Energy Landscape Sampling Reveals Ligand-Dependent Structural Dynamics of the Protease-Activated Receptor 1.
6 affiliations
- 1Institute for Drug Discovery, Leipzig University, Brüderstraße 34, 04103Leipzig, Germany.
- 2Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital Leipzig, Paul-List-Straße 13-15, 04103Leipzig, Germany.
- 3Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103Leipzig, Germany.
- 4LeiCeM─Leipzig Center of Metabolism, Leipzig University, 04103Leipzig, Germany.
- 5Interdisciplinary Center for Bioinformatics, Leipzig University, 04107Leipzig, Germany.
- 6Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105Leipzig, Germany.
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.
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BibTeX
@article{schwerin2026energy,
title = {{Energy Landscape Sampling Reveals Ligand-Dependent Structural Dynamics of the Protease-Activated Receptor 1.}},
author = {Inken Kaja Schwerin and Shihai Jiang and Claudia Stäubert and Berend Isermann and Georg Künze},
journal = {Journal of chemical information and modeling},
year = {2026},
month = oct,
doi = {10.1021/acs.jcim.6c01315},
url = {https://europepmc.org/article/MED/42912924},
note = {CC BY},
}
RIS
TY - JOUR
TI - Energy Landscape Sampling Reveals Ligand-Dependent Structural Dynamics of the Protease-Activated Receptor 1.
AU - Inken Kaja Schwerin
AU - Shihai Jiang
AU - Claudia Stäubert
AU - Berend Isermann
AU - Georg Künze
PY - 2026
DA - 2026/10/01
JO - Journal of chemical information and modeling
DO - 10.1021/acs.jcim.6c01315
UR - https://europepmc.org/article/MED/42912924
AB - 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.
SN - 1549-9596
SN - 1549-960X
ER -