Transporting Mechanisms of Sodium-Dependent Secondary Membrane Transporters: Insights form Computational Simulations

Recent progress in crystallographic studies of sodium-coupled secondary transporters has revealed striking similarities in the structural organization of ion and solute binding motifs and a well-conserved inverted-repeat topology between proteins from several gene families. Molecular Dynamics and free energy simulations are applied to study the mechanisms of selective binding of ion and substrate in LeuT, vSGLT, and Mhp1. We found that water molecules accessed from periplasm and cytoplasm to the binding sites play an important role in affinity and selectivity of the ion/substrate binding. String method is applied to study the transition from outward-facing state to inward-facing state, providing a minimal-free energy pathway of the transition. These studies identify the sequence of ion and substrate binding/releasing associated with the transporting cycle and provide microscopic mechanical mechanisms of gating.