title: Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations.
abstract: Rotary ATPases are involved in numerous physiological processes, with the three distinct types (F/A/V-ATPases) sharing functional properties and structural features. The basic mechanism involves the counter rotation of two motors, a soluble ATP hydrolyzing/synthesizing domain and a membrane-embedded ion pump connected through a central rotor axle and a stator complex. Within the A/V-ATPase family conformational flexibility of the EG stators has been shown to accommodate catalytic cycling and is considered to be important to function. For the A-ATPase three EG structures have been reported, thought to represent conformational states of the stator during different stages of rotary catalysis. Here we use long, detailed atomistic simulations to show that those structures are conformers explored through thermal fluctuations, but do not represent highly populated states of the EG stator in solution. We show that the coiled coil tail domain has a high persistence length (∼100 nm), but retains the ability to adapt to different conformational states through the presence of two hinge regions. Moreover, the stator network of the related V-ATPase has been suggested to adapt to subunit interactions in the collar region in addition to the nucleotide occupancy of the catalytic domain. The MD simulations reported here, reinforce this observation showing that the EG stators have enough flexibility to adapt to significantly different structural re-arrangements and accommodate structural changes in the catalytic domain whilst resisting the large torque generated by catalytic cycling. These results are important to understand the role the stators play in the rotary-ATPase mechanism. Proteins 2016; 84:1203-1212. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.|School of Molecular and Cellular Biology, University of Leeds, Leeds, England.
authors.forename: Kostas
authors.initials: K
authors.lastname: Papachristos
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.|School of Biomedical Sciences, University of Leeds, Leeds, England.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Muench
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.|School of Molecular and Cellular Biology, University of Leeds, Leeds, England.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D025243:Bacterial Proton-Translocating ATPases / Q000737:chemistry*; D055162:Biocatalysis; D020134:Catalytic Domain; D025261:Mitochondrial Proton-Translocating ATPases / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry*; D012399:Rotation; D016963:Thermus thermophilus / Q000737:chemistry* / Q000201:enzymology; D025262:Vacuolar Proton-Translocating ATPases / Q000737:chemistry*
chemical_list: D021122:Protein Subunits; D000255:Adenosine Triphosphate; D025243:Bacterial Proton-Translocating ATPases; D025262:Vacuolar Proton-Translocating ATPases; D025261:Mitochondrial Proton-Translocating ATPases
keywords: molecular dynamics; protein mechanics; rotary ATPases