Mechanism of the Alternating Access in Leut-Fold Na+-Coupled Secondary Transporters: A Computational Transition Path Study

Abstract

Na+-coupled LeuT-fold secondary transporters consist of many essential membrane proteins that utilize the concentration gradient of Na+ to transport solutes across the cell membrane against their concentration gradients. The solutes they transport include many physiologically important molecules such as neurotransmitters (serotonin, dopamine, etc.), sugar molecules, nucleotide bases, etc. Dysfunction of these transporters is implicated in various diseases and syndromes and they are targets of many clinical drugs including antidepressants. Recent progress in crystallographic studies of the LeuT structural family has revealed striking similarities in the structural organization of ion and solute binding, implying some general mechanisms of substrate translocation and transporter conformational changes. This presentation will focus on the transport mechanism of transporters in this structural family, featuring Mhp1, a bacterial homologue of cation nucleotide-base symporters. Three crystal structures of this protein in open-to-out, occluded-out, and open-to-in conformational states have become available recently [1, 2]. The optimal transition path connecting these states is obtained from the “string method with swarm of trajectories” [3]. Potential of Mean Force (PMFs) maps are computed to characterize the path. Free energy simulations reveal the coupling between the co-transported ion and the main substrate and a profile of the dynamical interactions between substrates, ions, and the protein. This computational study will reveal the molecular mechanisms that govern the transporter's conformational changes from open to one face of the membrane to open to the opposite face.[1] Shimamura, T.; Weyand, S.; Beckstein, O.; Rutherford, N.G.; Hadden, J.M.; Sharples, D.; Sansom, M.S.P.; Iwata, S.; Henderson, P.J.F.; Cameron, A.D., Science, 2010, 328, (5977), 470-473.[2] Yamashita, A.; Singh, S.K.; Kawate, T.; Jin, Y.; Gouaux, E., Nature, 2005, 437, (7056), 215-223.[3] Pan, A.C.; Sezer, D.; Roux, B., Journal of Physical Chemistry B, 2008, 112, (11), 3432-3440.