The mechanism of sodium and substrate release from the binding pocket of vSGLT

Abstract

Membrane co-transport proteins that use a five-helix inverted repeat motif have recently emerged as one of the largest structural classes of secondary active transporters1,2. However, despite many structural advances there is no clear evidence of how ion and substrate transport are coupled. Here we report a comprehensive study of the sodium/galactose transporter from Vibrio parahaemolyticus (vSGLT), consisting of molecular dynamics simulations, biochemical characterization and a new crystal structure of the inward-open conformation at a resolution of 2.7 Å. Our data show that sodium exit causes a reorientation of transmembrane helix 1 that opens an inner gate required for substrate exit, and also triggers minor rigid-body movements in two sets of transmembrane helical bundles. This cascade of events, initiated by sodium release, ensures proper timing of ion and substrate release. Once set in motion, these molecular changes weaken substrate binding to the transporter and allow galactose readily to enter the intracellular space. Additionally, we identify an allosteric pathway between the sodium-binding sites, the unwound portion of transmembrane helix 1 and the substrate-binding site that is essential in the coupling of co-transport.

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Figure 1: Structures and overlay of the inward-open and inward-occluded conformations.
Figure 2: Mechanism of galactose release.
Figure 3: The potential of mean force for galactose unbinding.
Figure 4: Conformational changes in the transition from the inward-occluded to the inward-open structure.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors of the inward-open vSGLT structure have been deposited in the Protein Data Bank under accession number 2XQ2.

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Acknowledgements

We thank T. Vondriska and K. Philipson as well as members of the Abramson, Wright and Grabe labs for useful discussions and for reading the manuscript. We would also like to thank S. Faham for contributions at the early stages of this work, S. Iwata for advance release of the Mhp1 coordinates (Protein Data Bank ID, 2X79), and R. Roskies for assistance with the computations. Simulations were carried out through a TeraGrid grant at the Pittsburgh Supercomputing Center and the Texas Advanced Computing Center. This work was supported by NIH grants GM078844 (J.A.), RGY0069 (J.A.) and DK19567 (E.M.W.), and a grant from the Human Frontier Science Program (J.A.). M.G. is an Alfred P. Sloan Research Fellow.

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Experiments were carried out and diffraction data collected by A.W., V.C. and J.A. Simulations were carried out by S.C. Data were analysed and the manuscript was prepared by all authors.

Corresponding authors

Correspondence to Michael Grabe or Jeff Abramson.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-6 with legends, Supplementary Table 1 and a legend for Supplementary Movie 1. (PDF 2560 kb)

41586_2010_BFnature09580_MOESM295_ESM.mov

This movie shows a 200 ns unrestrained MD simulation of galactose exiting from the sodium glucose transporter from Vibrio parahaemolyticus (see Supplementary Information file for full legend. (MOV 7132 kb)

Supplementary Movie 1

This movie shows a 200 ns unrestrained MD simulation of galactose exiting from the sodium glucose transporter from Vibrio parahaemolyticus (see Supplementary Information file for full legend. (MOV 7132 kb)

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Watanabe, A., Choe, S., Chaptal, V. et al. The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature 468, 988–991 (2010). https://doi.org/10.1038/nature09580

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