Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT

Biophys J. 2012 Sep 5;103(5):878-88. doi: 10.1016/j.bpj.2012.07.044.


Neurotransmitter:sodium symporter (NSS) proteins are secondary Na(+)-driven active transporters that terminate neurotransmission by substrate uptake. Despite the availability of high-resolution crystal structures of a bacterial homolog of NSSs-Leucine Transporter (LeuT)-and extensive computational and experimental structure-function studies, unanswered questions remain regarding the transport mechanisms. We used microsecond atomistic molecular-dynamics (MD) simulations and free-energy computations to reveal ion-controlled conformational dynamics of LeuT in relation to binding affinity and selectivity of the more extracellularly positioned Na(+) binding site (Na1 site). In the course of MD simulations starting from the occluded state with bound Na(+), but in the absence of substrate, we find a spontaneous transition of the extracellular vestibule of LeuT into an outward-open conformation. The outward opening is enhanced by the absence of Na1 and modulated by the protonation state of the Na1-associated Glu-290. Consistently, the Na(+) affinity for the Na1 site is inversely correlated with the extent of outward-open character and is lower than in the occluded state with bound substrate; however, the Na1 site retains its selectivity for Na(+) over K(+) in such conformational transitions. To the best of our knowledge, our findings shed new light on the Na(+)-driven transport cycle and on the symmetry in structural rearrangements for outward- and inward-open transitions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Extracellular Space / metabolism
  • Molecular Dynamics Simulation*
  • Plasma Membrane Neurotransmitter Transport Proteins / chemistry*
  • Plasma Membrane Neurotransmitter Transport Proteins / metabolism*
  • Protein Conformation / drug effects
  • Sodium / metabolism
  • Sodium / pharmacology*
  • Thermodynamics


  • Plasma Membrane Neurotransmitter Transport Proteins
  • Sodium