Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism

  1. J Robert Lane  Is a corresponding author
  2. Ara M Abramyan
  3. Pramisha Adhikari
  4. Alastair C Keen
  5. Kuo-Hao Lee
  6. Julie Sanchez
  7. Ravi Kumar Verma
  8. Herman D Lim
  9. Hideaki Yano
  10. Jonathan A Javitch  Is a corresponding author
  11. Lei Shi  Is a corresponding author
  1. University of Nottingham, United Kingdom
  2. National Institute on Drug Abuse, National Institutes of Health, United States
  3. Monash University, Australia
  4. Columbia University, United States

Abstract

By analyzing and simulating inactive conformations of the highly-homologous dopamine D2 and D3 receptors (D2R and D3R), we find that eticlopride binds D2R in a pose very similar to that in the D3R/eticlopride structure but incompatible with the D2R/risperidone structure. In addition, risperidone occupies a sub-pocket near the Na+ binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na+-sensitive eticlopride and Na+-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the D2R/risperidone structure to an extended conformation similar to that in the D3R/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of D2R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. J Robert Lane

    Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
    For correspondence
    Rob.Lane@nottingham.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  2. Ara M Abramyan

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Pramisha Adhikari

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Alastair C Keen

    Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Kuo-Hao Lee

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Julie Sanchez

    Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Ravi Kumar Verma

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Herman D Lim

    Department of Pharmacology and Medicinal Chemistry, Monash University, Parkville, Australia
    Competing interests
    The authors declare that no competing interests exist.
  9. Hideaki Yano

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Jonathan A Javitch

    Department of Psychiatry, Columbia University, New York, United States
    For correspondence
    jaj2@cumc.columbia.edu
    Competing interests
    The authors declare that no competing interests exist.
  11. Lei Shi

    Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
    For correspondence
    lei.shi2@nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4137-096X

Funding

National Institutes of Health (Z1A DA000606-03)

  • Lei Shi

National Institutes of Health (MH54137)

  • Jonathan A Javitch

National Health and Medical Research Council (APP1049564)

  • J Robert Lane

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Yibing Shan, DE Shaw Research, United States

Publication history

  1. Received: September 25, 2019
  2. Accepted: January 24, 2020
  3. Accepted Manuscript published: January 27, 2020 (version 1)
  4. Version of Record published: March 3, 2020 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 1,923
    Page views
  • 326
    Downloads
  • 21
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. J Robert Lane
  2. Ara M Abramyan
  3. Pramisha Adhikari
  4. Alastair C Keen
  5. Kuo-Hao Lee
  6. Julie Sanchez
  7. Ravi Kumar Verma
  8. Herman D Lim
  9. Hideaki Yano
  10. Jonathan A Javitch
  11. Lei Shi
(2020)
Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism
eLife 9:e52189.
https://doi.org/10.7554/eLife.52189

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Dario Segura-Peña, Oda Hovet ... Nikolina Sekulic
    Research Article Updated

    Aurora B, together with IN-box, the C-terminal part of INCENP, forms an enzymatic complex that ensures faithful cell division. The [Aurora B/IN-box] complex is activated by autophosphorylation in the Aurora B activation loop and in IN-box, but it is not clear how these phosphorylations activate the enzyme. We used a combination of experimental and computational studies to investigate the effects of phosphorylation on the molecular dynamics and structure of [Aurora B/IN-box]. In addition, we generated partially phosphorylated intermediates to analyze the contribution of each phosphorylation independently. We found that the dynamics of Aurora and IN-box are interconnected, and IN-box plays both positive and negative regulatory roles depending on the phosphorylation status of the enzyme complex. Phosphorylation in the activation loop of Aurora B occurs intramolecularly and prepares the enzyme complex for activation, but two phosphorylated sites are synergistically responsible for full enzyme activity.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Maura Greiser, Mariusz Karbowski ... Liron Boyman
    Research Article

    Mitochondrial ATP production in cardiac ventricular myocytes must be continually adjusted to rapidly replenish the ATP consumed by the working heart. Two systems are known to be critical in this regulation: mitochondrial matrix Ca2+ ([Ca2+]m) and blood flow that is tuned by local ventricular myocyte metabolic signaling. However, these two regulatory systems do not fully account for the physiological range of ATP consumption observed. We report here on the identity, location, and signaling cascade of a third regulatory system -- CO2/bicarbonate. CO2 is generated in the mitochondrial matrix as a metabolic waste product of the oxidation of nutrients that powers ATP production. It is a lipid soluble gas that rapidly permeates the inner mitochondrial membrane (IMM) and produces bicarbonate (HCO3-) in a reaction accelerated by carbonic anhydrase (CA). The bicarbonate level is tracked physiologically by a bicarbonate-activated adenylyl cyclase, soluble adenylyl cyclase (sAC). Using structural Airyscan super-resolution imaging and functional measurements we find that sAC is primarily inside the mitochondria of ventricular myocytes where it generates cAMP when activated by HCO3-. Our data strongly suggest that ATP production in these mitochondria is regulated by this cAMP signaling cascade operating within the inter-membrane space (IMS) by activating local EPAC1 (Exchange Protein directly Activated by cAMP) which turns on Rap1 (Ras-related protein 1). Thus, mitochondrial ATP production is shown to be increased by bicarbonate-triggered sAC signaling through Rap1. Additional evidence is presented indicating that the cAMP signaling itself does not occur directly in the matrix. We also show that this third signaling process involving bicarbonate and sAC activates the cardiac mitochondrial ATP production machinery by working independently of, yet in conjunction with, [Ca2+]m-dependent ATP production to meet the energy needs of cellular activity in both health and disease. We propose that the bicarbonate and calcium signaling arms function in a resonant or complementary manner to match mitochondrial ATP production to the full range of energy consumption in cardiac ventricular myocytes in health and disease.