecule ◽  
Nonequilibrium Statistical Mechanics ◽  
Model System ◽  
Fluctuation Theorem ◽  
Biological Model ◽  
Equilibrium Statistical Mechanics ◽  
Γ Subunit ◽  
Protein Motor ◽  
Rotary Motor

F1-ATPase (F1) is a rotary motor protein in which the rotor γ subunit rotates in the α3β3 ring hydrolyzing adenosine-5′-triphosphate (ATP). Several fluctuation theories of nonequilibrium statistical mechanics have been applied recently to the single-molecule experiments on F1. For example, the fluctuation theorem, a recent achievement in the field of nonequilibrium statistical mechanics, has been suggested to be useful for measuring the rotary torque of F1. In this paper, we introduce F1 as a good biological model for experimentally testing the theories of nonequilibrium statistical mechanics.

scholarly journals F0-F1 coupling and symmetry mismatch in ATP synthase resolved in every F0 rotation step

2021 ◽  
Author(s):  
Shintaroh Kubo ◽  
Toru Niina ◽  
Shoji Takada
Keyword(s):  
Electron Microscopy ◽  
Atp Synthase ◽  
Energy Production ◽  
Comprehensive Understanding ◽  
Cellular Energy ◽  
Cryo Electron Microscopy ◽  
Rotary Motors ◽  
Elastic Distortion ◽  
Dynamics Simulations ◽  
Symmetric Structures

The F0F1 ATP synthase, essential for cellular energy production, is composed of the F0 and F1 rotary motors. While both F0 and F1 have pseudo-symmetric structures, their symmetries do not match. How the symmetry mismatch is solved remains elusive due to missing intermediate structures of rotational steps. Here, for ATP synthases with 3- and 10-fold symmetries in F1 and F0, respectively, we uncovered the mechanical couplings between F0 and F1 at every 36° rotation step via molecular dynamics simulations and comparison of cryo-electron microscopy structures from three species. We found that the frustration is shared by several elements. The F1 stator partially rotates relative to the F0 stator via elastic distortion of the b-subunits. The rotor can be distorted. The c-ring rotary angles can be deviated from symmetric ones. Additionally, the F1 motor may take non-canonical structures relieving stronger frustration. Together, we provide comprehensive understanding to solve the symmetry mismatch.

scholarly journals Stepwise rotation of the γ-subunit of EF0F1-ATP synthase observed by intramolecular single-molecule fluorescence resonance energy transfer1

FEBS Letters ◽  
2002 ◽  
Vol 527 (1-3) ◽  
pp. 147-152 ◽  
Author(s):  
Michael Börsch ◽  
Manuel Diez ◽  
Boris Zimmermann ◽  
Rolf Reuter ◽  
Peter Gräber
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Resonance Energy ◽  
Single Molecule Fluorescence ◽  
Γ Subunit ◽  
Fluorescence Resonance

scholarly journals Fast ATP-dependent subunit rotation in reconstituted FoF1-ATP synthase trapped in solution

2021 ◽  
Author(s):  
Thomas Heitkamp ◽  
Michael Börsch
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Atp Synthesis ◽  
Electrochemical Potential ◽  
Ensemble Averaging ◽  
Subunit Rotation ◽  
Atp Synthases

ABSTRACTFoF1-ATP synthases are the ubiquitous membrane enzymes which catalyze ATP synthesis or ATP hydrolysis in reverse, respectively. Enzyme kinetics are controlled by internal subunit rotation, by substrate and product concentrations, by mechanical inhibitory mechanisms, but also by the electrochemical potential of protons across the membrane. By utilizing an Anti- Brownian electrokinetic trap (ABEL trap), single-molecule Förster resonance energy transfer (smFRET)-based subunit rotation monitoring was prolonged from milliseconds to seconds. The extended observation times for single proteoliposomes in solution allowed to observe fluctuating rotation rates of individual enzymes and to map the broad distributions of ATP-dependent catalytic rates in FoF1-ATP synthase. The buildup of an electrochemical potential of protons was confirmed to limit the maximum rate of ATP hydrolysis. In the presence of ionophores and uncouplers the fastest subunit rotation speeds measured in single reconstituted FoF1-ATP synthases were 180 full rounds per second, i.e. much faster than measured by biochemical ensemble averaging, but not as fast as the maximum rotational speed reported previously for isolated single F1 fragments without coupling to the membrane-embedded Fo domain of the enzyme.

scholarly journals Spotlighting motors and controls of single FoF1-ATP synthase

2013 ◽  
Vol 41 (5) ◽  
pp. 1219-1226 ◽  
Author(s):  
Michael Börsch ◽  
Thomas M. Duncan
Keyword(s):  
Escherichia Coli ◽  
Atp Synthase ◽  
Single Molecule ◽  
Conformational Changes ◽  
Structural Information ◽  
E Coli ◽  
Single Molecule Fret ◽  
Membrane Enzyme ◽  
Subunit Rotation ◽  
Fof1 Atp Synthase

Subunit rotation is the mechanochemical intermediate for the catalytic activity of the membrane enzyme FoF1-ATP synthase. smFRET (single-molecule FRET) studies have provided insights into the step sizes of the F1 and Fo motors, internal transient elastic energy storage and controls of the motors. To develop and interpret smFRET experiments, atomic structural information is required. The recent F1 structure of the Escherichia coli enzyme with the ϵ-subunit in an inhibitory conformation initiated a study for real-time monitoring of the conformational changes of ϵ. The present mini-review summarizes smFRET rotation experiments and previews new smFRET data on the conformational changes of the CTD (C-terminal domain) of ϵ in the E. coli enzyme.

scholarly journals High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F 1 -ATPase

2013 ◽  
Vol 368 (1611) ◽  
pp. 20120023 ◽  
Author(s):  
Thomas Bilyard ◽  
Mayumi Nakanishi-Matsui ◽  
Bradley C. Steel ◽  
Teuta Pilizota ◽  
Ashley L. Nord ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Molecule ◽  
Room Temperature ◽  
Atp Hydrolysis ◽  
Chemical Processes ◽  
Atp Binding ◽  
Γ Subunit ◽  
Rotary Motor ◽  
Resolution Single

The rotary motor F 1 -ATPase from the thermophilic Bacillus PS3 (TF 1 ) is one of the best-studied of all molecular machines. F 1 -ATPase is the part of the enzyme F 1 F O -ATP synthase that is responsible for generating most of the ATP in living cells. Single-molecule experiments have provided a detailed understanding of how ATP hydrolysis and synthesis are coupled to internal rotation within the motor. In this work, we present evidence that mesophilic F 1 -ATPase from Escherichia coli (EF 1 ) is governed by the same mechanism as TF 1 under laboratory conditions. Using optical microscopy to measure rotation of a variety of marker particles attached to the γ-subunit of single surface-bound EF 1 molecules, we characterized the ATP-binding, catalytic and inhibited states of EF 1 . We also show that the ATP-binding and catalytic states are separated by 35±3°. At room temperature, chemical processes occur faster in EF 1 than in TF 1 , and we present a methodology to compensate for artefacts that occur when the enzymatic rates are comparable to the experimental temporal resolution. Furthermore, we show that the molecule-to-molecule variation observed at high ATP concentration in our single-molecule assays can be accounted for by variation in the orientation of the rotating markers.

scholarly journals Determinants of directionality and efficiency of the ATP synthase Fo motor at atomic resolution

2021 ◽  
Author(s):  
Antoni Marciniak ◽  
Pawel Chodnicki ◽  
Kazi Amirul Hossain ◽  
Joanna Slabonska ◽  
Jacek Czub
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Protein Interactions ◽  
Structural Information ◽  
Mechanical Energy ◽  
Release Site ◽  
Tight Coupling ◽  
A Subunit ◽  
Energy Simulations ◽  
Rotary Motor

Fo subcomplex of ATP synthase is an membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor's directionality naturally arises from the interplay between intra-protein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.

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