Docking and homology modeling explain inhibition of the human vesicular glutamate transporters

• Published in: Protein science Vol. 16; no. 9; pp. 1819 - 1829
• Main Authors: Almqvist, Jonas, Huang, Yafei, Laaksonen, Aatto, Wang, Da‐Neng, Hovmöller, Sven
• Format: Journal Article
• Language: English
• Published: Bristol Cold Spring Harbor Laboratory Press 01-09-2007; Wiley-Blackwell
• Subjects: Amino Acid Sequence; Binding Sites; Computer Simulation; Conserved Sequence; docking; Escherichia coli; Glutamic Acid - metabolism; homology modeling; Humans; inhibitor; membrane protein structure; Models, Molecular; molecular dynamics; Molecular Sequence Data; NATURAL SCIENCES; NATURVETENSKAP; Protein Binding; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Substrate Specificity; Surface Properties; Transport Vesicles - metabolism; Vesicular Glutamate Transport Protein 1 - antagonists & inhibitors; Vesicular Glutamate Transport Protein 1 - chemistry; Vesicular Glutamate Transport Protein 2 - antagonists & inhibitors; Vesicular Glutamate Transport Protein 2 - chemistry; Vesicular Glutamate Transport Proteins - antagonists & inhibitors; Vesicular Glutamate Transport Proteins - chemistry; Vesicular Glutamate Transport Proteins - metabolism; vesicular glutamate transporter; Vesicular Transport Proteins - physiology; docking; homology modeling; inhibitor; membrane protein structure; molecular dynamics; vesicular glutamate transporter
• ISSN: 0961-8368; 1469-896X; 1469-896X
• DOI: 10.1110/ps.072944707

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.