ArticleBiophysical journal2010
Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 63 citations in OpenAlex.
- Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis.International journal of molecular sciences · 2024Article
- Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine AChem · 2024Article
- Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands.Frontiers in endocrinology · 2022Review
- Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study.Biomolecules · 2021Article
- Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations.Scientific reports · 2020Article
- Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor.PloS one · 2020Article
- Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.The Journal of membrane biology · 2019Review
- Insights from molecular dynamics simulations to exploit new trends for the development of improved opioid drugs.Neuroscience letters · 2019Review
- Allostery in G protein-coupled receptors investigated by molecular dynamics simulations.Current opinion in structural biology · 2019Review
- An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber.The Journal of chemical physics · 2018Article
- Structural Features and Ligand Selectivity for 10 Intermediates in the Activation Process of βACS omega · 2017Article
- Understanding the molecular basis of agonist/antagonist mechanism of human mu opioid receptor through gaussian accelerated molecular dynamics method.Scientific reports · 2017Article
- G-protein coupled receptors: advances in simulation and drug discovery.Current opinion in structural biology · 2016Review
- Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics.Physical chemistry chemical physics : PCCP · 2014Article
- Conformational flexibility of human casein kinase catalytic subunit explored by metadynamics.Biophysical journal · 2014Article
- Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods.Advances in experimental medicine and biology · 2014Review
- Heterologous expression of functional G-protein-coupled receptors in Caenorhabditis elegans.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2012Article
- Article
- Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the post-hydrolysis reactions.PloS one · 2012Article
- Activation mechanism of the β2-adrenergic receptor.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A major current focus of structural work on G-protein-coupled receptors (GPCRs) pertains to the investigation of their active states. However, for virtually all GPCRs, active agonist-bound intermediate states have been difficult to characterize experimentally owing to their higher conformational flexibility, and thus intrinsic instability, as compared to inactive inverse agonist-bound states. In this work, we explored possible activation pathways of the prototypic GPCR bovine rhodopsin by means of biased molecular dynamics simulations. Specifically, we used an explicit atomistic representation of the receptor and its environment, and sampled the conformational transition from the crystal structure of a photoactivated deprotonated state of rhodopsin to the low pH crystal structure of opsin in the presence of 11-trans-retinal, using adiabatic biased molecular dynamics simulations. We then reconstructed the system free-energy landscape along the predetermined transition trajectories using a path collective variable approach based on metadynamics. Our results suggest that the two experimental endpoints of rhodopsin/opsin are connected by at least two different pathways, and that the conformational transition is populated by at least four metastable states of the receptor, characterized by a different amplitude of the outward movement of transmembrane helix 6.
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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 OpenQuestion graph.