Na+/K+-ATPase Pumping Mechanism: Insights from Simulations

Abstract

The Na+/K+-ATPase resides in the plasma membrane and maintains the physiological K+ and Na+ concentration gradient across the cell membrane. It functions via a ping-pong mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. The E1 conformation binds three Na+ from the cytosol and exports them using the energy from ATP hydrolysis. The release of Na+ and the binding of K+ at the extracellular side trigger the structural transition to the E2(K2) state, which imports two K+, followed by the pump returning to the E1 conformation. Although the broad features of the pumping cycle are known, the transition mechanisms between the conformational states and why a given state preferentially binds K+ or Na+, two monovalent cations of very similar radius, is not understood. Starting from the available x-ray structures of the Na+/K+-ATPase and the SERCA Ca2+-pump, we use anisotropic network model pathway calculations and targeted molecular dynamics simulations to generate atomic models of the outward facing Na+/K+-ATPase, Na3E2-P and K2E2-P. Qualitative support of the models comes from a recent Na+/K+-ATPase x-ray structure and previous mutagenesis data. In addition to this, the gating charge and dissociation constants of the extracellular Na+/K+ binding calculated using the models are in excellent agreement with experimental data as well. The model generation process also produces the occlusion/de-occlusion transition pathways upon ion binding. To study the change in ion selectivity during the occlusion/de-occlusion process, free energy perturbation calculations are performed. The results reveal the molecular determinants of the 3Na-2K stoichiometry of the Na+/K+-ATPase.