Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT

PLoS Comput Biol. 2014 Dec 18;10(12):e1004017. doi: 10.1371/journal.pcbi.1004017. eCollection 2014 Dec.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Galactose / chemistry*
  • Galactose / metabolism*
  • Kinetics
  • Molecular Dynamics Simulation
  • Sodium / chemistry
  • Sodium / metabolism
  • Sodium-Glucose Transport Proteins / chemistry*
  • Sodium-Glucose Transport Proteins / metabolism*
  • Thermodynamics

Substances

  • Sodium-Glucose Transport Proteins
  • Sodium
  • Galactose

Grants and funding

We acknowledge the CINECA award N. HP10A1YTXK and N. HP10APNMLX for the availability of high performance computing resources and support (http://www.hpc.cineca.it/services/iscra). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.