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Structural and dynamic insights into the activation of the μ-opioid receptor by an allosteric modulator

Author

Listed:
  • Shun Kaneko

    (Center for Biosystems Dynamics Research (BDR)
    The University of Tokyo)

  • Shunsuke Imai

    (Center for Biosystems Dynamics Research (BDR))

  • Tomomi Uchikubo-Kamo

    (Center for Biosystems Dynamics Research (BDR))

  • Tamao Hisano

    (Center for Biosystems Dynamics Research (BDR))

  • Nobuaki Asao

    (Center for Biosystems Dynamics Research (BDR)
    The University of Tokyo)

  • Mikako Shirouzu

    (Center for Biosystems Dynamics Research (BDR))

  • Ichio Shimada

    (Center for Biosystems Dynamics Research (BDR)
    Hiroshima University)

Abstract

G-protein-coupled receptors (GPCRs) play pivotal roles in various physiological processes. These receptors are activated to different extents by diverse orthosteric ligands and allosteric modulators. However, the mechanisms underlying these variations in signaling activity by allosteric modulators remain largely elusive. Here, we determine the three-dimensional structure of the μ-opioid receptor (MOR), a class A GPCR, in complex with the Gi protein and an allosteric modulator, BMS-986122, using cryogenic electron microscopy. Our results reveal that BMS-986122 binding induces changes in the map densities corresponding to R1673.50 and Y2545.58, key residues in the structural motifs conserved among class A GPCRs. Nuclear magnetic resonance analyses of MOR in the absence of the Gi protein reveal that BMS-986122 binding enhances the formation of the interaction between R1673.50 and Y2545.58, thus stabilizing the fully-activated conformation, where the intracellular half of TM6 is outward-shifted to allow for interaction with the Gi protein. These findings illuminate that allosteric modulators like BMS-986122 can potentiate receptor activation through alterations in the conformational dynamics in the core region of GPCRs. Together, our results demonstrate the regulatory mechanisms of GPCRs, providing insights into the rational development of therapeutics targeting GPCRs.

Suggested Citation

  • Shun Kaneko & Shunsuke Imai & Tomomi Uchikubo-Kamo & Tamao Hisano & Nobuaki Asao & Mikako Shirouzu & Ichio Shimada, 2024. "Structural and dynamic insights into the activation of the μ-opioid receptor by an allosteric modulator," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47792-6
    DOI: 10.1038/s41467-024-47792-6
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    as
    1. Aashish Manglik & Andrew C. Kruse & Tong Sun Kobilka & Foon Sun Thian & Jesper M. Mathiesen & Roger K. Sunahara & Leonardo Pardo & William I. Weis & Brian K. Kobilka & Sébastien Granier, 2012. "Crystal structure of the µ-opioid receptor bound to a morphinan antagonist," Nature, Nature, vol. 485(7398), pages 321-326, May.
    2. Gustavo Fenalti & Patrick M. Giguere & Vsevolod Katritch & Xi-Ping Huang & Aaron A. Thompson & Vadim Cherezov & Bryan L. Roth & Raymond C. Stevens, 2014. "Molecular control of δ-opioid receptor signalling," Nature, Nature, vol. 506(7487), pages 191-196, February.
    3. Yuki Toyama & Hanaho Kano & Yoko Mase & Mariko Yokogawa & Masanori Osawa & Ichio Shimada, 2017. "Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses," Nature Communications, Nature, vol. 8(1), pages 1-15, April.
    4. Christopher J. Draper-Joyce & Rebecca Bhola & Jinan Wang & Apurba Bhattarai & Anh T. N. Nguyen & India Cowie-Kent & Kelly O’Sullivan & Ling Yeong Chia & Hariprasad Venugopal & Celine Valant & David M., 2021. "Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia," Nature, Nature, vol. 597(7877), pages 571-576, September.
    5. G. Glenn Gregorio & Matthieu Masureel & Daniel Hilger & Daniel S. Terry & Manuel Juette & Hong Zhao & Zhou Zhou & Jose Manuel Perez-Aguilar & Maria Hauge & Signe Mathiasen & Jonathan A. Javitch & Hare, 2017. "Single-molecule analysis of ligand efficacy in β2AR–G-protein activation," Nature, Nature, vol. 547(7661), pages 68-73, July.
    6. Geng Chen & Jun Xu & Asuka Inoue & Maximilian F. Schmidt & Chen Bai & Qiuyuan Lu & Peter Gmeiner & Zheng Liu & Yang Du, 2022. "Activation and allosteric regulation of the orphan GPR88-Gi1 signaling complex," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. M. J. Strohman & S. Maeda & D. Hilger & M. Masureel & Y. Du & B. K. Kobilka, 2019. "Local membrane charge regulates β2 adrenergic receptor coupling to Gi3," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    8. Andras S. Solt & Mark J. Bostock & Binesh Shrestha & Prashant Kumar & Tony Warne & Christopher G. Tate & Daniel Nietlispach, 2017. "Insight into partial agonism by observing multiple equilibria for ligand-bound and Gs-mimetic nanobody-bound β1-adrenergic receptor," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    9. Kaavya Krishna Kumar & Michael J. Robertson & Elina Thadhani & Haoqing Wang & Carl-Mikael Suomivuori & Alexander S. Powers & Lipin Ji & Spyros P. Nikas & Ron O. Dror & Asuka Inoue & Alexandros Makriya, 2023. "Structural basis for activation of CB1 by an endocannabinoid analog," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    10. David Chandler, 2005. "Interfaces and the driving force of hydrophobic assembly," Nature, Nature, vol. 437(7059), pages 640-647, September.
    11. Antoine Koehl & Hongli Hu & Shoji Maeda & Yan Zhang & Qianhui Qu & Joseph M. Paggi & Naomi R. Latorraca & Daniel Hilger & Roger Dawson & Hugues Matile & Gebhard F. X. Schertler & Sebastien Granier & W, 2018. "Structure of the µ-opioid receptor–Gi protein complex," Nature, Nature, vol. 558(7711), pages 547-552, June.
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