Paper Citing NAMD - Abstract
Kleinekathoefer, Ulrich; Isralewitz, Barry; Dittrich, Markus; Schulten, Klaus
Domain Motion of Individual F-1-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7267-7274, JUN 30 2011
F-1-ATPase is the catalytic domain of F1F0-ATP synthase and consists of a hexameric arrangement of three noncatalytic alpha and three catalytic beta subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated beta-subunits as a step toward explaining the function of the integral F-1 unit. To this end, we simulated the open (beta(E)) and the closed (beta(Tp)) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free beta(E) retains its open configuration over the course of the simulations. The same is true when the neighboring alpha subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated beta(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 beta-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.
