TCB Publications - Abstract

Ulrich Kleinekathoefer, Barry Isralewitz, Markus Dittrich, and Klaus Schulten. Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations. Journal of Physical Chemistry, 115:7267-7274, 2011. (PMC: 3121902)

KLEI2011 F$_1$-ATPase is the catalytic domain of F$_1$F$_{\rm o}$-ATP synthase and consists of an hexameric arrangement of three non-catalytic $\alpha$ and three catalytic $\beta$ subunits. We have used molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic equilibrium properties of isolated $\beta$-subunits as a step toward explaining the function of the integral F$_1$ unit. To this end, we equilibrated the open ($\beta_E$) and the closed ($\beta_{TP}$) conformations 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 neighbouring $\alpha$ 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 timescale of a few tens of nanoseconds.

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