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Mechanism of Tethered Agonist Binding to an Adhesion G-Protein-Coupled Receptor
Open accessPreprint — published as 10.1021/acs.jpcb.5c05305
Abstract
Adhesion GPCRs (ADGRs) contain a GPCR autoproteolysis-inducing (GAIN) domain that is proximal to the receptor N-terminus and undergoes autoproteolysis at a highly conserved GPCR proteolysis (GPS) site to generate the N-terminal fragment (NTF) and transmembrane C-terminal fragment (CTF). Dissociation of NTF reveals a peptide tethered agonist (TA) which is responsible for the activation of the ADGRs. The NTF-bound ADGRs contain the encrypted TA that assumes a β-strand configuration within the GAIN domain, which is markedly different from a U-shaped α-helical configuration of TA in the active cryo-EM structures of ADGRs. However, how the TA dramatically changes its configuration and binds to the ADGR CTF remains unknown. In this study, we have performed all-atom enhanced sampling simulations using a novel Peptide-Gaussian accelerated Molecular Dynamics (Pep-GaMD) method on TA binding to the ADGRD1. The Pep-GaMD simulations captured spontaneous binding of the TA into orthosteric pocket of the ADGRD1 and its large conformational transition from the extended β strand to the U-shaped α helical configuration. We were able to identify important low-energy conformations of the TA in the binding pathway, as well as different active and inactive states of ADGRD1, in the presence and absence of the Gs protein. Therefore, our Pep-GaMD simulations have revealed dynamic mechanism of the TA binding to an ADGR, which will facilitate rational design of peptide regulators of ADGRs. TOC Graphic: Peptide-Gaussian accelerated Molecular Dynamics (Pep-GaMD) simulations remarkably captured spontaneous binding of tethered agonist (TA) into the orthosteric pocket of adhesion G-protein–coupled receptor (ADGRD1) and large conformational transition of the TA from an extended β-strand to a U-shaped α-helical configuration. We were able to identify important low-energy conformations of the TA in the binding pathway and different states of the receptor from the Pep-GaMD simulations.
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Metadata
- Authors
- Joshi, K., & Miao, Y.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Miao, Yinglong
- Venue
- The Journal of Physical Chemistry B
- Publisher
- openRxiv
- Published
- 2025-08-04
- Volume
- 130
- Issue
- 1
- Pages
- 56-67
- ISSN
- 1520-5207 (ISSN-L)
- PMC
- PMC12340805
- OpenAlex
- W7116703999
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 4
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- Funders
- Extreme Science and Engineering Discovery Environment ACCESS (Allocation Award TG-MCB180049)
- Project M2874 through the National Energy Research Scientific Computing Center (Contract No. DE-AC02-05CH11231)
- National Institutes of Health (R01GM132572)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- adhesion G protein-coupled receptors, GAIN domain, autoproteolysis, peptide conformational transition, orthosteric binding pocket, Gs protein, receptor activation mechanism, enhanced sampling molecular dynamics
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