Molecular dynamics simulation of large biological macromolecules have reached the point where they can be used to provide meaningful insight on the function of complex systems. Free energy methodologies are particularly important to establish a strong connection to experiments. This will be illustrated with a few recent examples on (1) Src tyrosine kinases, (2) K+ channels, and the (3) sodium-potassium ATPase pump.

(1) Tyrosine kinases are crucial to cellular signaling that regulates cell growth, proliferation, metabolism, differentiation and migration. Therefore, they are attractive drug targets for curing certain types of cancers. Gleevec, a well-known cancer therapeutic agent, is a potent inhibitor of Abl kinases, but it is not an effective inhibitor of the highly homologous c-Src kinase.  Free energy MD simulations are used to explain why.

(2) Activation of a K+ channel typically leads to a transient period of ion conduction until the selectivity filter spontaneously undergoes a conformational change toward a constricted non-conductive state (inactivation). Subsequent removal of the stimulus closes the gate and allows the selectivity filter to return back to its conductive conformation (recovery). The recovery process can take up to several seconds, an extraordinarily long time. Yet, the structural differences between the conductive and inactivated filter are very small. MD simulations are used to explain the origin of the slow recovery process.

(3) The sodium-potassium (Na/K) pump is an ATPase that generates Na+ and K+ concentration gradients across the cell membrane. For each ATP molecule, the pump extrudes three Na+ and imports two K+ by alternating between outward- and inward-facing conformations that preferentially bind K+ or Na+, respectively. Remarkably, the selective K+ and Na+ binding sites share several residues, and how the pump is able to achieve the selectivity required for the functional cycle is unclear. Free energy MD simulations reveal that protonation of the acidic side-chains involved in the binding sites is critical to achieve the proper K+ selectivity.