Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling

  1. Oliver Fleetwood
  2. Jens Carlsson
  3. Lucie Delemotte  Is a corresponding author
  1. KTH Royal Institute of Technology, Sweden
  2. Uppsala University, Sweden

Abstract

Ligand binding stabilizes different G protein-coupled receptor states via a complex allosteric process that is not completely understood. Here, we have derived free energy landscapes describing activation of the β2 adrenergic receptor bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics (MD) simulations. These reveal shifts towards active-like states at the G protein binding site for receptors bound to partial and full agonists and that the ligands modulate the conformational ensemble of the receptor by tuning protein microswitches. We indeed find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cAMP signaling responses. Dimensionality reduction further reveals the similarity between the unique conformational states induced by different ligands and examining the output of classifiers highlights two distant hotspots governing agonism on transmembrane helices 5 and 7.

Data availability

The data necessary to reproduce the findings presented in this paper can be found on OSF (DOI 10.17605/OSF.IO/B5RAV). The code used to run and analyze simulations has been deposited on GitHub (https://github.com/delemottelab/demystifying, https://github.com/delemottelab/gpcr-string-method-2019 and https://github.com/delemottelab/state-sampling).

The following previously published data sets were used

Article and author information

Author details

  1. Oliver Fleetwood

    Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4277-2661
  2. Jens Carlsson

    Uppsala University, Uppsala, Sweden
    Competing interests
    No competing interests declared.
  3. Lucie Delemotte

    Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
    For correspondence
    lucie.delemotte@scilifelab.se
    Competing interests
    Lucie Delemotte, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0828-3899

Funding

Göran Gustafssons Stiftelse

  • Jens Carlsson
  • Lucie Delemotte

Science for Life Laboratory

  • Jens Carlsson
  • Lucie Delemotte

Vetenskapsrådet (2017-4676)

  • Jens Carlsson

Swedish strategic research program eSSENCE

  • Jens Carlsson

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

Reviewing Editor

  1. Toby W Allen, RMIT University, Australia

Version history

  1. Received: July 3, 2020
  2. Accepted: January 27, 2021
  3. Accepted Manuscript published: January 28, 2021 (version 1)
  4. Version of Record published: February 16, 2021 (version 2)
  5. Version of Record updated: November 24, 2022 (version 3)

Copyright

© 2021, Fleetwood et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,062
    views
  • 554
    downloads
  • 43
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Oliver Fleetwood
  2. Jens Carlsson
  3. Lucie Delemotte
(2021)
Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling
eLife 10:e60715.
https://doi.org/10.7554/eLife.60715

Share this article

https://doi.org/10.7554/eLife.60715

Further reading

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics
    Dimitrios Vismpas, Friedrich Förster
    Insight

    Advanced cryo-EM approaches reveal surprising insights into the molecular structure that allows nascent proteins to be inserted into the membrane of the endoplasmic reticulum.

    1. Developmental Biology
    2. Structural Biology and Molecular Biophysics
    Samuel C Griffiths, Jia Tan ... Hsin-Yi Henry Ho
    Research Article

    The receptor tyrosine kinase ROR2 mediates noncanonical WNT5A signaling to orchestrate tissue morphogenetic processes, and dysfunction of the pathway causes Robinow syndrome, Brachydactyly B and metastatic diseases. The domain(s) and mechanisms required for ROR2 function, however, remain unclear. We solved the crystal structure of the extracellular cysteine-rich (CRD) and Kringle (Kr) domains of ROR2 and found that, unlike other CRDs, the ROR2 CRD lacks the signature hydrophobic pocket that binds lipids/lipid-modified proteins, such as WNTs, suggesting a novel mechanism of ligand reception. Functionally, we showed that the ROR2 CRD, but not other domains, is required and minimally sufficient to promote WNT5A signaling, and Robinow mutations in the CRD and the adjacent Kr impair ROR2 secretion and function. Moreover, using function-activating and -perturbing antibodies against the Frizzled (FZ) family of WNT receptors, we demonstrate the involvement of FZ in WNT5A-ROR signaling. Thus, ROR2 acts via its CRD to potentiate the function of a receptor super-complex that includes FZ to transduce WNT5A signals.