Primary Citation PubMed: 10926528
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GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model.
(2005) Nucleic Acids Res 33
PubMed: 15980445 | PubMedCentral: PMC1160255 | DOI: 10.1093/nar/gki495
To calculate these parameters, the boundaries of the transmembrane helix and loop regions of GPCR sequences were determined from multiple alignments of known Class A families with bovine rhodopsin as ... three-dimensional structure template (PDB ID: 1f88) using CLUSTAL W ( 18 ).
Publication Year: 2005
The binding site for neohesperidin dihydrochalcone at the human sweet taste receptor.
(2007) BMC Struct Biol 7
PubMed: 17935609 | PubMedCentral: PMC2099433 | DOI: 10.1186/1472-6807-7-66
The alignment of the seven transmembrane helices of TAS1R3 receptor (SWISS-PROT: TS1R3_HUMAN, Q7RTX0) with the transmembrane helices of bovine rhodopsin (pdb ref code 1f88) and the 3D receptor-based p... armacophore modeling was described previously [ 22 ].
Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin x-ray structure (pdb ref code 1f88, Additional file 4 ) allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector.
Publication Year: 2007
Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.
(2003) BMC Genomics 4
PubMed: 12914674 | PubMedCentral: PMC212514 | DOI: 10.1186/1471-2164-4-34
The model was constructed using bacteriorhodopsin (PDB: 1C3W) and bovine retinal rhodopsin (PDB:1F88) as templates.
Publication Year: 2003
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation.
(2008) BMC Bioinformatics 9 Suppl 1
PubMed: 18315845 | PubMedCentral: PMC2259415 | DOI: 10.1186/1471-2105-9-S1-S14
c TMS of bovine rhodopsin based on the crystal structure (pdb code 1F88 A).
Modelling bovine rhodopsin and hGalR1 based on the Baldwin template and verification of the models using REPIMPS Transmembrane segments of bovine rhodopsin and hGalR1 Transmembrane segments of bovine rhodopsin (shown in Table 1 ) are based on the assignment indicated in the Protein Databank (RCSB) for the 1F88 A crystal structure and transmembrane segments proposed by Baldwin.
Publication Year: 2008
Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors.
PubMed: 18315847 | PubMedCentral: PMC2259417 | DOI: 10.1186/1471-2105-9-S1-S16
Methods Alignment An alignment of the seven-transmembrane helices of rat and human mGluR1, mGluR2, mGluR4, mGluR5 and mGluR7 with respect to the transmembrane helices of bovine rhodopsin (Protein Data... Bank code 1f88 [ 17 ]) was generated using ClustalW [ 62 ].
The crystal structure of dark, inactive bovine rhodopsin with pdb id 1f88 [ 17 ] and the ANM generated model of the activated state of rhodopsin [ 18 ] were used as the structural templates for generating the inactive and active models of mGluRs, respectively.
GPR50 is the mammalian ortholog of Mel1c: evidence of rapid evolution in mammals.
(2008) BMC Evol Biol 8
PubMed: 18400093 | PubMedCentral: PMC2323367 | DOI: 10.1186/1471-2148-8-105
3A ) Figure 3 Sequence alignment of human MT1, MT2 and GPR50 with bovine rhodopsin (pdb 1F88 ).
6 ) GPR50 homology modelling A model of the three-dimensional structure of the GPR50 transmembrane domain was obtained using the high resolution crystal structure of bovine rhodopsin (pdb 1F88 ) as a template.
Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region.
(2008) J Biol Chem 283
PubMed: 18463093 | PubMedCentral: PMC2440622 | DOI: 10.1074/jbc.C800040200
Squ_rhod , squid rhodopsin (PDB code: 2ZIY in this study); Bov_rhod , bovine rhodopsin (1F88 ( 5 ) or 1GZM ( 17 )); and ADRB2 (2RH1 ( 8 )).
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
(2009) PLoS One 4
PubMed: 19190775 | PubMedCentral: PMC2631154 | DOI: 10.1371/journal.pone.0004345
The sequences that are associated with or that are extremely similar to high resolution structures are noted [PDB identifiers 1F88  , 2VT4  , 3EML ... 5b;26] , 2RH1  , and 2R4R  ].
Publication Year: 2009
Modeling of human CCR5 as target for HIV-I and virtual screening with marine therapeutic compounds.
(2008) Bioinformation 3
PubMed: 19238197 | PubMedCentral: PMC2639675 | DOI: null
Coordinates from the reference protein (1F88) to the SCRs, structurally variable regions (SVRs), N-terminal and C-terminal were assigned to the target sequence based on the satisfaction of spatial res... raints.
Our PDB BLAST Hit for CCR5 target sequence gave a best hit of Rhodopsin crystal structure (PDB: 1F88) .
These pockets were compared with the Active site of the template (Bovine Rhodepsin PDB: 1f88) and by careful analysis of the entire predicted 14 Active sites, we found that 12 th predicted Active site (shown in Figure 2 ) with residues Asp2, pro8, Asn13, Tyr14, Tyr15, Thr16, Gln21 of CCR5 were similar to that of the catalytic site in 1f88 and Therefore its chosen as the most biologically favorable site for Docking study and other Identified Active sites were neglected.
Methodology Homology Modeling of CCR5 The Homology Model of Human CCR5 with Swiss-Prot ID: P51681 was generated using MODELLER [ 39 ] with ClustalW alignment of Bovine Rhodopsin sequence [accession number P02699] and its crystal structure [PDB: 1F88] as Template [ 40 ] chosen from PDB BLAST hit.
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.
(2009) BMC Bioinformatics 10 Suppl 8
PubMed: 19758467 | PubMedCentral: PMC2745585 | DOI: 10.1186/1471-2105-10-S8-S3
Protein name Mutation in literature Effect as reported in literature Stability change Compliance Bacteriorhodopsin PDB: 1brr UniProt: P02945 G113Q destabilized slightly destabilizing yes G113L destabi... ized destabilizing yes G116Q destabilized slightly destabilizing yes G116L destabilized destabilizing yes I117F destabilized slightly destabilizing yes I117A destabilized stabilizing no M145F still active destabilizing no Halorhodopsin PDB: 1e12 UniProt: P16102 H95A destabilized slightly destabilizing yes H95R destabilized slightly stabilizing no R108Q not functional slightly destabilizing yes T203V less active destabilizing yes Rhodospin PDB: 1f88 UniProt: P02699 T93P misfolded destabilizing yes T94I night blindness destabilizing yes C110F r. pigmentosa destabilizing yes C110Y r. pigmentosa destabilizing yes C110A r. pigmentosa slightly destabilizing yes E122Q still active slightly destabilizing no E122D still active slightly destabilizing no E122A slightly destabilizing E122R no retinal binding slightly destabilizing yes C185A wrong disulfide slightly destabilizing yes G188R misfolding slightly destabilizing yes S186A incr.
Calling International Rescue: knowledge lost in literature and data landslide!
(2009) Biochem J 424
PubMed: 19929850 | PubMedCentral: PMC2805925 | DOI: 10.1042/BJ20091474
Compare the structure of a bona fide GPCR [bovine rhodopsin, PDB code 1F88 ( e )] with the nisin cyclase structure shown in Illingworth's paper [PDB code 2G0D ( c )].
Homology modelling and spectroscopy, a never-ending love story.
(2010) Eur Biophys J 39
PubMed: 19718498 | PubMedCentral: PMC2841279 | DOI: 10.1007/s00249-009-0531-0
1 The most striking difference between the crystal structures of rhodopsin (PDBid 1f88, Palczewski et al.
Publication Year: 2010
Integration of open access literature into the RCSB Protein Data Bank using BioLit.
(2010) BMC Bioinformatics 11
PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220
of Articles 1JJ2 Large Ribosomal Subunit 27 1J5E 30S Ribosomal Subunit 19 1FFK Large Ribosomal Subunit 19 1LMB Lambda Repressor 19 1AAY Zinc Finger 17 1TSR P53 16 1F88 Rhodopsin 15 1BRS Barnase/Barsta... complex 14 The open access literature for RCSB PDB entries is available from the Literature tab for each structure entry at http://www.rcsb.org .
Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.
(2010) PLoS One 5
PubMed: 21042584 | PubMedCentral: PMC2962639 | DOI: 10.1371/journal.pone.0013596
Characterization of Transmemebrane Protein Structure We performed analyses on a structurally resolved (X-ray Crystallography) transmembrane protein called Bovine Rhodopsin (PDB: 1F88) in order to dete... mine the information contained in a pure population of embedded alignments  .
Membrane environment and endocannabinoid signaling.
(2010) Front Physiol 1
PubMed: 21423380 | PubMedCentral: PMC3059985 | DOI: 10.3389/fphys.2010.00140
Figure 1 Three-dimensional model of CB 1 , based on sequence alignment with visual rhodopsin in the inactivated state (PDB code: 1F88) .
Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics.
(2011) Int J Mol Sci 12
PubMed: 21541053 | PubMedCentral: PMC3083700 | DOI: 10.3390/ijms12021196
The seven TM domains (named TM1∼7) are boxed by a red border; ( B ) Superposition of template protein 1F88 chain A (green ribbon) and the DA D3 receptor model structure (red ribbon) from homol... gy modeling.
Blue and pink dot regions are the binding pocket of compound 9 and the template protein 1F88 chain A, respectively.
And as seen in Figure 7B , the template protein 1F88 chain A (green ribbon) are well superposed with the DA D3 receptor model structure (red ribbon) from homology modeling.
It is observed that this binding pocket is partly overlapped with the binding pocket in the template protein 1F88 chain A. Furthermore, the binding site we generated in the seven TM domains corresponds well to the studies of Frank Boeckler et al. [ 1 , 39 ].
( A ) Sequence alignment of bovine rhodopsin (1F88 chain A) and the DA D3 receptor homology model.
In this work, the rhodopsin X-ray structure (PDB entry: 1F88, chain A, 2.8 Å) has been applied since it belongs to the same subfamily of the GPCRs with dopamine receptors [ 40 , 44 ].
Publication Year: 2011
Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.
(2011) J Ophthalmol 2011
PubMed: 21785698 | PubMedCentral: PMC3138052 | DOI: 10.1155/2011/531380
We analyzed the location of the F293C mutation in the bovine rod opsin crystal structure (1F88.
Molecular Graphics The bovine rod rhodopsin crystal structure (1F88.
Investigation on quantitative structure activity relationships and pharmacophore modeling of a series of mGluR2 antagonists.
PubMed: 22016641 | PubMedCentral: PMC3189765 | DOI: 10.3390/ijms12095999
Using bovine Rhodopsin crystal structures 1F88 and 1GZM, which is also a transmembrane protein, to build TM structure of GPCRs (G protein-coupled receptor) like mGluR1 and mGluR5, is applied recently ... 20 – 22 ].
Activation of astroglial calcium signaling by endogenous metabolites succinate and gamma-hydroxybutyrate in the nucleus accumbens.
(2011) Front Neuroenergetics 3
PubMed: 22180742 | PubMedCentral: PMC3235779 | DOI: 10.3389/fnene.2011.00007
The SUCNR1 receptor model was built based on the bovine rhodopsin (RHO) structure (PDB code 1f88; Palczewski et al., 2000 ).
Progress in structure based drug design for G protein-coupled receptors.
(2011) J Med Chem 54
PubMed: 21615150 | PubMedCentral: PMC3308205 | DOI: 10.1021/jm200371q
Table 1 List of Published GPCR Crystal Structures receptor resolution (Å) PDB code date ref Rhodopsin: bovine rod outer segment 2.8 1F88 06/00 ( 52 ) Rhodopsin: bovine rod outer segment 2.6 1L... H 03/02 ( 176 ) Rhodopsin: bovine rod outer segment 2.65 1GZM 05/02 ( 177 ) Rhodopsin: bovine rod outer segment 2.2 1U19 07/04 ( 178 ) Rhodopsin, photoactivated: bovine rod outer segment 3.8–4.15 2I37 08/06 ( 179 ) Rhodopsin: recombinant bovine rhodopsin mutant, N2C/D282C 3.4 2J4Y 09/06 ( 180 ) Rhodopsin: squid 3.7 2ZIY 05/07 ( 181 ) Rhodopsin: squid 2.5 2Z73 08/07 ( 182 ) Human β 2 adrenergic receptor Fab5 complex.
PubMed ID is not available.
Published in 2012
Figure 3 Sequence alignment of human MT1, MT2 and GPR50 with bovine rhodopsin (pdb 1F88 ).
Publication Year: 2012
Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. Melanogaster.
(2012) Bioinform Biol Insights 6
PubMed: 22493562 | PubMedCentral: PMC3320116 | DOI: 10.4137/BBI.S8990
OR22a sequence and bovine rhodopsin (1F88: PDB ID) sequence were aligned ( Fig.
One using bovine rhodopsin (1F88) as template and the other two using both bovine rhodopsin and potassium ion channel as template corresponding to two different regions of the query.
Name TM 1 TM 2 TM 3 TM 4 TM 5 TM 6 TM 7 1f88 (Bovine rhodopsin) 30 30 33 23 26 31 21 2rh1 (Beta-2 AR) 32 30 34 25 33 32 24 OR83b 23 18 23 20 20 19 24 Loop 1 Loop 2 Loop 3 Loop 4 Loop 5 Loop 6 1f88 (Bovine rhodopsin) 12 17 20 30 30 8 2rh1 (Beta-2 AR) 6 8 10 + 160 38 27 7 OR83b 12 38 34 141 12 57 Notes: We do not find much variation in the length of TM helices between two templates, while bovine rhodopsin has loop lengths closer to the query compared to beta-2 adrenergic receptors.
The model was built using the software MODELLER 19 based on the manually edited alignment of OR83b and bovine rhodopsin 20 (1F88: PDB ID) sequence ( Supplementary Fig.
Action of molecular switches in GPCRs--theoretical and experimental studies.
(2012) Curr Med Chem 19
PubMed: 22300046 | PubMedCentral: PMC3343417 | DOI: null
Summary of All Available Crystal Structures of GPCRs (Based on [ 61 ]) GPCR Engineered Type of ligand Ligand name PDB ID (Resolution Å) [Reference] A 2A R (human) IC3 fusion Agonist UK-432097 ... QAK (2.71) [ 101 ] Inverse agonist ZM241385 3EML (2.6) [ 98 ] Point mutations Agonist Adenosine 2YDO (3.0) [ 105 ] Agonist NECA 2YDV (2.6) [ 105 ] Antagonist Caffeine 3RFM (3.60) [ 106 ] Antagonist XAC 3REY (3.31) [ 106 ] Inverse agonist ZM241385 3PWH (3.30) [ 106 ] β 1 AR (turkey) Point mutations Agonist Carmoterol 2Y02 (2.6) [ 104 ] Agonist Isoprenaline 2Y03 (2.85] [ 104 ] Antagonist Cyanopindolol 2VT4 (2.7) [ 74 ], 2YCX (3.25) [ 159 ], 2YCY (3.15) [ 159 ], 2YCZ (3.65) [ 159 ] Inverse agonist Carazolol 2YCW (3.0) [ 159 ] Partial agonist Dobutamine 2Y00 (2.5) [ 104 ], 2Y01 (2.6) [ 104 ] Partial agonist Salbutamol 2Y04 (3.05) [ 104 ] β 2 AR (human) IC3 fusion Agonist BI-167107, nanobody 3P0G (3.5) [ 96 ] Agonist FAUC50 3PDS (3.5) [ 96 ] Antagonist Alprenolol 3NYA (3.16) [ 97 ] Inverse agonist Carazolol 2RH1 (2.4) [ 18 ] Inverse agonist Compound #1 3NY9 (2.84) [ 97 ] Inverse agonist ICI118551 3NY8 (2.84 [ 97 ] Inverse agonist Timolol 3DS4 (2.8) [ 59 ] Inverse agonist FAB, not resolved 2R4R (3,4) [ 96 ], 2R4S (3.4) [ 96 ] Inverse agonist FAB, not resolved 3KJ6 (3.4) [ 135 ] N-terminal fusion Agonist BI-167107, Gαβγ, nanobody 3SN6 (3.2) [ 15 ] CXCR4 (human) IC3 fusion Antagonist CVX15 peptide 3OE0 (2.9) [ 33 ] Antagonist Molecule 1t 3ODU (2.5) [ 33 ], 3OE6 (3.2) [ 33 ], 3OE8 (3.1) [ 33 ], 3OE9 (3.1)[ 33 ] D 3 R (human) IC3 fusion Antagonist Eticlopride 3PBL (2.89) [ 99 ] H 1 R (human) IC3 fusion Inverse agonist Doxepin 3RZE (3.1) 36 [ 100 ] Opsin 3CAP (2.9) [ 89 ] Gα peptide 3DQB (3.2) [ 91 ] Rhodopsin (bovine) Agonist All- trans -retinal 2G87 (2.6) [ 139 ] Inverse agonist 11- cis -retinal 1F88 (2.8) [ 17 ], 1U19 (2.2) [ 83 ], 1GZM (2.65) [ 83 ], L9H (2.6) [ 83 ], 1HZX (2.8) [ 83 ], 2I37 (4.0) [ 83 ], 3OAX (2.6) [ 83 ], 3C9L (2.65) [ 83 ] Point mutations Agonist 11- trans -retinal, Ga peptide 2X72 (3.0) [ 122 ], 3PQR (2.85) [ 123 ], 3PXO (3.0) [ 123 ] 9- cis -retinal 2PED (2.95) 3385 [ 85 ] 2J4Y (3.4) 3 [ 83 ], 3C9M (3.4) [ 83 ] Rhodopsin (squid) Inverse agonist 11- cis -retinal 2ZIY (3.7) [ 86 ]
Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity.
(2012) BMC Bioinformatics 13 Suppl 7
PubMed: 22594995 | PubMedCentral: PMC3348020 | DOI: 10.1186/1471-2105-13-S7-S1
The coordinates corresponding to the residues 236-239 and 328-333 were not available in the crystal structure of 1F88 chain A due to poor electron density and hence these residues were removed from th... template sequence before the alignment.
Figure 1 Alignment of query (OR73) with template (1F88).
The crystal structure of the bovine rhodopsin [ 23 ] (PDB ID: 1f88 chain A) was used as a template for the comparative modelling of the query (OR73).
Molecular evolution of a peptide GPCR ligand driven by artificial neural networks.
(2012) PLoS One 7
PubMed: 22606313 | PubMedCentral: PMC3351444 | DOI: 10.1371/journal.pone.0036948
When this study was initiated only five x-ray structures of GPCRS were known: those of of two rhodopsins (PDB 1F88, 2Z73)  ,  , of the β2- and β1-adrenergic receptors (PDB 2RH1, ... VT4)  ,  and the structure of the A2A adenosine receptor (PDB 2RH1)  .
Activation biosensor for G protein-coupled receptors: a FRET-based m1 muscarinic activation sensor that regulates G(q).
PubMed: 23029161 | PubMedCentral: PMC3447775 | DOI: 10.1371/journal.pone.0045651
Miscellaneous Methods The homology-modeled structure of the M1 receptor was generated by SWISS-MODEL  using rhodopsin in its inactive state (pdb 1F88)  as a template.
A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors.
(2012) BMC Biophys 5
PubMed: 22748306 | PubMedCentral: PMC3478154 | DOI: 10.1186/2046-1682-5-13
Here, RT stands for the ligand binding domain in rhodopsin (PDB ID: 1F88).
In addition to comparing ligand binding pockets directly (i.e. extracting 5 Å residues in PDB ID: 1F88 for rhodopsin to identify the RT ligand binding pocket), we also generated the following combined sets of pocket residues to investigate similarities and differences between ligand binding pockets of different GPCRs (Table 1 ).
Homology modeling a fast tool for drug discovery: current perspectives.
(2012) Indian J Pharm Sci 74
PubMed: 23204616 | PubMedCentral: PMC3507339 | DOI: 10.4103/0250-474X.102537
In the year 2000 only a single crystal structure was available, bovine rhodopsin (bRho) (PDB code 1f88, 1l9h), before which bacterio-rhodopsin was used for modeling.
Structural Characterization of an LPA1 Second Extracellular Loop Mimetic with a Self-Assembling Coiled-Coil Folding Constraint.
(2013) Int J Mol Sci 14
PubMed: 23434648 | PubMedCentral: PMC3588015 | DOI: 10.3390/ijms14022788
Rhodopsin (1F88 [ 21 ], orange), β2-adrenoceptor (2RH1 [ 19 ], magenta), β1-adrenoceptor (2VT4 [ 18 ], cyan), adenosine A2a (3EML [ 17 ], pink), dopamine D3 (3PBL [ 15 ], brown), chemo... ine CXCR4 (3Oe0 [ 16 ], green), histamine H1 (3RZE [ 14 ], mustard), muscarinic acetylcholine M2 (3UON [ 22 ], brick red), muscarinic acetylcholine M3 (4DAJ [ 33 ], grey), κ-opioid (4DJH [ 23 ], red), μ-opioid (4DKL [ 24 ], purple), and S1P 1 (3V2Y [ 25 ], blue) are shown using ribbon representations.
Publication Year: 2013
Homology models of melatonin receptors: challenges and recent advances.
PubMed: 23584026 | PubMedCentral: PMC3645733 | DOI: 10.3390/ijms14048093
They used the first available crystal structure of rhodopsin (PDB ID: 1F88 [ 59 ]) to build the TM domains and the ECL2 portion of the MT 1 receptor.
Structure and activation of rhodopsin.
(2012) Acta Pharmacol Sin 33
PubMed: 22266727 | PubMedCentral: PMC3677203 | DOI: 10.1038/aps.2011.171
The photoactivated all- trans -retinal (PDB: 3PQR) is magenta and the ground-state 11- cis -retinal (PDB: 1F88, gray) is superposed on the activated all- trans -retinal for comparison.
Green shows the ground-state conformation (PDB: 1F88), and brown shows the activated conformation (PDB: 3PQR).
Eye (Lond) 1992 6 1 10 Dryja TP Hahn LB Cowley GS McGee TL Berson EL Mutation spectrum of the rhodopsin gene among patients with autosomal dominant retinitis pigmentosa Proc Natl Acad Sci U S A 1991 88 9370 4 1833777 Souied E Gerber S Rozet JM Bonneau D Dufier JL Ghazi I Five novel missense mutations of the rhodopsin gene in autosomal dominant retinitis pigmentosa Hum Mol Genet 1994 3 1433 4 7987331 Farrar GJ Kenna P Redmond R Shiels D McWilliam P Humphries MM Autosomal dominant retinitis pigmentosa: a mutation in codon 178 of the rhodopsin gene in two families of Celtic origin Genomics 1991 11 1170 1 1783387 Matias-Florentino M Ayala-Ramirez R Graue-Wiechers F Zenteno JC Molecular screening of rhodopsin and peripherin/RDS genes in Mexican families with autosomal dominant retinitis pigmentosa Curr Eye Res 2009 34 1050 6 19958124 Liu X Garriga P Khorana HG Structure and function in rhodopsin: correct folding and misfolding in two point mutants in the intradiscal domain of rhodopsin identified in retinitis pigmentosa Proc Natl Acad Sci U S A 1996 93 4554 9 8643442 Macke JP Davenport CM Jacobson SG Hennessey JC Gonzalez-Fernandez F Conway BP Identification of novel rhodopsin mutations responsible for retinitis pigmentosa: implications for the structure and function of rhodopsin Am J Hum Genet 1993 53 80 9 8317502 Farrar GJ Findlay JB Kumar–Singh R Kenna P Humphries MM Sharpe E Autosomal dominant retinitis pigmentosa: a novel mutation in the rhodopsin gene in the original 3q linked family Hum Mol Genet 1992 1 769 71 1302614 Haim M Grundmann K Gal A Rosenberg T Novel rhodopsin mutation (M216R) in a Danish family with autosomal dominant retinitis pigmentosa Ophthalmic Genet 1996 17 193 7 9010870 Al-Maghtheh M Inglehearn C Lunt P Jay M Bird A Bhattacharya S Two new rhodopsin transversion mutations (L40R; M216K) in families with autosomal dominant retinitis pigmentosa Hum Mutat 1994 3 409 10 8081400 Sieving PA Richards JE Naarendorp F Bingham EL Scott K Alpern M Dark-light: model for nightblindness from the human rhodopsin Gly-90 → Asp mutation Proc Natl Acad Sci U S A 1995 92 880 4 7846071 Dryja TP Berson EL Rao VR Oprian DD Heterozygous missense mutation in the rhodopsin gene as a cause of congenital stationary night blindness Nat Genet 1993 4 280 3 8358437 Nakayama TA Khorana HG Mapping of the amino acids in membrane-embedded helices that interact with the retinal chromophore in bovine rhodopsin J Biol Chem 1991 266 4269 75 1999419 Hwa J Garriga P Liu X Khorana HG Structure and function in rhodopsin: packing of the helices in the transmembrane domain and folding to a tertiary structure in the intradiscal domain are coupled Proc Natl Acad Sci U S A 1997 94 10571 6 9380676 Sheffield VC Fishman GA Beck JS Kimura AE Stone EM Identification of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis Am J Hum Genet 1991 49 699 706 1897520 Natochin M Gasimov KG Moussaif M Artemyev NO Rhodopsin determinants for transducin activation: a gain-of-function approach J Biol Chem 2003 278 37574 81 12860986 Fuchs S Kranich H Denton MJ Zrenner E Bhattacharya SS Humphries P Three novel rhodopsin mutations (C110F, L131P, A164V) in patients with autosomal dominant retinitis pigmentosa Hum Mol Genet 1994 3 1203 7981701 Richards JE Scott KM Sieving PA Disruption of conserved rhodopsin disulfide bond by Cys187Tyr mutation causes early and severe autosomal dominant retinitis pigmentosa Ophthalmology 1995 102 669 77 7724183 Hwa J Klein-Seetharaman J Khorana HG Structure and function in rhodopsin: Mass spectrometric identification of the abnormal intradiscal disulfide bond in misfolded retinitis pigmentosa mutants Proc Natl Acad Sci U S A 2001 98 4872 6 11320236 Huber T Botelho AV Beyer K Brown MF Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure Biophys J 2004 86 2078 100 15041649 Rodriguez JA Herrera CA Birch DG Daiger SP A leucine to arginine amino acid substitution at codon 46 of rhodopsin is responsible for a severe form of autosomal dominant retinitis pigmentosa Hum Mutat 1993 2 205 13 8364589 Sung CH Schneider BG Agarwal N Papermaster DS Nathans J Functional heterogeneity of mutant rhodopsins responsible for autosomal dominant retinitis pigmentosa Proc Natl Acad Sci U S A 1991 88 8840 4 1924344 Inglehearn CF Keen TJ Bashir R Jay M Fitzke F Bird AC A completed screen for mutations of the rhodopsin gene in a panel of patients with autosomal dominant retinitis pigmentosa Hum Mol Genet 1992 1 41 5 1301135 Bunge S Wedemann H David D Terwilliger DJ van den Born LI Aulehla-Scholz C Molecular analysis and genetic mapping of the rhodopsin gene in families with autosomal dominant retinitis pigmentosa Genomics 1993 17 230 3 8406457 Kranich H Bartkowski S Denton MJ Krey S Dickinson P Duvigneau C Autosomal dominant 'sector' retinitis pigmentosa due to a point mutation predicting an Asn-15-Ser substitution of rhodopsin Hum Mol Genet 1993 2 813 4 8353500 Chuang JZ Vega C Jun W Sung CH Structural and functional impairment of endocytic pathways by retinitis pigmentosa mutant rhodopsin-arrestin complexes J Clin Invest 2004 114 131 40 15232620 Scott KM Sieving PA Bingham E Bhagat VJ Sullivan J Alpern M Rhodopsin mutations associated with autosomal dominant retinitis pigmentosa Am J Hum Genet 1993 53 147 Li Y Lambert MH Xu HE Activation of nuclear receptors: a perspective from structural genomics Structure 2003 11 741 6 12842037 Jacobson KA Gao ZG Liang BT Neoceptors: reengineering GPCRs to recognize tailored ligands Trends Pharmacol Sci 2007 28 111 6 17280720 Costanzi S On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor J Med Chem 2008 51 2907 14 18442228 Nolte RT Wisely GB Westin S Cobb JE Lambert MH Kurokawa R Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma Nature 1998 395 137 43 9744270 Cronet P Petersen JF Folmer R Blomberg N Sjoblom K Karlsson U Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family Structure 2001 9 699 706 11587644 Xu HE Lambert MH Montana VG Plunket KD Moore LB Collins JL Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors Proc Natl Acad Sci U S A 2001 98 13919 24 11698662 Figure 1 Overall structure of ground sate bovine rhodopsin and its key features (PDB: 1F88).
(B) 11- cis -retinal (in gray) in the ligand binding pocket is associated with the surrounding residues of the protein moiety (green, PDB: 1F88).
Structure of the chemokine receptor CXCR1 in phospholipid bilayers.
(2012) Nature 491
PubMed: 23086146 | PubMedCentral: PMC3700570 | DOI: 10.1038/nature11580
In the second stage, we used the resulting molecular fragment database, together with the experimental DC restraints and the structure of rhodopsin (PDB ID: 1F88) 25 as topology template, to fold 20,0... 0 structural models with the coarse-grained and implicit membrane potentials of Rosetta.
Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands.
(2010) Pharmaceuticals (Basel) 3
PubMed: 24009470 | PubMedCentral: PMC3760430 | DOI: 10.3390/ph3103324
Cartoon representation of (A) rhodopsin (PDBID: 1L9H) with the different zinc binding sites, as well as (B) rhodopsin (PDBID: 1F88), and (C) opsin (PDBID: 3CAP) both highlighting the top 4 potential b... nding pockets predicted using Pocket-Finder tool implemented based on the Ligsite algorithm [ 47 ].
Sphingosine 1-phosphate receptor 1 as a useful target for treatment of multiple sclerosis.
(2012) Pharmaceuticals (Basel) 5
PubMed: 24281561 | PubMedCentral: PMC3763654 | DOI: 10.3390/ph5050514
A model of S1P 1 was constructed by the homology model protocol in Discovery Studio 1.7 (Accelrys Software Inc.) based on the bovine rhodopsin crystal structure (PDB code 1F88) as a template.
Accounting for epistatic interactions improves the functional analysis of protein structures.
(2013) Bioinformatics 29
PubMed: 24021383 | PubMedCentral: PMC3799481 | DOI: 10.1093/bioinformatics/btt489
For instance, in the rhodopsin structure [PDBID 1f88], ET found the G-protein interaction determinants instead of the retinal binding site noted in the crystal structure ( Berman et al., 2000 ).
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