Molecular basis of proton sensing by G protein-coupled receptors

Affiliations

¹ Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
² Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Biophysics graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.
³ Department of Pharmacology and the National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
⁴ Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
⁵ Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA.
⁶ Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
⁷ Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA.
⁸ Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA.
⁹ Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
¹⁰ Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: willow.coyote-maestas@ucsf.edu.
¹¹ Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA. Electronic address: aashish.manglik@ucsf.edu.

PMID: 39753132
PMCID: PMC11849372 (available on 2026-02-06)
DOI: 10.1016/j.cell.2024.11.036

Molecular basis of proton sensing by G protein-coupled receptors

Matthew K Howard et al. Cell. 2025.

. 2025 Feb 6;188(3):671-687.e20.

doi: 10.1016/j.cell.2024.11.036. Epub 2025 Jan 2.

Affiliations

¹ Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
² Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Biophysics graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.
³ Department of Pharmacology and the National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
⁴ Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
⁵ Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA.
⁶ Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
⁷ Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA.
⁸ Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA.
⁹ Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
¹⁰ Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: willow.coyote-maestas@ucsf.edu.
¹¹ Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA. Electronic address: aashish.manglik@ucsf.edu.

PMID: 39753132
PMCID: PMC11849372 (available on 2026-02-06)
DOI: 10.1016/j.cell.2024.11.036

Abstract

Three proton-sensing G protein-coupled receptors (GPCRs)-GPR4, GPR65, and GPR68-respond to extracellular pH to regulate diverse physiology. How protons activate these receptors is poorly understood. We determined cryogenic-electron microscopy (cryo-EM) structures of each receptor to understand the spatial arrangement of proton-sensing residues. Using deep mutational scanning (DMS), we determined the functional importance of every residue in GPR68 activation by generating ∼9,500 mutants and measuring their effects on signaling and surface expression. Constant-pH molecular dynamics simulations provided insights into the conformational landscape and protonation patterns of key residues. This unbiased approach revealed that, unlike other proton-sensitive channels and receptors, no single site is critical for proton recognition. Instead, a network of titratable residues extends from the extracellular surface to the transmembrane region, converging on canonical motifs to activate proton-sensing GPCRs. Our approach integrating structure, simulations, and unbiased functional interrogation provides a framework for understanding GPCR signaling complexity.

Keywords: GPCR; cryo-EM; proton; proton sensing; signaling; structure.

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Conflict of interest statement

Declaration of interests A.M. is a founder of Epiodyne and Stipple Bio, consults for Abalone, and serves on the scientific advisory board of Septerna. D.M. is the founder and chief scientific officer of Dioclea Labs. L.D. is the chief scientific advisor of the Dioclea Labs advisory board.

Update of

Molecular basis of proton-sensing by G protein-coupled receptors.
Howard MK, Hoppe N, Huang XP, Macdonald CB, Mehrota E, Grimes PR, Zahm A, Trinidad DD, English J, Coyote-Maestas W, Manglik A. Howard MK, et al. bioRxiv [Preprint]. 2024 Apr 18:2024.04.17.590000. doi: 10.1101/2024.04.17.590000. bioRxiv. 2024. Update in: Cell. 2025 Feb 06;188(3):671-687.e20. doi: 10.1016/j.cell.2024.11.036. PMID: 38659943 Free PMC article. Updated. Preprint.

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Molecular basis of proton sensing by G protein-coupled receptors

Affiliations

Molecular basis of proton sensing by G protein-coupled receptors

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials