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Published online before print July 27, 2007, 10.1110/ps.072944707
Protein Science (2007), 16:1819-1829. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Docking and homology modeling explain inhibition of the human vesicular glutamate transporters

Jonas Almqvist1, Yafei Huang1, Aatto Laaksonen2, Da-Neng Wang3, and Sven Hovmöller1

1 Division of Structural Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
2 Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
3 Kimmel Center for Biology and Medicine of the Skirball Institute, and Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA

(RECEIVED April 12, 2007; FINAL REVISION May 23, 2007; ACCEPTED May 28, 2007)

As membrane transporter proteins, VGLUT1–3 mediate the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. This function is crucial for exocytosis and the role of glutamate as the major excitatory neurotransmitter in the central nervous system. The three transporters, sharing 76% amino acid sequence identity in humans, are highly homologous but differ in regional expression in the brain. Although little is known regarding their three-dimensional structures, hydropathy analysis on these proteins predicts 12 transmembrane segments connected by loops, a topology similar to other members in the major facilitator superfamily, where VGLUT1–3 have been phylogenetically classified. In this work, we present a three-dimensional model for the human VGLUT1 protein based on its distant bacterial homolog in the same superfamily, the glycerol-3-phosphate transporter from Escherichia coli. This structural model, stable during molecular dynamics simulations in phospholipid bilayers solvated by water, reveals amino acid residues that face its pore and are likely to affect substrate translocation. Docking of VGLUT1 substrates to this pore localizes two different binding sites, to which inhibitors also bind with an overall trend in binding affinity that is in agreement with previously published experimental data.

Keywords: vesicular glutamate transporter; homology modeling; membrane protein structure; inhibitor; docking; molecular dynamics


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