Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Biophysical Journal

• Publication date

  2008-07-15

• Fields of study

  Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1529/biophysj.107.120691PMID 18390613PMCID PMC2440475
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Single-Molecule Experiments in Vitro and in Silico

  2007cited by this paper
• GPCR Engineering Yields High-Resolution Structural Insights into β2-Adrenergic Receptor Function

  2007cited by this paper
• Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD.

  2007cited by this paper
• Crystal structure of the human beta2 adrenergic G-protein-coupled receptor.

  2007cited by this paper
• High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.

  2007cited by this paper
• Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.

  2007cited by this paper
• The signaling pathway of rhodopsin.

  2007cited by this paper
• Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

  2007cited by this paper
• Crystal structure of the human β2 adrenergic G-protein-coupled receptor

  2007cited by this paper
• Modeling activated states of GPCRs: the rhodopsin template

  2007cited by this paper
• Convergence of molecular dynamics simulations of membrane proteins

  2007cited by this paper
• Linkage between the intramembrane H-bond network around aspartic acid 83 and the cytosolic environment of helix 8 in photoactivated rhodopsin.

  2007cited by this paper
• High-Resolution Crystal Structure of an Engineered Human β2-Adrenergic G Protein–Coupled Receptor

  2007cited by this paper
• Structural analysis and dynamics of retinal chromophore in dark and meta I states of rhodopsin from 2H NMR of aligned membranes.

  2007cited by this paper
• Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

  2007cited by this paper
• How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

  2006cited by this paper
• Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

  2006cited by this paper
• Modeling activated states of GPCRs: the rhodopsin template

  2006cited by this paper
• A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

  2006cited by this paper
• G protein-coupled receptor rhodopsin.

  2006cited by this paper
• Predisposition of the dark state of rhodopsin to functional changes in structure

  2006cited by this paper
• Anisotropic network model: systematic evaluation and a new web interface

  2006cited by this paper
• A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids

  2006cited by this paper
• Interactions in native binding sites cause a large change in protein dynamics.

  2006cited by this paper
• Solid-state 2H NMR structure of retinal in metarhodopsin I.

  2006cited by this paper
• Crystal structure of a photoactivated deprotonated intermediate of rhodopsin

  2006cited by this paper
• Probing the β2 Adrenoceptor Binding Site with Catechol Reveals Differences in Binding and Activation by Agonists and Partial Agonists*

  2005cited by this paper
• Normal mode analysis : theory and applications to biological and chemical systems

  2005cited by this paper
• Normal-modes-based prediction of protein conformational changes guided by distance constraints.

  2005cited by this paper
• Allostery in a coarse-grained model of protein dynamics.

  2005cited by this paper
• Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor.

  2005cited by this paper
• Intrinsic dynamics of an enzyme underlies catalysis

  2005cited by this paper
• The role of shape in determining molecular motions.

  2005cited by this paper
• The role of Glu181 in the photoactivation of rhodopsin.

  2005cited by this paper
• Coarse-grained normal mode analysis in structural biology.

  2005cited by this paper
• Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.

  2005cited by this paper
• Allosteric Mechanisms of Signal Transduction

  2005cited by this paper
• Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin.

  2005cited by this paper
• Scalable molecular dynamics with NAMD

  2005cited by this paper
• Conformational sampling and dynamics of membrane proteins from 10‐nanosecond computer simulations

  2004cited by this paper
• Toward the active conformations of rhodopsin and the β2‐adrenergic receptor

  2004cited by this paper
• Structural Models of the Photointermediates in the Rhodopsin Photocascade, Lumirhodopsin, Metarhodopsin I, and Metarhodopsin II

  2004cited by this paper
• Deuterium NMR structure of retinal in the ground state of rhodopsin.

  2004cited by this paper
• Coupling of retinal isomerization to the activation of rhodopsin.

  2004cited by this paper
• Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure.

  2004cited by this paper
• Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin

  2003cited by this paper
• Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change.

  2003cited by this paper
• Rhodopsin structure, dynamics, and activation: a perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking.

  2003cited by this paper
• Modelling of Photointermediates Suggests a Mechanism of the Flip of the β‐Ionone Moiety of the Retinylidene Chromophore in the Rhodopsin Photocascade

  2003cited by this paper
• Molecular dynamics simulations of peptides and proteins with amplified collective motions.

  2003cited by this paper
• Mutagenesis and modelling of the alpha(1b)-adrenergic receptor highlight the role of the helix 3/helix 6 interface in receptor activation.

  2002cited by this paper
• Convergence of sampling in protein simulations.

  2002cited by this paper
• Structural studies of metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin.

  2002cited by this paper
• Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations.

  2002cited by this paper
• Dynamics in Rhodopsin

  2002cited by this paper
• Functional role of internal water molecules in rhodopsin revealed by x-ray crystallography

  2002cited by this paper
• Rhodopsin: insights from recent structural studies.

  2002cited by this paper
• Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch.

  2002cited by this paper
• Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin.

  2002cited by this paper
• Function of extracellular loop 2 in rhodopsin: glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II.

  2002cited by this paper
• Anisotropy of fluctuation dynamics of proteins with an elastic network model.

  2001cited by this paper
• Structure and function in rhodopsin: mapping light-dependent changes in distance between residue 65 in helix TM1 and residues in the sequence 306-319 at the cytoplasmic end of helix TM7 and in helix H8.

  2001cited by this paper
• Probing the dark state tertiary structure in the cytoplasmic domain of rhodopsin: proximities between amino acids deduced from spontaneous disulfide bond formation between cysteine pairs engineered in cytoplasmic loops 1, 3, and 4.

  2001cited by this paper
• Structure and function in rhodopsin: Mass spectrometric identification of the abnormal intradiscal disulfide bond in misfolded retinitis pigmentosa mutants

  2001cited by this paper
• Probing the dark state tertiary structure in the cytoplasmic domain of rhodopsin: proximities between amino acids deduced from spontaneous disulfide bond formation between Cys316 and engineered cysteines in cytoplasmic loop 1.

  2001cited by this paper
• Activation of the β2-Adrenergic Receptor Involves Disruption of an Ionic Lock between the Cytoplasmic Ends of Transmembrane Segments 3 and 6*

  2001cited by this paper
• Receptor activation: what does the rhodopsin structure tell us?

  2001cited by this paper
• Conformational change of proteins arising from normal mode calculations.

  2001cited by this paper
• Rhodopsin: structural basis of molecular physiology.

  2001cited by this paper
• Steered molecular dynamics investigations of protein function.

  2001cited by this paper
• Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor

  2000cited by this paper
• The effect of mutations in the DRY motif on the constitutive activity and structural instability of the histamine H(2) receptor.

  2000cited by this paper
• Similarities between principal components of protein dynamics and random diffusion

  2000cited by this paper
• Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach.

  2000cited by this paper
• Crystal structure of rhodopsin: A G protein-coupled receptor.

  2000cited by this paper
• Movement of retinal along the visual transduction path.

  2000cited by this paper
• Efficient sampling in collective coordinate space

  2000cited by this paper
• Uncovering molecular mechanisms involved in activation of G protein-coupled receptors.

  2000cited by this paper
• Structural features and light-dependent changes in the sequence 306-322 extending from helix VII to the palmitoylation sites in rhodopsin: a site-directed spin-labeling study.

  1999cited by this paper
• Structure and function in rhodopsin: further elucidation of the role of the intradiscal cysteines, Cys-110, -185, and -187, in rhodopsin folding and function.

  1999cited by this paper
• Single-cysteine substitution mutants at amino acid positions 55-75, the sequence connecting the cytoplasmic ends of helices I and II in rhodopsin: reactivity of the sulfhydryl groups and their derivatives identifies a tertiary structure that changes upon light-activation.

  1999cited by this paper
• Single-cysteine substitution mutants at amino acid positions 306-321 in rhodopsin, the sequence between the cytoplasmic end of helix VII and the palmitoylation sites: sulfhydryl reactivity and transducin activation reveal a tertiary structure.

  1999cited by this paper
• Investigating protein dynamics in collective coordinate space.

  1999cited by this paper
• Mutation of a highly conserved aspartic acid in the beta2 adrenergic receptor: constitutive activation, structural instability, and conformational rearrangement of transmembrane segment 6.

  1999cited by this paper
• Structural features and light-dependent changes in the sequence 59-75 connecting helices I and II in rhodopsin: a site-directed spin-labeling study.

  1999cited by this paper
• Rhodopsin: a prototypical G protein-coupled receptor.

  1998cited by this paper
• Analysis of domain motions by approximate normal mode calculations

  1998cited by this paper
• Functional Microdomains in G-protein-coupled Receptors

  1998cited by this paper
• Model‐free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

  1997cited by this paper
• Expression of a mutant opsin gene increases the susceptibility of the retina to light damage

  1997cited by this paper
• Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

  1997cited by this paper
• Structure and function in rhodopsin: topology of the C-terminal polypeptide chain in relation to the cytoplasmic loops.

  1997cited by this paper
• How receptors talk to trimeric G proteins.

  1997cited by this paper
• Requirement of Rigid-Body Motion of Transmembrane Helices for Light Activation of Rhodopsin

  1996cited by this paper
• Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study.

  1996cited by this paper
• Constitutively active mutants of the alpha 1B‐adrenergic receptor: role of highly conserved polar amino acids in receptor activation.

  1996cited by this paper
• Principal Component Analysis and Long Time Protein Dynamics

  1996cited by this paper
• An extended sampling of the configurational space of HPr from E. coli

  1996cited by this paper
• An efficient method for sampling the essential subspace of proteins.

  1996cited by this paper
• Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F

  1996cited by this paper

• Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems

  2023cites this paper
• Activation and Speciation Mechanisms in Class A GPCRs

  2022cites this paper
• Problems of Quantum-Classical Modeling Of the Primary Photoreaction in Rhodopsin

  2022cites this paper
• Systematic profiling of temperature- and retinal-sensitive rhodopsin variants by deep mutational scanning

  2021cites this paper
• Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.

  2021cites this paper
• Allostery as Structure‐Encoded Collective Dynamics

  2020cites this paper
• Conformational Changes of Protein Analyzed Based on Structural Perturbation Method

  2020cites this paper
• Allosteric interactions in the parathyroid hormone GPCR–arrestin complex formation

  2020cites this paper
• Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling

  2020cites this paper
• CHEMORECEPTOR DYNAMICS AND SIGNALING: NMR MEASUREMENTS WITHIN FUNCTIONAL COMPLEXES

  2019cites this paper
• Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies

  2019cites this paper
• Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

  2019cites this paper
• Quantum-classical modeling of rhodopsin photoisomerization

  2018cites this paper
• Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.

  2018cites this paper
• Investigation of Rhodopsin Chromophore Photoisomerization Based on the Quantum-Classical Model

  2018cites this paper
• Ligand-induced action of the W2866.48 rotamer toggle switch in the β2-adrenergic receptor.

  2017cites this paper
• Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters

  2017cites this paper
• Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations.

  2017cites this paper
• Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.

  2017cites this paper
• Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin

  2016cites this paper
• Revealing an outward-facing open conformational state in a CLC Cl–/H+ exchange transporter

  2016cites this paper
• Oncogenic mutations weaken the interactions that stabilize the p110α‐p85α heterodimer in phosphatidylinositol 3‐kinase α

  2015cites this paper
• Energy landscape of LeuT from molecular simulations.

  2015cites this paper
• Ensemble-Based Docking Using Biased Molecular Dynamics

  2014cites this paper
• Molecular dynamics study of enhanced Man5B enzymatic activity

  2014cites this paper
• Elastic network normal mode dynamics reveal the GPCR activation mechanism

  2014cites this paper
• Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

  2014cites this paper
• An introduction to biomolecular simulations and docking

  2014cites this paper
• Simulating Large-Scale Conformational Changes of Proteins by Accelerating Collective Motions Obtained from Principal Component Analysis.

  2014cites this paper
• Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation

  2014cites this paper
• Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.

  2013cites this paper
• Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation.

  2013cites this paper
• Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.

  2013cites this paper
• Structural Dynamics and Allosteric Signaling in Ionotropic Glutamate Receptors

  2013cites this paper
• Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.

  2012cites this paper
• 9.3 In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies

  2012cites this paper
• 9.8 G Protein Coupled Receptors

  2012cites this paper
• Identification of motions in membrane proteins by elastic network models and their experimental validation.

  2012influential citation
• Model of Abnormal Chromophore-Protein Interaction for Е181К Rhodopsin Mutation: Computer Molecular Dynamics Study

  2012cites this paper
• Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.

  2012cites this paper
• Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes

  2012cites this paper
• The cytoplasmic rhodopsin-protein interface: potential for drug discovery.

  2012cites this paper
• The effects of rigid motions on elastic network model force constants

  2012cites this paper
• Light activation of the isomerization and deprotonation of the protonated Schiff base retinal

  2011cites this paper
• Predicting large‐scale conformational changes in proteins using energy‐weighted normal modes

  2011cites this paper
• Harmonic Vibrational Analysis in Delocalized Internal Coordinates.

  2011cites this paper
• Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

  2011cites this paper
• Domain decomposition‐based structural condensation of large protein structures for understanding their conformational dynamics

  2011cites this paper
• Searching Peptide Conformational Space.

  2011cites this paper
• Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

  2011cites this paper
• Cooperative dynamics of proteins unraveled by network models

  2011cites this paper
• Coarse-Grained Modeling of Large Protein Complexes for Understanding Their Conformational Dynamics

  2011cites this paper
• Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors.

  2011cites this paper
• The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

  2011cites this paper
• Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors.

  2011cites this paper
• Understanding functional residues of the cannabinoid CB1.

  2010cites this paper
• On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

  2010cites this paper
• Dynamics and flexibility of G-protein-coupled receptor conformations and their relevance to drug design.

  2010cites this paper
• The role of conformational ensembles of seven transmembrane receptors in functional selectivity.

  2010cites this paper
• Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.

  2010cites this paper
• Structural insight into the role of thrombospondin-1 binding to calreticulin in calreticulin-induced focal adhesion disassembly.

  2010influential citation
• Understanding Functional Residues of the Cannabinoid CB1 Receptor for Drug Discovery

  2010cites this paper
• Elastic Network Models For Biomolecular Dynamics: Theory and Application to Membrane Proteins and Viruses

  2009cites this paper
• Modeling small molecule-compound binding to G-protein-coupled receptors.

  2009cites this paper
• Adrenergic Receptors: Model Systems for Investigation of GPCR Structure and Function

  2009cites this paper
• Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter

  2009cites this paper
• Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

  2009cites this paper
• Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

  2009cites this paper
• Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex.

  2009cites this paper
• Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.

  2009cites this paper
• Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy †

  2009cites this paper
• Symmetry, dynamics and function: Biological macromolecules studied by elastic network models

  2009cites this paper
• Residue Network Construction and Predictions of Elastic Network Models

  2008cites this paper
• Computational Microscopy Petascale Computing Resource Allocations (prac)

  2008cites this paper
• Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors.

  2008cites this paper