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.

3D-localization of the a -subunit in F 0 F 1 -ATP synthase by time resolved single-molecule FRET

2006 ◽  
Author(s):  
Monika G. Düser ◽  
Nawid Zarrabi ◽  
Yumin Bi ◽  
Boris Zimmermann ◽  
Stanley D. Dunn ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Time Resolved ◽  
Single Molecule Fret ◽  
3D Localization ◽  
A Subunit

scholarly journals Structure of a proton-powered molecular motor that drives protein transport and gliding motility

2020 ◽  
Author(s):  
Rory Hennell James ◽  
Justin C. Deme ◽  
Andreas Kjӕr ◽  
Felicity Alcock ◽  
Augustinas Silale ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Single Molecule ◽  
Protein Transport ◽  
Transmembrane Domain ◽  
Structural Information ◽  
Cell Envelope ◽  
Molecular Motor ◽  
Gliding Motility ◽  
Protonmotive Force ◽  
Inner Membrane

SummaryIon-driven motors are rare in biology. The archetypes of the three classes identified to date are ATP synthase, the bacterial flagellar motor, and a proton-driven motor that powers gliding motility and protein secretion in Bacteroidetes bacteria. Whilst the molecular mechanism of ATP synthase is now well understood, structural information is lacking for the other two classes of motor. Here we present the structure of the Bacteroidetes gliding motility motor determined by cryo-electron microscopy. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM proteins are positioned within a ring of five GldL proteins. Combining mutagenesis and single-molecule tracking, we identify protonatable amino acid residues within the transmembrane domain of the complex that are important for motor function. Our data imply a mechanism in which proton flow leads the periplasm-spanning GldM dimer to rotate with respect to the intra-membrane GldL ring to drive processes at the bacterial outer membrane. This work provides a molecular basis for understanding how the gliding motility motor is able to transduce the energy of the inner membrane protonmotive force across the bacterial cell envelope.

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.

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 Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 Å resolution

2015 ◽  
Vol 112 (43) ◽  
pp. 13231-13236 ◽  
Author(s):  
Edgar Morales-Rios ◽  
Martin G. Montgomery ◽  
Andrew G. W. Leslie ◽  
John E. Walker
Keyword(s):  
Atp Synthase ◽  
Paracoccus Denitrificans ◽  
Release Site ◽  
Membrane Domain ◽  
X Ray ◽  
X Ray Crystallography ◽  
Central Stalk ◽  
C Subunit ◽  
A Subunit ◽  
Α Helix

The structure of the intact ATP synthase from the α-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by X-ray crystallography at 4.0 Å resolution. The ζ-protein is bound via its N-terminal α-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The δ-subunit component of the peripheral stalk binds to the N-terminal regions of two α-subunits. The stalk extends via two parallel long α-helices, one in each of the related b and b′ subunits, down a noncatalytic interface of the F1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F1 domain, and, together, the central stalk and c-ring form the enzyme’s rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four α-helices in the a-subunit that are tilted at ∼30° to the plane of the membrane. Conserved polar residues in the two α-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine.

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

2020 ◽  
Vol 27 (37) ◽  
pp. 6306-6355 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Structural Features ◽  
Protein Protein Interactions ◽  
Modular Architecture ◽  
Post Translational Modifications ◽  
Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

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