Evidence map›Paper›PMID 39753132›Full record

ArticleCell2025

Molecular basis of proton sensing by G protein-coupled receptors.

Matthew K Howard, Nicholas Hoppe, Xi-Ping Huang, Darko Mitrovic, Christian B Billesbølle, Christian B Macdonald, Eshan Mehrotra, Patrick Rockefeller Grimes, Donovan D Trinidad, Lucie Delemotte and 3 more

Abstract read
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.

0numbers the graph read from it
0cells of the map it votes in
40citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

40 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Temporal coding expands the bandwidth of GPCR-mediated neuromodulation.bioRxiv : the preprint server for biology · 2026
    Article
  9. Article
  10. Functional dissection ofProceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  11. Deep mutational scan of the pore of the cold-sensing TRPM8 channel.bioRxiv : the preprint server for biology · 2026
    Article
  12. Article
  13. Article
  14. Article
  15. Review
  16. Article
  17. Article
  18. Review
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Matthew K HowardTetrad 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.
Nicholas HoppeDepartment 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.
Xi-Ping HuangDepartment 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.
Darko MitrovicScience for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
Christian B BillesbølleDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA.
Christian B MacdonaldDepartment of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
Eshan MehrotraTetrad 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.
Patrick Rockefeller GrimesDepartment of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.
Donovan D TrinidadDepartment of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA.
Lucie DelemotteScience for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
Justin G EnglishDepartment of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
Willow Coyote-MaestasDepartment 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.
Aashish ManglikDepartment 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.

Funding

The Stanford-SLAC CryoEM Center supplementU24GM129541 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH, HEDMAN, BRITT · 2018 to 2023
$54.8M
Medical Scientist Training Program (T32 NRSA Training Grant)T32GM141323 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Aimee Kao · 2021 to 2026
$10.5M
Tetrad: Genetics, Cell Biology, Biochemistry and Molecular Biology Training GrantT32GM139786 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Natalia Jura, David Paul Toczyski · 2021 to 2026
$6.5M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
Directed Evolution of Cell-Type Specific On-Demand Signaling Control SystemsDP2GM146247 · NIGMS · UNIVERSITY OF UTAH · PI ENGLISH, JUSTIN G. · 2021 to 2024
$2.3M
Acquisition of an electron microscope for high-resolution single particle cryo-EMS10OD021741 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2016 to 2016
$2.0M
Glacios™ Cryo Transmission Electron Microscope with 200 kV XFEG opticsS10OD026881 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2019 to 2019
$1.8M
Designing and developing PAM-antagonists for GPR68R21MH120422 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HUANG, XI-PING, KENAKIN, TERRENCE PETER · 2019 to 2020
$460k
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
Connecting structure and fitness landscapes to overcome antibiotic resistanceF32GM152977 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MACDONALD, CHRISTIAN BERNARD · 2023 to 2024
$146k
Understanding the mechanisms of ESX secretion systems in mycobacteriaF31AI157438 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TRINIDAD, DONOVAN DAVID · 2021 to 2023
$127k
Molecular mechanisms of proton-sensing in CO2-dependent breathingF31HL164045 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HOPPE, NICK · 2022 to 2023
$46k
NHLBI NIH HHS F31 HL164045NIAID NIH HHS F31 AI157438NIAID NIH HHS T32 AI060537NIGMS NIH HHS DP2 GM146247NIGMS NIH HHS F32 GM152977NIGMS NIH HHS T32 GM139786NIGMS NIH HHS T32 GM141323NIGMS NIH HHS U24 GM129541NIH HHS S10 OD020054NIH HHS S10 OD021741NIH HHS S10 OD026881NIMH NIH HHS R21 MH120422
6 · The paper itself

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.

Indexed as

ProtonsReceptors, G-Protein-CoupledAnimalsCryoelectron MicroscopyHEK293 CellsHumansHydrogen-Ion ConcentrationMolecular Dynamics SimulationSignal TransductionGPR4 protein, humanGPR65 protein, humanGPR68 protein, humanProtonsReceptors, G-Protein-Coupledcryo-EMGPCRprotonproton sensingsignalingstructure

Identifiers

PMID39753132
PMCPMC11849372

What Socratic holds

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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.