title: Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT.
abstract: Sodium-Galactose Transporter (SGLT) is a secondary active symporter which accumulates sugars into cells by using the electrochemical gradient of Na+ across the membrane. Previous computational studies provided insights into the release process of the two ligands (galactose and sodium ion) into the cytoplasm from the inward-facing conformation of Vibrio parahaemolyticus sodium/galactose transporter (vSGLT). Several aspects of the transport mechanism of this symporter remain to be clarified: (i) a detailed kinetic and thermodynamic characterization of the exit path of the two ligands is still lacking; (ii) contradictory conclusions have been drawn concerning the gating role of Y263; (iii) the role of Na+ in modulating the release path of galactose is not clear. In this work, we use bias-exchange metadynamics simulations to characterize the free energy profile of the galactose and Na+ release processes toward the intracellular side. Surprisingly, we find that the exit of Na+ and galactose is non-concerted as the cooperativity between the two ligands is associated to a transition that is not rate limiting. The dissociation barriers are of the order of 11-12 kcal/mol for both the ion and the substrate, in line with kinetic information concerning this type of transporters. On the basis of these results we propose a branched six-state alternating access mechanism, which may be shared also by other members of the LeuT-fold transporters.
authors.affiliation: SISSA, Trieste, Italy.
authors.forename: Ina
authors.initials: I
authors.lastname: Bisha
authors.affiliation: SISSA, Trieste, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: SISSA, Trieste, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Laio
authors.affiliation: CNR-IOM-Democritos National Simulation Center, SISSA, Trieste, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Magistrato
mesh_terms: D005690:Galactose / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D012964:Sodium / Q000737:chemistry / Q000378:metabolism; D051247:Sodium-Glucose Transport Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D051247:Sodium-Glucose Transport Proteins; D012964:Sodium; D005690:Galactose