Toward understanding membrane channels
Membrane channels play key roles in all living cells. Owing to recent advances in protein crystallography, atomic-resolution structures for a representative set of membrane channels have become available. Transport of materials through these channels, however, is a dynamic process and cannot be fully understood from static structural information alone. Molecular dynamics simulations are in a unique position to describe the dynamics of channel transport in the cases in which the structures of channel proteins are known. However, simulation of channel permeability and gating in the native environment of lipid bilayer and water involves large systems with 100,000 - 300,000 atoms.
This review article focuses on four case studies that demonstrate the power of molecular dynamics simulations in unraveling the mechanisms underlying the function of membrane channels. Simulations of AQP water channels present a prime example of the effectiveness and usefulness of molecular dynamics in simulating conduction and explaining selectivity. A detailed energetic analysis of ion permeation through chloride channels proposes a two- ion permeation mechanism that reconciles naturally structural and physiological data. The study of ion and water permeation through hemolysin exemplifies how accurately one can simulate today even very large membrane channel systems. Finally, the study of mechanical gating of MscS shows that molecular dynamics can account even for complex gating motions of channels.