Exploring the State of the F₁-ATPase after ATP Binding and before ADP Release: Effects of Conformational Changes on Phosphate Displacement

Abstract

Single-molecule imaging experiments provide information that is not available from ensemble experiments. We are interested in the interpretation of dynamical studies imaging and manipulation in F₁-ATPase single-molecules. One key question that has arisen in single molecule stalling experiments is the erratic behavior a rotor angle of 55° between the binding and hydrolysis dwell angles of 0 and 80°, respectively. In our previous theoretical work, we used the elastic property of the rotor-stator structure to treat the experiments on controlled rotation. Our modeling suggests that there has to be a change in the bonding network, for example, of hydrogen bonds, as the system transitions between the two dwell points, perhaps at 55°, as indicated by an unusual stalling behavior around that angle. Therefore, in order to get further insights on these events, we have performed full-atomistic molecular dynamics (MD) simulations on the F₁-ATPase to explore the relationship between the conformational changes and the phosphate displacement. The pK_a values for phosphoric acid are 2.2, 7.2, and 12.3; although the effective pK_a for H₂PO₄⁻ within the binding site could be different. Hence, both protonation states (i.e., H₂PO₄⁻ and HPO₄²⁻) were assessed, performing molecular dynamics for 650 ns at 298.15K (Nose-Hoover thermostat) using the CHARMM36 force field. After the analysis of five MD trajectories, we found that the displacement of the phosphate was, to some extent, correlated with the dynamics of the protein. Moreover, one of the MD trajectories led to the complete release of the diprotic phosphate.