title: Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations.
abstract: F(1)-ATPase is the catalytic domain of F(1)F(o)-ATP synthase and consists of a hexameric arrangement of three noncatalytic α and three catalytic β subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated β-subunits as a step toward explaining the function of the integral F(1) unit. To this end, we simulated the open (β(E)) and the closed (β(TP)) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free β(E) retains its open configuration over the course of the simulations. The same is true when the neighboring α subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated β(TP) subunits show a significant trend toward the open conformation during our simulations, with one trajectory per case opening completely. Hence, our simulations suggest that the equilibrium conformation of a nucleotide-free β-subunit is the open conformation and that the transition from the closed to the open conformation can occur on a time scale of a few tens of nanoseconds.
authors: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany. u.kleinekathoefer@jacobs-university.de
authors: Ulrich
authors: U
authors: Kleinekathöfer
authors: Barry
authors: B
authors: Isralewitz
authors: Markus
authors: M
authors: Dittrich
authors: Klaus
authors: K
authors: Schulten
mesh_terms: D000409:Alanine / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D020134:Catalytic Domain; D002417:Cattle; D018360:Crystallography, X-Ray; D005998:Glycine / Q000737:chemistry / Q000378:metabolism; D008928:Mitochondria / Q000201:enzymology; D056004:Molecular Dynamics Simulation; D009038:Motion; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry* / Q000378:metabolism; D006180:Proton-Translocating ATPases / Q000737:chemistry* / Q000378:metabolism; D013997:Time Factors
chemical_list: D021122:Protein Subunits; D006180:Proton-Translocating ATPases; D000409:Alanine; D005998:Glycine