ArticleBiophysical journal2008
Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 76 citations in OpenAlex.
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Activation and Speciation Mechanisms in Class A GPCRs.Journal of molecular biology · 2022Article
- Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.The Journal of chemical physics · 2021Article
- Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation.Nature chemical biology · 2020Article
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters.The journal of physical chemistry. B · 2017Article
- Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin.Doklady. Biochemistry and biophysics · 2016Article
- Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter.eLife · 2016Article
- Energy landscape of LeuT from molecular simulations.The Journal of chemical physics · 2015Article
- Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α.The FEBS journal · 2015Article
- Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation.BMC structural biology · 2014Article
- Molecular dynamics study of enhanced Man5B enzymatic activity.Biotechnology for biofuels · 2014Article
- Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.Biophysical journal · 2013Article
- Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.The Journal of chemical physics · 2013Article
- Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation.Journal of the American Chemical Society · 2013Article
- Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.The journal of physical chemistry letters · 2012Article
- Article
- Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.Biophysical journal · 2012Article
- The cytoplasmic rhodopsin-protein interface: potential for drug discovery.Current drug targets · 2012Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
As one of the best studied members of the pharmaceutically relevant family of G-protein-coupled receptors, rhodopsin serves as a prototype for understanding the mechanism of G-protein-coupled receptor activation. Here, we aim at exploring functionally relevant conformational changes and signal transmission mechanisms involved in its photoactivation brought about through a cis-trans photoisomerization of retinal. For this exploration, we propose a molecular dynamics simulation protocol that utilizes normal modes derived from the anisotropic network model for proteins. Deformations along multiple low-frequency modes of motion are used to efficiently sample collective conformational changes in the presence of explicit membrane and water environment, consistent with interresidue interactions. We identify two highly stable regions in rhodopsin, one clustered near the chromophore, the other near the cytoplasmic ends of transmembrane helices H1, H2, and H7. Due to redistribution of interactions in the neighborhood of retinal upon stabilization of the trans form, local structural rearrangements in the adjoining H3-H6 residues are efficiently propagated to the cytoplasmic end of these particular helices. In the structures obtained by our simulations, all-trans retinal interacts with Cys(167) on H4 and Phe(203) on H5, which were not accessible in the dark state, and exhibits stronger interactions with H5, while some of the contacts made (in the cis form) with H6 are lost.
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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.