Exploration of Na⁺,K⁺-ATPase ion permeation pathways via molecular dynamic simulation and electrostatic analysis

Abstract

Biologically-inspired nanodevices can serve as “natural” alternatives to conventional semiconductor devices in many applications from information storage to mechanical rotors. In this work we consider an ATP-powered transmembrane protein, the Na⁺,K⁺-ATPase, which has appealing functionality but still lacks an “atomistic” picture capable of elucidating its operation. The vast collection of experimental literature on the Na⁺,K⁺-ATPase gives a unique advantage to this protein in developing and validating computational tools. We have performed extensive molecular dynamic simulations of the Na⁺,K⁺-ATPase in an accurate biological environment, followed by time-averaged electrostatic analysis, to investigate the ion-binding loci and access/egress pathways that cations may take through the protein as they are transported across the membrane.