{
  "abstract": "Protease-activated receptor 1 (PAR1) is a class A G protein-coupled receptor activated by proteolytic cleavage and exposure of a tethered agonist. While existing structures have revealed inactive and active conformations, the ligand-dependent conformational energy landscape governing PAR1 activation remains poorly understood. Here, we employed enhanced-sampling molecular dynamics simulations using the string method with swarms of trajectories to quantify how extracellular ligands and G-protein binding modulate PAR1 activation. Free-energy landscapes were computed for five receptor states (apo, tethered agonist, thrombin receptor-activating peptide (TRAP), vorapaxar (VPX), and VPX + Na+) using five transmembrane (TM) helix distance metrics as collective variables. In the apo state, PAR1 samples inactive, intermediate, and active-like conformations, indicating substantial intrinsic receptor flexibility. VPX increases the free energy of active conformations and restricts TM helix 5 and 6 rearrangements, while VPX + Na+ eliminates intermediate basins and stabilizes the inactive state. In contrast, the tethered agonist stabilizes the active state as the global minimum and promotes TM6 displacement of up to ∼1 nm. The simulations reveal a continuous activation pathway linking extracellular ligand engagement to intracellular motifs, including the connector, DRF, intracellular loop 3 (ICL3), and KRK motifs, with intracellular chloride ion coordination contributing to inactive-state stabilization. Gαq binding reduces TM6 flexibility and shifts the free-energy minimum toward more active-like conformations. Alanine mutagenesis and Gq-CASE BRET assays validate predicted roles of key residues in activation and G-protein coupling. Together, these results provide a detailed understanding of ligand- and transducer-dependent PAR1 signaling and inform the design of pathway-selective PAR1 modulators.",
  "abstract_shown": true,
  "affiliations": [
    "Institute for Drug Discovery, Leipzig University, Brüderstraße 34, 04103Leipzig, Germany.",
    "Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital Leipzig, Paul-List-Straße 13-15, 04103Leipzig, Germany.",
    "Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103Leipzig, Germany.",
    "LeiCeM─Leipzig Center of Metabolism, Leipzig University, 04103Leipzig, Germany.",
    "Interdisciplinary Center for Bioinformatics, Leipzig University, 04107Leipzig, Germany.",
    "Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105Leipzig, Germany."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Inken Kaja Schwerin"
    },
    {
      "affs": [
        1
      ],
      "name": "Shihai Jiang",
      "orcid": "0000-0002-0559-6160"
    },
    {
      "affs": [
        2
      ],
      "name": "Claudia Stäubert"
    },
    {
      "affs": [
        1,
        3
      ],
      "name": "Berend Isermann"
    },
    {
      "affs": [
        0,
        4,
        5
      ],
      "name": "Georg Künze",
      "orcid": "0000-0003-1799-346X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b229yc793kkwn.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jcim.6c01315",
  "fulltext_url": "https://europepmc.org/articles/PMC13664097",
  "id": "b229yc793kkwn",
  "issns": [
    "1549-9596",
    "1549-960X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42912924",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Receptor Mechanisms and Signaling"
    ]
  ],
  "openalex": "W7214112859",
  "pdf_url": "https://europepmc.org/articles/PMC13664097?pdf=render",
  "pmcid": "PMC13664097",
  "pmid": "42912924",
  "published": "2026-10-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b229yc793kkwn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:14Z",
      "native_id": "MED:42912924",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42912924"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Receptor Mechanisms and Signaling",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Energy Landscape Sampling Reveals Ligand-Dependent Structural Dynamics of the Protease-Activated Receptor 1.",
  "title_text": "Energy Landscape Sampling Reveals Ligand-Dependent Structural Dynamics of the Protease-Activated Receptor 1.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:20:14Z",
  "url": "https://research.draconitic.com/paper/b229yc793kkwn",
  "venue": "Journal of chemical information and modeling",
  "versions": []
}