The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Journal of Molecular Biology

• Publication date

  2004-09-10

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/J.JMB.2004.07.044PMID 15327956
• 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.

• Protein-induced bonding perturbation of the rhodopsin chromophore detected by double-quantum solid-state NMR.

  2004cited by this paper
• The Nature of the Complex Counterion of the Chromophore in Rhodopsin

  2004cited by this paper
• Vertebrate ultraviolet visual pigments: protonation of the retinylidene Schiff base and a counterion switch during photoactivation.

  2004cited 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
• 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
• Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin.

  2003cited by this paper
• Thr94 and Wat2b effect protonation of the retinal chromophore in rhodopsin.

  2003cited by this paper
• Perspectives on the counterion switch-induced photoactivation of the G protein-coupled receptor rhodopsin

  2003cited by this paper
• Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin

  2003cited by this paper
• Exploring the Opsin shift with ab initio methods: Geometry and counterion effects on the electronic spectrum of retinal.

  2003cited by this paper
• Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals.

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

  2002cited by this paper
• 11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

  2002cited by this paper
• Crystal Structure of Rhodopsin: A G‐Protein‐Coupled Receptor

  2002influential reference
• G protein-coupled receptors: dominant players in cell-cell communication.

  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
• On the bioactive conformation of the rhodopsin chromophore: absolute sense of twist around the 6-s-cis bond.

  2001cited by this paper
• Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs).

  2001cited by this paper
• Nonempirical Calculation of Polymethine Excited States.

  2001cited by this paper
• Inherent chirality of the retinal chromophore in rhodopsin-A nonempirical theoretical analysis of chiroptical data.

  2001cited by this paper
• Activation of rhodopsin: new insights from structural and biochemical studies.

  2001cited by this paper
• A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method

  2001cited by this paper
• Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event

  2001cited by this paper
• Preparation and analysis of two-dimensional crystals of rhodopsin.

  2000cited by this paper
• Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method

  2000cited by this paper
• Fast Photoisomerization of a Rhodopsin Model-An Ab Initio Molecular Dynamics Study This work was supported by the Deutsche Forschungsgemeinschaft (Graduate College "Struktur und Dynamikheterogener Systeme").

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

  2000cited by this paper
• XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

  1999cited by this paper
• Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems

  1999cited by this paper
• Retinylidene ligand structure in bovine rhodopsin, metarhodopsin-I, and 10-methylrhodopsin from internuclear distance measurements using 13C-labeling and 1-D rotational resonance MAS NMR.

  1999cited by this paper
• Crystallography & NMR system: A new software suite for macromolecular structure determination.

  1998influential reference
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• ABSOLUTE SENSE OF TWIST OF THE C12-C13 BOND OF THE RETINAL CHROMOPHORE IN RHODOPSIN : SEMIEMPIRICAL AND NONEMPIRICAL CALCULATIONS OF CHIROPTICAL DATA

  1998cited by this paper
• Influence of DFT-calculated electron correlation on energies and geometries of retinals and of retinal derivatives related to the bacteriorhodopsin and rhodopsin chromophores

  1998cited by this paper
• Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties

  1998cited by this paper
• Retinoids and related compounds. Part 20.1 Synthesis of(11Z)-8,18-ethanoretinal and a conformational study of therhodopsin chromophore

  1997cited by this paper
• An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors.

  1997cited by this paper
• Structure and wavelength modification in retinylidene iminium salts

  1996cited by this paper
• Synergy in the spectral tuning of retinal pigments: complete accounting of the opsin shift in bacteriorhodopsin.

  1994cited by this paper
• Raster3D Version 2.0. A program for photorealistic molecular graphics.

  1994cited by this paper
• The tube' structure of 1,7-bis(dimethylamino)-heptamethinium tetrafluoroborate, a streptocyanine dye

  1994cited by this paper
• Protonation states of membrane-embedded carboxylic acid groups in rhodopsin and metarhodopsin II: a Fourier-transform infrared spectroscopy study of site-directed mutants.

  1993cited by this paper
• A program to produce both detailed and schematic plots of protein structures

  1991cited by this paper
• Crystal structure of N-Methyl-N-phenylretinal iminium perchlorate: A structural model for the bacteriorhodopsin chromophore

  1990cited by this paper
• How photoreceptor cells respond to light.

  1987cited by this paper
• Two-photon spectroscopy of locked-11-cis-rhodopsin: evidence for a protonated Schiff base in a neutral protein binding site.

  1985cited by this paper
• A NOVEL RHODOPSIN ANALOGUE POSSESSING THE CYCLOPENTATRIENYLIDENE STRUCTURE AS THE LL-CIS-LOCKED AND THE FULL PLANAR CHROMOPHORE

  1982cited by this paper
• Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

  1976cited by this paper
• Experimental evidence of Bond‐angle and Hybridisation Alteration caused by π‐electron density alternation

  1973cited by this paper
• CIRCULAR DICHROISM OF VISUAL PIGMENTS IN THE VISIBLE AND ULTRAVIOLET SPECTRAL REGIONS*

  1966cited by this paper

• Dragonfly red opsins share a common tuning mechanism with mammalian red opsins and further enhancement of near-infrared sensitivity

  2026cites this paper
• Bacteriorhodopsin proton-pumping mechanism: successes and challenges in computational approaches.

  2025cites this paper
• Activation Mechanism of Jumping Spider Rhodopsin-1 Revealed by Classical Molecular Dynamics.

  2025cites this paper
• Molecular basis underlying the specificity of an antagonist AA92593 for mammalian melanopsins

  2025cites this paper
• Photodynamics of Microbial Rhodopsin Mimic M1-L121E: Insights from Computational Modeling.

  2025cites this paper
• A back-to-back structured bionic visual sensor for adaptive perception

  2025cites this paper
• A repertoire of visible light–sensitive opsins in the deep-sea hydrothermal vent shrimp Rimicaris hybisae

  2025cites this paper
• V-synthes2 - the Next Generation Tool for Structure-based Virtual Screening of Giga-scale Chemical Spaces

  2025cites this paper
• Multistep 11-cis to All-trans Retinal Photoisomerization in Bestrhodopsin, an Unusual Microbial Rhodopsin

  2025cites this paper
• Effects of Membrane Cholesterol on the Structure and Function of Selected Class A GPCRsChallenges and Future Perspectives

  2025cites this paper
• Conformational Heterogeneity Underlying Divergent Signaling in Class A G Protein-Coupled Receptors.

  2025cites this paper
• Light-induced FTIR spectroscopy of visual rhodopsin microcrystals grown in lipidic cubic phase.

  2025cites this paper
• Signal termination of the chemokine receptor CCR9 is governed by an arrestin-independent phosphorylation mechanism.

  2025cites this paper
• Deprotonation of retinal Schiff base and structural dynamics in the early photoreaction of primate blue cone visual pigment

  2025cites this paper
• CCR9 signal termination is governed by an arrestin-independent phosphorylation mechanism

  2024cites this paper
• Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes

  2024cites this paper
• Comparative quantum-classical dynamics of natural and synthetic molecular rotors show how vibrational synchronization modulates the photoisomerization quantum efficiency

  2024cites this paper
• Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins

  2024cites this paper
• Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies

  2024cites this paper
• Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin.

  2024cites this paper
• Photoisomerization in rhodopsins: Shape-changing reactions of retinal at low temperatures

  2024cites this paper
• Characterization and engineering of a blue-sensitive, Gi/o-biased, and bistable ciliary opsin from a fan worm

  2024cites this paper
• GPER binding site detection and description: a flavonoid-based docking and molecular dynamics simulations study.

  2024cites this paper
• Comprehensive understanding of the role of GPER in estrogen receptor-alpha negative breast cancer.

  2024cites this paper
• Cryo-EM structures of human cone visual pigments

  2024cites this paper
• Glu1022.53-Mediated Early Conformational Changes in the Process of Light-Induced Green Cone Pigment Activation

  2024cites this paper
• Convergent mechanism underlying the acquisition of vertebrate scotopic vision

  2024cites this paper
• Adaptive Evolution of Nearctic Deepwater Fish Vision: Implications for Assessing Functional Variation for Conservation

  2024cites this paper
• Color Tuning in Bovine Rhodopsin through Polarizable Embedding.

  2024cites this paper
• Graph‐based algorithms to dissect long‐distance water‐mediated H‐bond networks for conformational couplings in GPCRs

  2024influential citation
• Thermal isomerization rates in retinal analogues using Ab‐Initio molecular dynamics

  2023cites this paper
• A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis

  2023cites this paper
• Investigating the mechanism of photoisomerization in jellyfish rhodopsin with the counterion at an atypical position

  2023influential citation
• Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor

  2023cites this paper
• Multiple parallel expansions of bilaterian-like phototransduction gene families in the eyeless Anthozoa

  2023cites this paper
• New simulation insights on the structural transition mechanism of bovine rhodopsin activation

  2023cites this paper
• Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel.

  2023cites this paper
• Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect

  2023cites this paper
• Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection

  2023cites this paper
• Similarity and difference in the photochemistry of type I and II rhodopsins

  2023cites this paper
• Role of Monomer/Tetramer Equilibrium of Rod Visual Arrestin in the Interaction with Phosphorylated Rhodopsin

  2023influential citation
• Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods.

  2023cites this paper
• Hydrophobic interaction between the TM1 and H8 is essential for rhodopsin trafficking to vertebrate photoreceptor outer segments

  2023cites this paper
• Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1

  2023cites this paper
• Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment.

  2023cites this paper
• Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans).

  2023cites this paper
• Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K.

  2023cites this paper
• Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins

  2023cites this paper
• Osmotic stress studies of G-protein-coupled receptor rhodopsin activation.

  2023cites this paper
• New insights into the molecular mechanism of rhodopsin retinitis pigmentosa from the biochemical and functional characterization of G90V, Y102H and I307N mutations

  2022cites this paper
• Conserved hydrogen-bond motifs of membrane transporters and receptors.

  2022cites this paper
• Isorhodopsin: An Undervalued Visual Pigment Analog

  2022cites this paper
• Quantum–classical simulations of rhodopsin reveal excited-state-population splitting and its effects on quantum efficiency

  2022cites this paper
• Identification of Small Molecular Chaperones Binding P23H Mutant Opsin through an In Silico Structure-Based Approach

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

  2022cites this paper
• The endocannabinoid system in the visual process

  2022cites this paper
• Ultrafast structural changes direct the first molecular events of vision

  2022cites this paper
• Best Practices in Constant pH MD Simulations: Accuracy and Sampling

  2022cites this paper
• Rhodopsin, light-sensor of vision.

  2022cites this paper
• Conformational selection guides β-arrestin recruitment at a biased G protein–coupled receptor

  2022cites this paper
• Energy Transport and Its Function in Heptahelical Transmembrane Proteins.

  2022cites this paper
• Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

  2022cites this paper
• Bidirectional Photochemistry of Antarctic Microbial Rhodopsin: Emerging Trend of Ballistic Photoisomerization from the 13-cis Resting State

  2022cites this paper
• A model for how Gβγ couples Gα to GPCR

  2022cites this paper
• Structural basis of GPCR coupling to distinct signal transducers: implications for biased signaling.

  2022cites this paper
• Computational Investigation of Functional Water Molecules Upon GPCR Bound to G protein or Arrestin

  2022cites this paper
• A method for selective 19F‐labeling absent of probe sequestration (SLAPS)

  2022cites this paper
• Convergent evolutionary counterion displacement of bilaterian opsins in ciliary cells

  2022influential citation
• Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin

  2022cites this paper
• Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

  2022cites this paper
• Phospholipid Scrambling by G Protein-Coupled Receptors.

  2021cites this paper
• Lipids and Phosphorylation Conjointly Modulate Complex Formation of β2-Adrenergic Receptor and β-arrestin2

  2021cites this paper
• Conformational insights into the C-terminal mutations of human rhodopsin in retinitispigmentosa.

  2021cites this paper
• Creation of photocyclic vertebrate rhodopsin by single amino acid substitution

  2021cites this paper
• Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery

  2021cites this paper
• Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors

  2021cites this paper
• Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action

  2021cites this paper
• Entry Pathway for the Inverse Agonist Ligand in the G Protein-Coupled Receptor Rhodopsin

  2021cites this paper
• S1PR1 signaling in cancer: A current perspective.

  2021cites this paper
• Motions around conserved helical weak spots facilitate GPCR activation

  2021cites this paper
• Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima

  2021cites this paper
• Model of Environmental Membrane Field for Transmembrane Proteins

  2021cites this paper
• Vitamin A1/A2 chromophore exchange: its role in spectral tuning and visual plasticity.

  2021cites this paper
• Protein Response Effects on Cofactor Excitation Energies from First Principles: Augmenting Subsystem Time-Dependent Density-Functional Theory with Many-Body Expansion Techniques.

  2021cites this paper
• Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

  2021cites this paper
• Structural aspects of rod opsin and their implication in genetic diseases

  2021cites this paper
• Sub-picosecond C=C bond photo-isomerization: evidence for the role of excited state mixing

  2021cites this paper
• Dimeric Rhodopsin R135L Mutant-Transducin-like Complex Sheds Light on Retinitis Pigmentosa Misfunctions.

  2021cites this paper
• Energetic Materials: From Cradle to Grave

  2021cites this paper
• C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins

  2021cites this paper
• Progress in GPCR structure determination

  2020cites this paper
• Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude.

  2020cites this paper
• Zinc and Its Critical Role in Retinitis pigmentosa: Insights from DFT/SMD Calculations.

  2020cites this paper
• On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems

  2020cites this paper
• Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

  2020cites this paper
• Molecular Evolution of a Collage of Cholesterol Interaction Motifs in Transmembrane Helix V of the Serotonin1A Receptor.

  2020cites this paper
• Computational Studies towards the Identification of Novel Rhodopsin-Binding Compounds as Chemical Chaperones for Misfolded Opsins

  2020influential citation
• Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins

  2020cites this paper
• An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima.

  2020cites this paper
• Viral rhodopsins 1 are an unique family of light-gated cation channels

  2020cites this paper