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The hidden energetics of ligand binding and activation in a glutamate receptor

Nature Structural & Molecular Biology volume 18, pages 283–287 (2011)Cite this article

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Abstract

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate most excitatory synaptic transmission in the central nervous system. The free energy of neurotransmitter binding to the ligand-binding domains (LBDs) of iGluRs is converted into useful work to drive receptor activation. We have computed the principal thermodynamic contributions from ligand docking and ligand-induced closure of LBDs for nine ligands of GluA2 using all-atom molecular dynamics free energy simulations. We have validated the results by comparison with experimentally measured apparent affinities to the isolated LBD. Features in the free energy landscapes that govern closure of LBDs are key determinants of binding free energies. An analysis of accessible LBD conformations transposed into the context of an intact GluA2 receptor revealed that the relative displacement of specific diagonal subunits in the tetrameric structure may be key to the action of partial agonists.

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Figure 1: Ligands of GluA2.
Figure 2: LBD conformational distributions.
Figure 3: Comparison of calculated free energy contributions with experimentally measured effective ligand-binding affinities to the isolated GluA2 LBD.
Figure 4: LBD conformational distributions in the context of an intact receptor.
Figure 5: Inter-LBD distance distributions.

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Acknowledgements

We thank E. Gouaux, V. Jayaraman, C. Landes, M. Mayer, R. Oswald and H. Weinstein for review of the manuscript, and W. Gan for discussions. This work was supported by grant MCB-0920261 from the National Science Foundation and grant GM062342 from the US National Institutes of Health. Computational resources were provided by the National Center for Supercomputing Applications (NCSA) through grant MCA01S018.

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  1. Albert Y Lau

    Present address: Present address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,

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  1. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA

    Albert Y Lau & Benoît Roux

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A.Y.L. and B.R. designed the research, analyzed the data and wrote the manuscript. A.Y.L. performed the computations.

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Supplementary Figures 1–5, Supplementary Tables 1–5 and Supplementary Methods (PDF 1074 kb)

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Lau, A., Roux, B. The hidden energetics of ligand binding and activation in a glutamate receptor. Nat Struct Mol Biol 18, 283–287 (2011). https://doi.org/10.1038/nsmb.2010

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