Towards the Simulation of a Complete ATP Synthase: Unravelling the Structural Basis of the Enzyme's Reversible Action

Abstract

The most prominent bioenergetic macromolecuar-motor in all life forms is ATP synthase that transforms an ion gradient existing across the cell membrane into the synthesis of ATP from ADP. Even with a wealth of available biochemical and structural information derived from numerous past and ongoing experiments, the exact mechanism of ATP synthase function remains unknown. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a suite of transition path sampling methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis have been investigated. The simulation suggests ADP unbinding is followed by ATP uptake which, in turn, leads to the torque generation step, i.e., rotation of the center stalk. The trajectory yields multiple intermediates, a couple of which have been isolated in independent crystallography experiments. The simulation further infers, in agreement with single-molecule experiments, that ATP binding is not the torque generation step. Finally, using data from four different high-resolution PDB structures a complete model of ATP synthase has been constructed. An evaluation of the elastic energy stored in the different ATP synthase subunits provides a structural basis for the reversible action of the synthase.