ArticleBiophysical journal2015
Retinal Conformation Changes Rhodopsin's Dynamic Ensemble.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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.
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Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- Conformational signatures of native ligand and pharmacochaperone binding in rhodopsin.Structure (London, England : 1993) · 2026Article
- Long-Time Scale Simulations Reveal Key Dynamics That Drive the Onset of the N State in the Proteorhodopsin Photocycle.The journal of physical chemistry. B · 2024Article
- Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin.Structure (London, England : 1993) · 2018Article
- Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions.Biophysical journal · 2018Article
- Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].Living journal of computational molecular science · 2018Article
- Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction.Methods in enzymology · 2017Article
- Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
G protein-coupled receptors are vital membrane proteins that allosterically transduce biomolecular signals across the cell membrane. However, the process by which ligand binding induces protein conformation changes is not well understood biophysically. Rhodopsin, the mammalian dim-light receptor, is a unique test case for understanding these processes because of its switch-like activity; the ligand, retinal, is bound throughout the activation cycle, switching from inverse agonist to agonist after absorbing a photon. By contrast, the ligand-free opsin is outside the activation cycle and may behave differently. We find that retinal influences rhodopsin dynamics using an ensemble of all-atom molecular dynamics simulations that in aggregate contain 100 μs of sampling. Active retinal destabilizes the inactive state of the receptor, whereas the active ensemble was more structurally homogenous. By contrast, simulations of an active-like receptor without retinal present were much more heterogeneous than those containing retinal. These results suggest allosteric processes are more complicated than a ligand inducing protein conformational changes or simply capturing a shifted ensemble as outlined in classic models of allostery.
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Registered trials
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.