Modeling of Binding Sites and Electrostatics in the Ion-Motive Sodium Pump

The present work establishes a unique framework for the simulation study of ion-motive pumps in general and the Na⁺/K⁺-ATPase, or sodium pump, in particular. We shall discuss the implications of electrostatic analysis, valence calculations, and protein cavity data, each coupled with molecular dynamics simulations on the structure-function relationship of Na⁺/K⁺-ATPase. These approaches will be used to investigate atomic-level characteristics that remain undetermined such as ion binding and accessibility.