Identifying Conformational Changes of Membrane Transporter MHP1 By Molecular Dynamics Simulations

All-atom Molecular Dynamics (MD) simulation provides insight into individual atomic motions to predict the detail of the structural changes caused by the forward and backward conformational transitions. In this study, we implemented Umbrella Sampling (US) to characterize the conformational changes between both ligand-free outward-facing open and outward-facing occluded state of Mhp1. Mhp1 is a secondary active membrane transport protein that exploits sodium and obtains the potential energy to transport molecules across the membrane. The Mhp1 structure is formed by 14 Transmembrane-Spanning Helices (TMHs). The loop between TMHs 9 and 10 is extended enough to partially seal the substrate-site from the exterior to close the outward-facing cavity. Sequentially, choosing the Ψ dihedral angle of the residues on the loop region as the reaction coordinate of the US simulation, we measured the free energy difference between the open and occluded state of the Mhp1 protein. Our result shows that the free energy change is △G = 5.7±0.5 K_bT. We conclude that the transition pathway of the short helix TMH-10 along with the loop determines a consistent and reversible pathway for the conformational changes of outward-facing open and outward-facing occluded state of the ligand-free Mhp1 protein.