Coarse-grained simulations of proton-dependent conformational changes in lactose permease.

During lactose/H(+) symport, the Escherichia coli lactose permease (LacY) undergoes a series of global conformational transitions between inward-facing (open to cytoplasmic side) and outward-facing (open to periplasmic side) states. However, the exact local interactions and molecular mechanisms dictating those large-scale structural changes are not well understood. All-atom molecular dynamics simulations have been performed to investigate the molecular interactions involved in conformational transitions of LacY, but the simulations can only explore early or partial global structural changes because of the computational limits (< 100 ns). In this work, we implement a hybrid force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the proton-dependent dynamics and conformational changes of LacY. The effects of the protonation states on two key glutamate residues (Glu325 and Glu269) have been studied. Our results on the salt-bridge dynamics agreed with all-atom simulations at early short time period, validating our simulations. From our microsecond simulations, we were able to observe the complete transition from inward-facing to outward-facing conformations of LacY. Our results showed that all helices have participated during the global conformational transitions and helical movements of LacY. The inter-helical distances measured in our simulations were consistent with the double electron-electron resonance experiments at both cytoplasmic and periplasmic sides. Our simulations indicated that the deprotonation of Glu325 induced the opening of the periplasmics side and partial closure of the cytoplasmic side of LacY, while protonation of the Glu269 caused a stable cross-domain salt-bridge (Glu130-Arg344) and completely closed the cytoplasmic side. Proteins 2016; 84:1067-1074.