Conformational Space and Dynamics of Sodium-Coupled Symporters

Abstract

Secondary transporters utilize the free energy stored in the sodium gradient to move a solute against a concentration gradient. The transport process involves a sequence of conformational changes that exposes the substrate and ion binding sites alternatively to the extracellular and the intracellular compartment. At least three conformational states are required for this “alternating access model”: An outward facing open state, connecting ion and substrate binding site to the outside; an occluded state where ion and substrate are buried inside the protein; and an inward facing open state that allows egress of substrate into the cytosol. We recently published a study of these three crystallographically defined states in the prokaryotic nucleobase:sodium symporter Mhp1 [1], which has a similar fold to many other transporters such as LeuT, vSGLT or BetB. We showed that alternating access can be understood as a sequence of multiple gating events. Here we present long, micro-second molecular dynamics simulations that further explore the conformational space available to the gating elements. They reveal that the two “thin gates”, formed by the ends of helices TM5 and TM10 move on the 100 ns time scale. The state of the thin gates is coupled to the “thick gate” (formed by a 30 degree rotation of the “hash” domain relative to the “bundle”). The extracellular thin gate can only open if the thick gate is in the outward facing conformation, a synchronization necessary for the alternating access model. The protein also transitions spontaneously into a fourth “inward-facing occluded” state. Comparison to simulations of LeuT and vSGLT indicates that the gating elements in those transporters can function in similar manner to Mhp1. Our results suggest a structural model of the transport cycle in sodium-coupled symporters.[1] T. Shimamura et al., Science, 328 (2010) 470-473.