ArticleBiophysical journal1997
The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints.
Article in Biophysical journal, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins.bioRxiv : the preprint server for biology · 2024Article
- Translation of structure-activity relationships from cyclic mixed efficacy opioid peptides to linear analogues.Biopolymers · 2014Article
- Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations.PLoS computational biology · 2013Article
- Modulation of opioid receptor ligand affinity and efficacy using active and inactive state receptor models.Chemical biology & drug design · 2012Article
- FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.Proteins · 2010Article
- Pentapeptides displaying mu opioid receptor agonist and delta opioid receptor partial agonist/antagonist properties.Journal of medicinal chemistry · 2009Article
- Docking studies suggest ligand-specific delta-opioid receptor conformations.Journal of molecular modeling · 2009Article
- A strategy using NMR peptide structures of thromboxane A2 receptor as templates to construct ligand-recognition pocket of prostacyclin receptor.BMC biochemistry · 2005Article
- Homology modeling of opioid receptor-ligand complexes using experimental constraints.The AAPS journal · 2005Review
- Interactions of human melanocortin 4 receptor with nonpeptide and peptide agonists.Biochemistry · 2005Article
- Sphingosine 1-phosphate analogue recognition and selectivity at S1P4 within the endothelial differentiation gene family of receptors.The Biochemical journal · 2005Article
- Pharmacophore and receptor models for neurokinin receptors.Journal of computer-aided molecular design · 2003Article
- G protein-coupled receptor rhodopsin: a prospectus.Annual review of physiology · 2003Review
- The crystallographic model of rhodopsin and its use in studies of other G protein-coupled receptors.Annual review of biophysics and biomolecular structure · 2003Review
- Unique mechanisms of excitation energy transfer, electron transfer and photoisomerization in biological systems.Journal of biological physics · 2002Article
- Interatomic potentials and solvation parameters from protein engineering data for buried residues.Protein science : a publication of the Protein Society · 2002Article
- Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors.Journal of computer-aided molecular design · 2001Article
- Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations.Biophysical journal · 2001Article
- Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs).Biochemistry · 2001Review
- A sequence and structural study of transmembrane helices.Journal of computer-aided molecular design · 2001Article
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3 authors.
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Abstract
A 3D model of the transmembrane 7-alpha-bundle of rhodopsin-like G-protein-coupled receptors (GPCRs) was calculated using an iterative distance geometry refinement with an evolving system of hydrogen bonds, formed by intramembrane polar side chains in various proteins of the family and collectively applied as distance constraints. The alpha-bundle structure thus obtained provides H bonding of nearly all buried polar side chains simultaneously in the 410 GPCRs considered. Forty evolutionarily conserved GPCR residues form a single continuous domain, with an aliphatic "core" surrounded by six clusters of polar and aromatic side chains. The 7-alpha-bundle of a specific GPCR can be calculated using its own set of H bonds as distance constraints and the common "average" model to restrain positions of the helices. The bovine rhodopsin model thus determined is closely packed, but has a few small polar cavities, presumably filled by water, and has a binding pocket that is complementary to 11-cis (6-s-cis, 12-s-trans, C = N anti)-retinal or to all-trans-retinal, depending on conformations of the Lys296 and Trp265 side chains. A suggested mechanism of rhodopsin photoactivation, triggered by the cis-trans isomerization of retinal, involves rotations of Glu134, Tyr223, Trp265, Lys296, and Tyr306 side chains and rearrangement of their H bonds. The model is in agreement with published electron cryomicroscopy, mutagenesis, chemical modification, cross-linking, Fourier transform infrared spectroscopy, Raman spectroscopy, electron paramagnetic resonance spectroscopy, NMR, and optical spectroscopy data. The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets.
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