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Coupling of receptor conformation and ligand orientation determine graded activity

Nature Chemical Biology volume 6, pages 837–843 (2010)Cite this article

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Abstract

Small molecules stabilize specific protein conformations from a larger ensemble, enabling molecular switches that control diverse cellular functions. We show here that the converse also holds true: the conformational state of the estrogen receptor can direct distinct orientations of the bound ligand. 'Gain-of-allostery' mutations that mimic the effects of ligand in driving protein conformation allowed crystallization of the partial agonist ligand WAY-169916 with both the canonical active and inactive conformations of the estrogen receptor. The intermediate transcriptional activity induced by WAY-169916 is associated with the ligand binding differently to the active and inactive conformations of the receptor. Analyses of a series of chemical derivatives demonstrated that altering the ensemble of ligand binding orientations changes signaling output. The coupling of different ligand binding orientations to distinct active and inactive protein conformations defines a new mechanism for titrating allosteric signaling activity.

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Figure 1: An energy landscape model of ligand binding.
Figure 2: WAY-169916 is an ERα-partial agonist.
Figure 3: The structure of WAY-169916 bound to the active conformation of ERα.
Figure 4: An unconstrained inactive conformation of ERα shows two nonoverlapping orientations of WAY-169916.
Figure 5: Protein substates define a pathway of ligand dynamics.
Figure 6: Activity profiles of WAY-169916 derivatives.
Figure 7: Ligand binding ensembles direct ERα activity profiles.

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Acknowledgements

This work was supported by the US National Institutes of Health PHS R37 DK15556 (J.A.K.), DK53002 (C.L.S.), CA132022 and DK077085 (K.W.N.) and the Frenchman's Creek Women for Cancer Research (G.G.). We would like to thank J. Cleveland for comments on the manuscript, L. Potterton and S. McNicholas (University of York) for help with CCP4MG and K. Carlson (University of Illinois) for performing the ERα ligand-binding assays.

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  1. John B Bruning and Alexander A Parent: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA.,

    John B Bruning, German Gil, Min Zhao, Jason Nowak & Kendall W Nettles

  2. Department of Chemistry, University of Illinois, Urbana, Illinois, USA

    Alexander A Parent & John A Katzenellenbogen

  3. Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA

    Margaret C Pace & Carolyn L Smith

  4. Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Pavel V Afonine & Paul D Adams

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Contributions

A.A.P. synthesized compounds, G.G. and M.C.P. performed cell-based assays, J.B.B., A.A.P., M.Z., J.N. and P.V.A. performed X-ray crystallography and data analysis, A.A.P., J.B.B., C.L.S., P.D.A., J.A.K. and K.W.N. designed and supervised experiments, and K.W.N. wrote the manuscript with input from all the authors.

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Correspondence to Kendall W Nettles.

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Bruning, J., Parent, A., Gil, G. et al. Coupling of receptor conformation and ligand orientation determine graded activity. Nat Chem Biol 6, 837–843 (2010). https://doi.org/10.1038/nchembio.451

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