Quantitative Simulations of Alternating Access in Sodium-Solute Symporters

Abstract

Sodium-solute symporters (SSS) exploit the sodium ion concentration gradients to transports solute across the plasma membrane. Through a series of conformational changes, collectively described as alternating access, transporters expose their substrate cavity from one side to the other of the membrane, and eventually release their cargo. How substrates and energizing ions coordinate to drive this processes remains elusive and is likely very different from one structural family to the next. I will use the Weighted Ensemble enhanced sampling technique together with a novel progress coordinate based on structural similarity to simulate alternating access of the bacterial sodium galactose transporter (vSGLT) starting from the apo and sugar bound inward-facing states using the outward-facing structure of the closely related sialic acid transporter (SiaT) as a target. Thanks to these two structures we can explore the biophysics of the transport cycle at the atomic level to answer to the following questions: 1) what is the order of binding?, and 2) how does sodium and substrate coupling drive conformational change? It is very likely that information gained through these studies will shed light on the transport cycle of mammalian homologues (hSGLT1/2) and other members in the Leucine Transporter superfamily.