Primary Citation PubMed: 17962520
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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 )).
Squid rhodopsin in this study is shown in orange , bovine rhodopsin in the trigonal crystal (1GZM) ( 17 ) is blue , and β 2 AR (2RH1) excluding the T4 lysozyme part of CL3 ( 8 ) is sky blue .
Publication Year: 2008
Virtual screening of GPCRs: an in silico chemogenomics approach.
(2008) BMC Bioinformatics 9
PubMed: 18775075 | PubMedCentral: PMC2553090 | DOI: 10.1186/1471-2105-9-363
In our case, receptor flexibility might influence the definition of the binding pocket, since it initially relies on the identification of residues in the two reference structures ( 1U19 and 2RH1 ) th... t present at least one atom situated at less than 6 Å of the ligand.
(a) The two known structures, PDB entries 1U19 and 2RH1 [ 62 , 63 ], were superimposed using the STAMP algorithm [ 64 ].
For the two ligands for which it was known, i.e. , retinal and 3-(isopropylamino)propan-2-ol from PDB entries 1U19 and 2RH1 respectively, we found that the predicted conformation, using the same method as for all other molecules, was very close to the experimental conformation, with RMSD values of less than 1 Å.
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
SDR: a database of predicted specificity-determining residues in proteins.
(2009) Nucleic Acids Res 37
PubMed: 18927118 | PubMedCentral: PMC2686543 | DOI: 10.1093/nar/gkn716
The distance of each residue's C β atom to the closest atom on the inverse agonist, carbazol, in the recent β2 adrenergic receptor structure (pdb code 2RH1), is also listed.
( B ) The predicted specificity-determining residues of the amine subfamily of class A GPCRs are shown on the human β2 adrenergic receptor ( 21 ) (pdb code 2RH1).
SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins.
PubMed: 19429894 | PubMedCentral: PMC2703960 | DOI: 10.1093/nar/gkp338
Alternative conformations (red) for loop 2 of the human β 2 -adrenergic receptor (2rh1.
Allosteric modulation of adenosine receptors.
(2009) Purinergic Signal 5
PubMed: 18615273 | PubMedCentral: PMC2721769 | DOI: 10.1007/s11302-008-9105-3
7 The location of amino acid residues involved in allosteric modulation of A 1 , A 2A , and A 3 receptors as displayed in a receptor homology model of the adenosine receptor (side and top vie... ) based on the structure of the β 2 -adrenergic receptor cocrystallized with its ligand carazolol (PDB coordinates: 2rh1).
Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.
PubMed: 19756152 | PubMedCentral: PMC2738427 | DOI: 10.1371/journal.pone.0007011
Protein name Gene name Species from PDB code Unique identifier Adenosine-2A receptor AA2AR Homo sapiens 3EML hAA2AR Beta-1 adrenergic receptor B1AR Meleagris gallopavo 2VT4 tB1AR Beta-2 adrenergic rec... ptor B2AR Homo sapiens 2RH1 hB2AR Rhodopsin RHO Todarodes pacificus 2Z73 sRHO Rhodopsin RHO Bos taurus 1U19 bRHO 10.1371/journal.pone.0007011.
Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor.
(2010) Nature 463
PubMed: 20054398 | PubMedCentral: PMC2805469 | DOI: 10.1038/nature08650
Evidence for a buried ligand binding site J Biol Chem 1990 265 16891 7 1976626 34 Baker JG The selectivity of beta-adrenoceptor antagonists at the human beta1, beta2 and beta3 adrenoceptors Br J Pharm... col 2005 144 317 22 15655528 35 Otwinowski Z Minor W Processing of X-ray diffraction data collected in oscillation mode Macromolecular Crystallography, Pt A 1997 276 307 326 36 Brunger AT Crystallography & NMR system: A new software suite for macromolecular structure determination Acta Crystallographica Section D-Biological Crystallography 1998 54 905 921 37 Adams PD PHENIX: building new software for automated crystallographic structure determination Acta Crystallographica Section D-Biological Crystallography 2002 58 1948 1954 Figure 1 Extracellular domains of carazolol-bound β 2 AR (PDB: 2RH1) a, The extracellular surface (ECS) of β 2 AR showing extracellular loop 2 (ECL2, cyan, Met171-Ala198), extracellular loop 3 (ECL3, dark blue, His296-Glu306), Lys305 7.32 (magenta), Asp192 (yellow), and inverse agonist carazolol (green).
Colored helices, loops, and side chains represent the carazolol-bound crystal structure (PDB: 2RH1).
Publication Year: 2010
Tuning microbial hosts for membrane protein production.
(2009) Microb Cell Fact 8
PubMed: 20040113 | PubMedCentral: PMC2807855 | DOI: 10.1186/1475-2859-8-69
Protein Expression Host PDB coordinates Resolution (Å) Reference TRANSMEMBRANE PROTEINS: BETA-BARREL Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane Human VDAC-1 voltage dependent ... nion channel E. coli 2K4T 1 , 2JK4 2 4 [ 210 , 211 ] Murine VDAC-1 voltage dependent anion channel E. coli 3EMN 2.3 [ 212 ] TRANSMEMBRANE PROTEINS: ALPHA-HELICAL G Protein-Coupled Receptors Rhodopsin: Bovine Rod Outer Segment mutant N2C/D282C COS cells 2J4Y 3.4 [ 122 ] Engineered turkey β 1 adrenergic receptor Trichoplusia ni 2VT4 2.7 [ 1 ] Human β 2 adrenergic receptor, from β 2 AR365-Fab5 ( 2R4R ) and β 2 AR24/365- Fab5 complexes ( 2R4S ) Spodoptera frugiperda 2R4R , 2R4S 3.4/3.7 [ 2 ] Engineered human β 2 adrenergic receptor Spodoptera frugiperda 2RH1 , 3D4S 2.4/2.8 [ 3 , 4 ] Human A 2A adenosine receptor, In complex with a high-affinity subtype-selective antagonist ZM241385.
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
2006 ) and the beta-2 adrenergic receptor (PDBid 2rh1, Cherezov et al.
Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach.
(2010) BMC Struct Biol 10
PubMed: 20233425 | PubMedCentral: PMC2850907 | DOI: 10.1186/1472-6807-10-8
Table 1 Alignment among GPR17 model and X-ray templates of GPCRs RMSD (Å) after alignment of α -helical carbon 3EML 2R4R 2RH1 3D4S 2VT4 GPR17 2.867 2.458 2.688 2.738 2.413 b Rh 1.955 2... 210 2.362 2.277 2.862 Globally, the helical pack was highly conserved among all the structures, and also the alignment of the α -helical domains to the GPR17 bundle yielded a good fit, as shown in Figure 1 .
Recently, thanks to protein engineering, the modified structures of two human GPCRs have been solved, providing new templates suitable for homology modeling: the adenosine A 2 A receptor (A 2 A R) bound to the high-affinity antagonist ZM241385 (PDB code 3EML ) [ 22 ]; the β 2 -adrenergic receptor-Fab ( β 2 AR-Fab) (PDB code 2R4R ) [ 23 ] and the β 2 -adrenergic receptor-T4 ( β 2 AR-T4) (PDB code 2RH1 ) [ 24 , 25 ], both bound to their inverse agonist carazolol; the mutated β 2 -adrenergic receptor-(E122W)-T4 ( β 2 AR(E122W)-T4) (PDB code 3D4S ) bound to cholesterol and its partial inverse agonist timolol [ 26 ].
Ribbon representation of the β 2 AR-Fab ( 2R4R ), β 2 AR-T4 ( 2RH1 ), β 2 AR(E122W)-T4 ( 3D4S ), β 1 AR ( 2VT4 ) and A 2 A R structures after alignment of the α -helical domains to GPR17 model (in gray) are reported in cyan, orange, green, magenta and yellow respectively.
Lessons from free energy simulations of delta-opioid receptor homodimers involving the fourth transmembrane helix.
(2010) Biochemistry 49
PubMed: 20617813 | PubMedCentral: PMC2914489 | DOI: 10.1021/bi100686t
Materials and Methods Molecular Modeling The TM region of mouse δOR was built by homology modeling with Modeler 9v3 ( 23 ), using the X-ray crystal structure of β2-adrenergic receptor ... β2AR) at 2.4 Å resolution (Protein Data Bank entry 2RH1 ) as a structural template ( 24 ), and the β2AR-δOR sequence alignment deposited in the GPCR database ( 25 ), which is based on highly conserved functional residues in the TM segments.
Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach.
(2010) Chem Biol Drug Des 76
PubMed: 20626410 | PubMedCentral: PMC2918726 | DOI: 10.1111/j.1747-0285.2010.01012.x
The 2.4 Å crystal structure of carazolol-bound human β 2 AR [PDB code 2RH1 ( 15 )] was used for human β 2 AR, with carazolol removed from the OS.
Induced effects of sodium ions on dopaminergic G-protein coupled receptors.
(2010) PLoS Comput Biol 6
PubMed: 20711351 | PubMedCentral: PMC2920834 | DOI: 10.1371/journal.pcbi.1000884
In our study, the high resolution X-ray structure of the β 2 adrenergic receptor (PDB entry 2RH1, resolution 2.40 Å) was selected as a template for the D 2 receptor modeling ( Figure 1... ).
Methods For the realistic, three-dimensional structural molecular system, a D 2 homology model was built based on the β 2 adrenergic receptor (PDB ID 2RH1) according to a previously used protocol  .
Results/Discussion Recent advances in GPCR engineering and X-ray crystallography techniques has allowed the resolution of the structures of GPCRs closely-related phylogenetically to the D 2 receptor (PDB ID codes: 2RH1 and 3D4S, 2VT4, 3EML).
Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor.
(2010) PLoS One 5
PubMed: 20811630 | PubMedCentral: PMC2928277 | DOI: 10.1371/journal.pone.0012394
Homology models of the receptor are here based on all the solved GPCRs structures (PDB codes 1U19, 2I37, 2RH1, 2VT4, 2ZTS, 3CAP, 3DQB, 3EML).
From left to right: Adenosine-receptor based model (template PDB code: 3EML), Beta-1 adrenergic receptor based model (template PDB code: 2VT4) and Beta2 adrenergic receptor based model (template PDB code: 2RH1).
Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues.
(2010) BMC Res Notes 3
PubMed: 20979597 | PubMedCentral: PMC2991341 | DOI: 10.1186/1756-0500-3-270
By following the published scheme the following templates are suitable for the different transmembrane helices, TM1: 2VT4 [PDB: 2VT4 ], TM2: 2RH1 [PDB: 2RH1 ], TM3: 2VT4 [PDB: 2VT4 ] or 2RH1 [PDB: 2RH... ], TM4: 2VT4 [PDB: 2VT4 ], TM5: 1U19 [PDB: 1U19 ], TM6: 2VT4 [PDB: 2VT4 ], TM7: 1U19 [PDB: 1U19 ].
Predicting novel binding modes of agonists to ? adrenergic receptors using all-atom molecular dynamics simulations.
(2011) PLoS Comput Biol 7
PubMed: 21253557 | PubMedCentral: PMC3017103 | DOI: 10.1371/journal.pcbi.1001053
Methods All simulations are based on the crystal structure of human β 2 Adrenergic Receptor (Protein Data Bank code: 2RH1)  , and on chain B of the crystal structure of part... ally mutated (β 1 AR-m23) turkey β 1 Adrenergic Receptor (Protein Data Bank code: 2VT4)  .
Publication Year: 2011
The structural basis for agonist and partial agonist action on a ?(1)-adrenergic receptor.
(2011) Nature 469
PubMed: 21228877 | PubMedCentral: PMC3023143 | DOI: 10.1038/nature09746
(a) β 2 AR with the antagonist carazolol bound (PDB code 2RH1); (b) β 1 AR with the antagonist cyanopindolol bound (PDB code 2VT4); (c) β 1 AR with the agonist isoprenaline bou... d.
Chemogenomic analysis of G-protein coupled receptors and their ligands deciphers locks and keys governing diverse aspects of signalling.
(2011) PLoS One 6
PubMed: 21326864 | PubMedCentral: PMC3033908 | DOI: 10.1371/journal.pone.0016811
Furthermore, the crystal structure of the beta2-adrenergic receptor  complexed with the inverse agonist carazolol (pdb entry 2RH1) evidenced interactions (H-bonds) of this ligand t... residues at TMH3, 5, and 7.
Making structural sense of dimerization interfaces of delta opioid receptor homodimers.
(2011) Biochemistry 50
PubMed: 21261298 | PubMedCentral: PMC3050604 | DOI: 10.1021/bi101474v
Briefly, we built the TM region of mouse DOR by homology modeling using the crystal structure of the β2 adrenergic receptor at 2.4 Å resolution (Protein Data Bank entry 2RH1 ) ( 35 ), ... nd a sequence alignment based on conserved residues and motifs that are present in family A GPCRs as inputs to Modeler 9v3 ( 36 ).
Structure of a nanobody-stabilized active state of the ?(2) adrenoceptor.
PubMed: 21228869 | PubMedCentral: PMC3058308 | DOI: 10.1038/nature09648
The search models were 1) the high-resolution carazolol-bound β 2 AR structure, PDB id 2RH1, but with T4L and all water, ligand and lipid molecules removed) and a nanobody (PDB id 3DWT, water ... olecules removed) as search models.
Selective orthosteric free fatty acid receptor 2 (FFA2) agonists: identification of the structural and chemical requirements for selective activation of FFA2 versus FFA3.
(2011) J Biol Chem 286
PubMed: 21220428 | PubMedCentral: PMC3060514 | DOI: 10.1074/jbc.M110.210872
Molecular Modeling and Ligand Docking Homology modeling of hFFA2 and hFFA3 receptors using the β 2 -adrenergic receptor (Protein Data Bank code 2RH1 ) as a template was conducted using MOE sof... ware (Molecular Operating Environment, 2009, Chemical Computing Group, Inc., Montreal, Quebec, Canada) with a default homology modeling protocol.
?2-Adrenergic ion-channel coupled receptors as conformational motion detectors.
PubMed: 21464970 | PubMedCentral: PMC3064670 | DOI: 10.1371/journal.pone.0018226
Helix H8 and β-bridge β1 are predicted from the β 2 AR (PDB code: 2RH1) and chimeric Kir3.1 (PDB code: 2QKS) structures, respectively.
Structure and function of an irreversible agonist-?(2) adrenoceptor complex.
PubMed: 21228876 | PubMedCentral: PMC3074335 | DOI: 10.1038/nature09665
However, the orientation of T4L relative to the receptor closely resembles the original carazolol-bound structure (PDB ID 2RH1).
The separated structures of the receptor and T4L components of the high-resolution carazolol-bound β 2 AR structure (PDB ID 2RH1 with all non protein atoms removed), were used as search models.
System setup and simulation protocol Hydrogens were added to the crystal structures of carazolol-bound β 2 AR ( β 2 AR-Cz; PDB entry 2RH1) and β 2 AR-NB80/BI-167107 (companion paper) using Maestro (Schrödinger LLC, New York NY) as described previously 19 .
GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.
(2011) BMC Bioinformatics 12
PubMed: 21605354 | PubMedCentral: PMC3113946 | DOI: 10.1186/1471-2105-12-185
Template selection and homology modelling A profile hidden markov model (HMM) was used to align the 5025 GPCRs to the five template structures available at the time (before November 2010) (PDB codes: ... U19 , 2Z73 , 2VT4 , 2RH1 and 3EML ) [ 22 ].
In order to assess the impact of increased template similarity on the accuracy of the homology models we used different sets of templates for modelling, based on their sequence similarity across the entire serpentine domain: 1) Bovine rhodopsin (PDB: 1U19 ) and Japanese flying squid rhodopsin (PDB: 2Z73 2) 1U19, 2Z73 and human Adenosine receptor A2A (PDB: 3EML ) 3) 1U19, 2Z73, 3EML, common turkey Beta-1 adrenergic receptor (PDB; 2VT4 ) and human Beta-2 adrenergic receptor (PDB: 2RH1 ) In order to assess the impact of using multiple templates for building homology models compared to using the single most similar template, we also built a model for each of the two GPCRs using only the GPCR structure with the highest sequence similarity across the entire serpentine domain, which in both cases was: 4) 2VT4 5) Finally, we used I-TASSER [ 29 ], which was ranked 1 in the server category of the Critical Assessment of Structure Prediction (CASP) 2007-2009, to build a model of both drd3_human and cxcr4_human, excluding their respective crystal structures from template selection.
Table 1 The RMSD of cxcr4_human and drd3_human homology models compared to their crystal structures Method used for template selection Templates used Accuracy cxcr4_human (RMSD) 1 Accuracy drd3_human (RMSD) 2 Sequence similarity across entire serpentine domain 2VT4 1.72 0.94 Sequence similarity for each TMH 1U19 and 2Z73 1.78 1.21 SSFE workflow or sequence similarity for each TMH 1U19, 2Z73 and 3EML 1.97 1.04 SSFE workflow 1U19, 2Z73, 3EML, 2VT4 and 2RH1 1.73 0.88 I-TASSER Crystal structure of query protein excluded 1.91 0.82 1 RMSD between cxcr4_human model and 3ODU (TMH region) 2 RMSD between drd3_human model and 3PBL (TMH region) We also did a comparable analysis of the five template structures and observed similar results to those observed for drd3_human and cxcr4_human, although in some instances the models produced by I-TASSER are significantly worse due to part of the transmembrane domain being modelled on the T4 lysozyme insertion found in some GPCR crystal structures (See additional file 2 , Tables S1-S5).
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.
PubMed: 21831265 | PubMedCentral: PMC3162937 | DOI: 10.1186/1471-2105-12-332
In Figure 4B the crystal structure of the ADRB2 receptor, co-crystalized with carazolol (pdbid: 2RH1 ) is visualized with the residues disrupting ligand binding colored green.
B: Crystal structure of ADRB2 co-crystalized with carazolol (pdbid: 2RH1 ), residues disrupting ligand binding upon mutation are colored green.
Molecular basis of ligand dissociation in ?-adrenergic receptors.
PubMed: 21915263 | PubMedCentral: PMC3168429 | DOI: 10.1371/journal.pone.0023815
Methods Molecular models and identification of ligand access channels The high-resolution crystal structures of the β 1 AR  and β 2 AR  were obtained from the Protein Data Bank... (PDB entries 2VT4 and 2RH1 respectively).
Investigation of the structure requirement for 5-HT? binding affinity of arylsulfonyl derivatives: a computational study.
(2011) Int J Mol Sci 12
PubMed: 21954341 | PubMedCentral: PMC3179148 | DOI: 10.3390/ijms12085011
The template protein (PDB code: 2RH1 chain A, obtained from the Protein Data Bank [ 43 ], a high resolution (2.4 Å) crystal structure of human β 2 -adrenergic G protein-coupled recepto... [ 44 ], was employed to generate the 3D protein structure.
Homology Modeling Results Figure 4 shows the structural superposition of the 5-HT 6 receptor homology model to the X-ray crystal structure of the template molecule (PDB ID: 2RH1).
( A ) Sequence alignment of 2RH1 (Chain A) and the 5-HT 6 receptor model, where the important transmembrane domains (TM1-TM7) are marked in red frame; ( B ) Superposition of the template protein 2RH1 chain A (red ribbon) and the 5-HT 6 receptor model structure (yellow ribbon) from homology modeling.
Seemingly, the sequence identity between 5-HT 6 receptor model and template 2RH1 is not so high (29% obtained from the automated mode report from [ 35 ]).
As seen in Figure 4B , compound 198 is docked into the pocket of the 5-HT 6 receptor, and the template protein 2RH1 chain A (red ribbon) are well superposed with the 5-HT 6 receptor model structure (yellow ribbon) obtained from the homology modeling, especially, around the binding pocket area.
Crystal structure of the ?2 adrenergic receptor-Gs protein complex.
(2011) Nature 477
PubMed: 21772288 | PubMedCentral: PMC3184188 | DOI: 10.1038/nature10361
In order, the search models used were: the β and γ subunits from a Gi heterotrimer (PDB ID: 1GP2), the Gs alpha ras-like domain (PDB ID: 1AZT), the active-state β 2 AR (PDB ID:... 3P0G), a β 2 AR binding nanobody (PDB ID: 3P0G), T4 lysozyme (PDB ID: 2RH1), and the Gs alpha helical domain (PDB ID: 1AZT).
Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques.
PubMed: 22022248 | PubMedCentral: PMC3192824 | DOI: 10.1371/journal.pcbi.1002193
Unliganded Receptor An activation pathway from the inactive to the active B2AR crystal structures (PDB codes 2RH1 and 3P0G, respectively) was obtained by ABMD following the protocol described in the M... terials and Methods section.
Materials and Methods System and Simulation Setup A model of the B2AR ( Figure S1 was prepared starting from one of the available crystal structures of this receptor (PDB ID: 2RH1), removing the lysozyme insertion, and modeling the missing intracellular loop 3 (IL3) with the Rosetta ab-initio loop modeling protocol  .
The intracellular loop 2 (IL2), which is probably misfolded  ,  in the inactive structure of the B2AR (2RH1), but in a helical conformation in the active nanobody-stabilized crystal (3P0G) of the receptor, was also replaced by the lowest-energy Rosetta model with a helical fold.
The outward movement is described by the difference in d TM6 values between any given conformation and the reference inactive crystal structure, i.e. by Δd TM6 = d TM6 –d TM6 (2RH1).
Ligand Docking Ligands for which an experimental crystal structure in complex with the B2AR is available, i.e. 2RH1 for carazolol  , 3NY8 for ICI- 118,551  , and 3NYA for alprenolol  , were positioned in the binding pocket accordingly.
On the other hand, representative structures of the energy basin at s∼0.2 (data not shown) corresponded to conformations of the helix bundle very similar to the inactive crystal structure of B2AR (Cα RMSD from 2RH1 is ∼1.0 Å).
The reference states R j (1≤ j ≤ n ) were numbered assigning j = 1 to the cluster closer to the inactive state (Cα RMSD from 2RH1 ∼0.4 Å) and j = 10 to the one closer to the active state (Cα RMSD from 3P0G ∼0.3 Å).
Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
(2011) Nat Chem Biol 7
PubMed: 21926995 | PubMedCentral: PMC3197762 | DOI: 10.1038/nchembio.662
Methods Homology Models The initial alignment was generated using PROMALS3D 46 using a sequence profile that included all dopamine receptor sequences as well as the β 1 and β 2 adrener... ic receptor sequences (PDB: 2VT4(chain B) 3 and 2RH1(chain A) 2 ).
Differential modulation of Beta-adrenergic receptor signaling by trace amine-associated receptor 1 agonists.
PubMed: 22073124 | PubMedCentral: PMC3205048 | DOI: 10.1371/journal.pone.0027073
The putative helix dimensions and loop regions are assigned according to observable features in the crystal structure of the inactivated β2-adrenergic receptor (pdb entry code 2RH1).
A ) The pocket-like ligand binding region (inner crevice surface) of the human β2-adrenergic receptor (pdb entry code 2RH1) is surrounded by amino acids (lilac sticks, labeled) which are also known from mutagenesis studies to be important for ligand binding and signal transduction.
For modeling of the human TAARs 1, 2, 5, 6, 8, and 9 we used the inactive structural conformation of the β-2 adrenergic receptor (pdb entry 2RH1,  ), based on high sequence similarity between hTAAR1 and β-adrenergic receptor 2 (39% similarity, Blosum62 matrix).
Prediction of the Human EP1 Receptor Binding Site by Homology Modeling and Molecular Dynamics Simulation.
Sci Pharm 79
PubMed: 22145106 | PubMedCentral: PMC3221501 | DOI: 10.3797/scipharm.1106-24
There are some crystal structures of members of GPCRs receptors available: Bovine rhodopsin (PDB code: 1L9H) [ 9 ], β 2 -adrenergic receptor (PDB code: 2RH1 ) [ 10 ], active β 2 -adren... rgic receptor (PDB code: 3P0G) [ 11 ] and CXCR4 chemokine receptor (PDB code: 3ODU) [ 12 ].
Publication Year: null
Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs.
PubMed: 22132188 | PubMedCentral: PMC3221691 | DOI: 10.1371/journal.pone.0027990
bRho - bovine Rhodopsin (PDB code:1L9H), hB2ADR - human β2-adrenergic receptor (2RH1), hA2AR - human A 2A adenosine receptor (3EML).
These multiple-template models are based on X-ray structures of bovine Rhodopsin (PDB codes: 1L9H)  , the human β2-adrenergic receptor (2RH1)  , and the human A 2A -adenosine receptor (3EML)  .
(A) Cyanopindolol redocked to β1adr crystal structure (PDB code: 2VT4), (B) Carazolol redocked to β1adr crystal structure (2YCW), (C) Carazolol redocked to β2adr crystal structure (2RH1), (D) Cyanopindolol docked to β1adr homology model, (E) Carazolol docked to β1adr homology model and (F) Carazolol docked to β2adr homology model.
The β1adr homology model is based on 4 different β2adr crystal structures (PDB codes – 3SN6, 2RH1, 3NY8, and 3d4S); the β2adr model is based on the crystal structures of β1adr (2VT4, 2YCW), the Dopamine D3 receptor (3PBL), and the histamine H1 receptor (3RZE).
Global analysis of small molecule binding to related protein targets.
(2012) PLoS Comput Biol 8
PubMed: 22253582 | PubMedCentral: PMC3257267 | DOI: 10.1371/journal.pcbi.1002333
The model was constructed from template structures of the Histamine H1 receptor (3rze), as well as the dopamine D3 receptor (3pbl), the human beta 2 adrenergic (2rh1, 3d4s, 3ny8, 3nya) and the turkey ... eta 1 adrenergic receptor (2vt4).
The model was constructed from template structures of the Histamine H1 receptor (3rze), as well as the dopamine D3 receptor (3pbl), the human beta 2 adrenergic (2rh1, 3d4s, 3ny8, 3nya) and the turkey beta 1 adrenergic receptor (2vt4).
Publication Year: 2012
Site-directed mutations and the polymorphic variant Ala160Thr in the human thromboxane receptor uncover a structural role for transmembrane helix 4.
(2012) PLoS One 7
PubMed: 22272267 | PubMedCentral: PMC3260207 | DOI: 10.1371/journal.pone.0029996
Panel A , Molecular model of TP bound SQ 29,548 superimposed with the structures of rhodopsin (PDB ID 1U19) and antagonist bound β 2 -AR (PDB ID 2RH1).
Figure 7A shows the homology model of SQ 29,548 bound TP model superimposed with the structures of rhodopsin (PDB ID, 1U19) and antagonist bound β 2 -AR (PDB ID, 2RH1).
Drug design for ever, from hype to hope.
(2012) J Comput Aided Mol Des 26
PubMed: 22252446 | PubMedCentral: PMC3268973 | DOI: 10.1007/s10822-011-9519-9
When the structure of the human β2 adrenoceptor bound to carazolol was solved by X-ray [PDBid 2RH1; 202 ], it showed indeed two hydrogen bonds between Asn-719 and this similar ligand (see Fig&... x000a0; 4 ).
A novel G protein-coupled receptor of Schistosoma mansoni (SmGPR-3) is activated by dopamine and is widely expressed in the nervous system.
(2012) PLoS Negl Trop Dis 6
PubMed: 22389736 | PubMedCentral: PMC3289605 | DOI: 10.1371/journal.pntd.0001523
The model was generated using the β-2 adrenergic receptor (PDB Accession # 2rh1) as a structural template, as described in the Methods.
Prior to generating the model, SmGPR-3 was aligned with the sequences of GPCR crystal structures available in the general protein database (PDB) (Accession numbers: 2rh1, 3eml, 1u19, 2vt4, 2z73) and the β-2 adrenergic receptor (2hr1) was selected as the best template based on similarity scores.
A homology model of SmGPR-3 was obtained from a structural alignment with the β2-adrenergic receptor (2rh1) and used for docking simulations.
Designing allosteric modulators for active conformational state of m-glutamate G-protein coupled receptors.
(2012) Bioinformation 8
PubMed: 22419835 | PubMedCentral: PMC3301996 | DOI: 10.6026/97320630008170
The structure of human B2- adrenergic G protein-coupled receptor was taken from PDB database having the PDB ID 2RH1 in the activated state and the structure was generated for mGlur1 its sequence was o... tained from NCBI,GenBank [ 7 , 8 ].
Progress in structure based drug design for G protein-coupled receptors.
(2011) J Med Chem 54
PubMed: 21615150 | PubMedCentral: PMC3308205 | DOI: 10.1021/jm200371q
Figure 5 TMD binding sites of published GPCRs illustrating protein–ligand interactions for agonists (cyan ligands) compared with antagonists (pink ligands): (A) general changes on antagonist t... agonist transition exemplified using rhodopsin (red) and opsin (green); (B) rhodopsin agonist structure (green) 2X72 vs antagonist structure (red) 1HZX ; (C) β 2 AR agonist structure (green) 3POG vs antagonist structure (red) 2RH1 ; (D) A 2A R agonist structure (green) 3QAK vs antagonist structure (red) 3EML .
Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study.
PubMed: 22479344 | PubMedCentral: PMC3314010 | DOI: 10.1371/journal.pone.0032864
X-ray structures of bovine rhodopsin (1U19), β 2 AR (2RH1), A 2A AR (3EML) were aligned over recent CXCR4 (3ODU) structure.
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
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 (Bo... ine 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.
A novel evolutionarily conserved domain of cell-adhesion GPCRs mediates autoproteolysis.
(2012) EMBO J 31
PubMed: 22333914 | PubMedCentral: PMC3321182 | DOI: 10.1038/emboj.2012.26
The seven-pass transmembrane domain (orange) was modelled by homology using the crystal structure of the β2 adrenergic GPCR structure (PDB ID 2RH1) ( Cherezov et al, 2007 ; Rosenbaum et al, 20... 7 ), and the GAIN and HormR domains were taken from the crystal structure of CL1.
Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties.
PubMed: 22532793 | PubMedCentral: PMC3330085 | DOI: 10.1371/journal.pcbi.1002473
In all simulations, C7.70 was palmitoylated by moving the coordinates of the palmitoyl chain (PALM) from PDB 2RH1  onto the C7.70 of 5-HT 2A R. Loop structures determined from ab inito loop predic... ion To enable full-scale 5-HT 2A R simulations, we refined the loops in 5-HT 2A R homology model described recently  using the Monte Carlo-Scaled Collective Variables ab initio method  ,  .
Comparative analysis of the heptahelical transmembrane bundles of G protein-coupled receptors.
PubMed: 22545139 | PubMedCentral: PMC3335790 | DOI: 10.1371/journal.pone.0035802
A 7TM bundle of 200 residues was successfully extracted from 80 chains and superposed on that of the highest resolution inactivated form of β2-adrenergic receptor (PDB entry 2RH1).
Stereo view of molecular overlay of helix VI within 7TM bundles: inactivated (red, PDB ID: 1U19-A) and activated (pink, PDB ID: 3PXO) bovine rhodopsin, inactivated (blue, PDB ID: 2RH1) and activated (cyan, PDB ID: 3SN6) β2 receptor, inactivated (yellow, PDB ID: 3EML) and activated (lemon, PDB ID: 3QAK) A2A receptor.
All of the 200 residue 7TM bundles were superposed on that of the highest resolution inactivated form of β2-adrenergic receptor (PDB entry 2RH1) by a secondary structure matching (SSM) algorithm  implemented in Coot  , from which 10 representative chains are shown in Figure 1 .
The colors of receptors are red, bovine rhodopsin (1U19-A); pink, squid rhodopsin (2Z73-A); blue, β2 receptor (2RH1); cyan, β1 receptor (2VT4-B); yellow, A2A receptor (3EML); gray, CXCR4 receptor (3ODU-A); magenta, D3 receptor (3PBL-A); purple, H1 receptor (3RZE); green, M2 receptor (3UON); light green, S1P1 receptor (3V2Y).
Using 9 representative chains (1U19-A for bovine rhodopsin, 2Z73-A for squid rhodopsin, 2RH1 for β2 receptor, 3EML for A2A receptor, 3ODU-A for CXCR4 receptor, 3PBL-A for D3 receptor, 3RZE for H1 receptor, 3UON for M2 receptor and 3V2Y for S1P1 receptor), deviations at 200 positions were calculated for all possible 36 pairs by CCP4  , demonstrating that the SSM fitting worked well because the Cα atoms of highly conserved residues (such as *.50s of Ballesteros & Weinstein numbering  for GPCRs, in which * is to be replaced with the number of helix) exhibited very small shifts among the chains from different receptors ( Figure 2 ).
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 ]
Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
(2012) Nature 482
PubMed: 22278061 | PubMedCentral: PMC3345277 | DOI: 10.1038/nature10753
Structure solution and refinement The structure was solved by molecular replacement using Phaser 37 , 38 with the structure of the inactive β 2 adrenergic receptor and T4 lysozyme used as sear... h models (PDB ID: 2RH1).
Molecular evolution of a peptide GPCR ligand driven by artificial neural networks.
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)  .
Structure of the human ?-opioid receptor in complex with JDTic.
(2012) Nature 485
PubMed: 22437504 | PubMedCentral: PMC3356457 | DOI: 10.1038/nature10939
( c ) Side and ( d ) extracellular views of a structural alignment of hKOR (yellow); CXCR4 (PDB ID: 3ODU; magenta) and β 2 AR (PDB ID: 2RH1; cyan).
Investigation of D? receptor-agonist interactions using a combination of pharmacophore and receptor homology modeling.
(2012) ChemMedChem 7
PubMed: 22315215 | PubMedCentral: PMC3382189 | DOI: 10.1002/cmdc.201100545
As mentioned above, Rasmussen et al., 46 together with Cherezov, Rosenbaum, and co-workers, 16 solved the 3D structure of the human β 2 adrenergic receptor (adrb2; PDB codes: 2R4S and 2RH1).
11 , 14 The ionic lock is not, however, present in the inactive states of the recently solved β 1 and β 2 adrenergic receptor structures (adrb1 [PDB code: 2VT4], adrb2 [2RH1], respectively) or in the adenosine A 2A (ad2a [PDB code: 3EML]) receptor structure.
Therefore, in the present study we chose the adrb2 structure (2RH1) as the template in the homology modeling procedure; 2RH1 has a resolution of 2.4 Å, which is the highest resolution of all crystal structures of monoaminergic GPCRs obtained so far.
The main difference between the 2RH1 structure and the true receptor structure is that the third intracellular loop (IC3) had to be replaced with T4 lysozyme (T4L) in order to stabilize the receptor for crystallization.
The adjustments in the initial alignment were: Figure 2 The final sequence alignment of the human adrenergic β 2 receptor (adrb2, 2RH1) and the human dopamine D 2 receptor (drd2).
Figure 3 Two orthogonal views of the dopamine D 2 receptor (drd2) homology model (yellow) with the full agonist ( R )-2-OH-NPA present in the binding site, and the structure of the adrenergic β2 receptor (adrb2; 2RH1) in red.
Investigation of D? receptor-agonist interactions and D?/D? agonist selectivity using a combination of pharmacophore and receptor homology modeling.
PubMed: 22315216 | PubMedCentral: PMC3382191 | DOI: 10.1002/cmdc.201100546
29 , 30 Dopamine D 1 receptor structure models with all loops except the third intracellular loop (IC3) were built by using the structure of the human β 2 adrenergic receptor (adrb2; PDB code:... 2RH1) as template.
Results and Discussion Multiple sequence alignment and manual adjustments A multiple sequence alignment of the human adrenergic β 2 (adrb2, PDB code: 2RH1), drd1, and drd2 was performed by using Clustal W (version 2.0.11).
Figure 1 The refined multiple sequence alignment of the human adrenergic β 2 receptor (adrb2, 2RH1) and the dopamine D 1 (drd1) and D 2 (drd2) receptors.
D 1 receptor homology modeling The D 1 homology model was built with the high-resolution β 2 receptor structure (2RH1) as template.
Assessing the relative stability of dimer interfaces in g protein-coupled receptors.
PubMed: 22916005 | PubMedCentral: PMC3420924 | DOI: 10.1371/journal.pcbi.1002649
Materials and Methods Initial Model Systems Initial molecular models of human B1AR and B2AR were built using available inactive crystal structures of the turkey B1AR and human B2AR (PDB identification... codes: 2VT4  , chain B, and 2RH1  , respectively) as structural templates.
We observed that some of the small number of long-resident cholesterols near to the TM1/H8 interface (illustrated here by the ROH bead only, colored by residue, one bead per frame, over the whole trajectory), congregated in similar positions to the cholesterol molecules found in the crystal structures of B2AR (PDB ID: 2RH1,yellow sticks) (e.g. blue, purple beads), although not exclusively (e.g. red and green beads).
Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function.
(2012) J Mol Model 18
PubMed: 22643967 | PubMedCentral: PMC3429779 | DOI: 10.1007/s00894-012-1431-2
Even within the group of inactive structures (PDB IDs: 2RH1, 3D4S, 3NYA, Fig.
1 ), we selected four different conformational states of the β 2 AR in complex with partial inverse agonists carazolol (PDB ID: 2RH1 [ 15 ]) and timolol (PDB ID: 3D4S [ 16 ]), the neutral antagonist alprenolol (PDB ID: 3NYA [ 17 ]) and an agonist (PDB ID: 3P0G [ 20 ]).
Fig. 2 Top left: structural superimposition of the active (PDB ID: 3P0G) and the inactive (PDB ID: 2RH1) β 2 AR showing both receptors from the intracellular side as well as two structural insets in surface representation highlighting differences between the inactive and the active β 2 AR.
The dotted circle highlights differences in the roughness pattern Table 3 Average roughness of the β 2 AR in different conformational states accompanied by the standard deviation (SD) for the orthosteric and the cholesterol binding sites at TM4 3D4S 2RH1 3NYA 3P0G Complete receptor (exposed residues) 2.1215 ± 0.0347 2.1210 ± 0.0363 2.1227 ± 0.0416 2.1196 ± 0.0352 Orthosteric binding site Trp109 3.28 , Asp113 3.32 , Val114 3.33 , Val117 3.36 , Ser203 5.42 , Phe289 6.51 , Phe290 6.52 , Asn312 7.39 , Tyr316 7.43 2.1567 ± 0.0501 2.1521 ± 0.0424 2.1572 ± 0.0577 2.1592 ± 0.0367 Cholesterol binding site (TM4) Val81 2.52 , Phe108 3.27 , Ile112 3.31 , Leu115 3.34 , Ile154 4.46 , Trp158 4.50 2.1424 ± 0.0400 2.1430 ± 0.0411 2.1679 ± 0.0317 2.1303 ± 0.0394 The obtained data for orthosteric binding sites of different β 2 AR structures (Table 3 ) shows clearly that the average roughness values for residues interacting directly with timolol (PDB ID: 3D4S), carazolol (PDB ID: 2RH1), alprenolol (PDB ID: 3NYA), and an agonist (PDB ID: 3P0G) are higher (2.1521 – 2.1592) than the average for the whole receptor (exposed residues: 2.1196 – 2.1227).
Fig. 1 Workflow for the calculation of surface roughness and exposure ratio for different conformational states of the β 2 AR Materials and methods Studied X-ray structures Four X-ray structures of the β 2 AR in different conformational states were studied: in complex with partial inverse agonists carazolol (PDB ID: 2RH1 [ 15 ]) and timolol (PDB ID: 3D4S [ 16 ]), the neutral antagonist alprenolol (PDB ID: 3NYA [ 17 ]) and an agonist (PDB ID: 3P0G [ 20 ]).
Blue lines correspond to inactive structures (PDB IDs: 2RH1, 3D4S, 3NYA) whereas the red line corresponds to the active structure (PDB ID: 3P0G) Exposure ratio of β 2 AR residues in different conformational states The calculation of exposure ratio of helix-forming residues for each transmembrane segment is described in detail in the Materials and methods section.
2 , red line) with the inactive ones (PDB IDs: 3D4S, 2RH1, 3NYA, Fig.
Interestingly, the roughness profile between conformationally different structures (PDB IDs: 2RH1, 3D4S, 3NYA, 3P0G, Fig.
Blue lines correspond to inactive structures (PDB IDs: 2RH1, 3D4S, 3NYA) and the red line – to the active structure (PDB ID: 3P0G) Roughness versus exposure ratio We have shown above for GPCRs that both the exposure ratio and the surface roughness expressed as the fractal dimension exhibit a periodic pattern (Figs.
In the active structure of the β 2 AR (PDB ID: 3P0G) the intracellular side of the receptor (site of G protein binding) is much more open in comparison to the inactive β 2 AR conformation (PDB IDs: 2RH1, 3D4S, and 3NYA, Fig.
6 , a – d; Table 3 : 2.1521 – 2.1592) are found between active (PDB ID: 3POG) and inactive (PDB IDs: 3D4S, 2RH1, 3NYA) conformations of β 2 ARs .
Homology modeling of dopamine D2 and D3 receptors: molecular dynamics refinement and docking evaluation.
PubMed: 22970199 | PubMedCentral: PMC3435408 | DOI: 10.1371/journal.pone.0044316
The homology models of these GPCRs were built in complex with haloperidol (previously aligned to the β 2 -adrenergic inverse agonist s-carazolol), using the crystal structure of β 2 -a... renergic receptor (2RH1); the complexes were subsequently simulated in a POPC bilayer for 1.5 ns.
N-terminal T4 lysozyme fusion facilitates crystallization of a G protein coupled receptor.
PubMed: 23056231 | PubMedCentral: PMC3464249 | DOI: 10.1371/journal.pone.0046039
E. ICL2 in the β 2 AR-T4L structure (pdb 2RH1).
Comparison of T4L-β 2 AR-Δ-ICL3 and β 2 AR-T4 structures The structures of the β 2 AR in T4L-β 2 AR-Δ-ICL3 (pdb 4GBR) and β 2 AR-T4L (pdb 2RH1) are very similar to each other ( Fig. 6 ), with an overall root mean square deviation of 0.32 Å.
A. The superimposed structures of the T4L-β 2 AR-ΔICL3 and the β 2 AR-T4L (pdb 2RH1).
The cutoff value is 3 and 268 out of 282 Cα atoms of the two structures (4GBR and 2RH1) were included in the structural alignment.
Why GPCRs behave differently in cubic and lamellar lipidic mesophases.
(2012) J Am Chem Soc 134
PubMed: 22931253 | PubMedCentral: PMC3469068 | DOI: 10.1021/ja3056485
To assess this hypothesis in the context of structural information available for GPCRs, we examined crystallographic contact interfaces for 12 different structures of rhodopsin-like GPCRs obtained by ... eans of the in meso technology (β 2 receptor – PBD codes: 2RH1 , 3PDS , 3SN6 ; A2A receptor – PDB codes: 3EML , 3QAK ; Chemokine CXCR4 receptor – PDB codes: 3ODU , 3OE0 , 3OE6 , 3OE8 , 3OE9 ; Dopamine D3 receptor – PDB code: 3PBL , and Histamine H1 receptor – PDB code: 3RZE ).
Molecular characterization of oxysterol binding to the Epstein-Barr virus-induced gene 2 (GPR183).
(2012) J Biol Chem 287
PubMed: 22875855 | PubMedCentral: PMC3471686 | DOI: 10.1074/jbc.M112.387894
A, view from the extracellular side of the human CXCR4 ( gray ; Protein Data Bank code 3ODU ), the human β 2 -adrenoreceptor ( dark blue ; Protein Data Bank code 2RH1 , and the human S1P1 rece... tor ( red ; Protein Data Bank code 3V2Y ) crystal structures as aligned by PyMOL software.
Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes.
PubMed: 23094046 | PubMedCentral: PMC3477165 | DOI: 10.1371/journal.pone.0047332
MM/CG Simulations of Human β2-adrenergic Receptor (hβ2AR) in Complex with S-carazolol (S-Car) or R-isoprenaline (R-Iso) The calculations are based on the X-ray structure of the h... 2;2AR in complex with S-Car (PDB code 2RH1)  .
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
The PDB structures used in the figure are 1U19, 2Z73, 2VT4, 2Y00, 2Y02, 2Y03, 2Y04, 2RH1, 3D4S, 3NY8, 3NY9, 3NYA, 3P0G, 3PDS, 3EML, 3PBL, 3ODU and 3OE0.
Table 1 GPCR summary table Receptor PDB IDs [number of structures] Ligands Bovine Rhodopsin ( BR ) 1 F88, 1GZM, 1HZX, 1JFP, 1L9H, 1LN6, 1U19, 2 G87, 2HPY, 2I35, 2I36, 2I37, 2J4Y, 2PED, 3C9L, 3C9M, 3CAP, 3DQB [ 18 ] RT, Ligand free Squid Rhodopsin ( SR ) 2Z73, 2ZIY [ 2 ] RT Turkey β1 adrenergic receptor ( β1AR ) 2VT4, 2Y00, 2Y01, 2Y02, 2Y03, 2Y04 [ 6 ] Cyanopindilol, Dobutamine Carmoterol, Isoprenaline Salbutamol Human β2 adrenergic receptor ( β2AR ) 2R4R, 2R4S, 2RH1, 3D4S, 3KJ6, 3NY8, 3NY9, 3NYA, 3P0G, 3PDS [ 10 ] Carazalol, Timolol, ICI 118,551, (molecule from Kolb et al., 2009), Alprenolol, BI-167107, FAUC50 Human A2A adenosine receptor ( A2A ) 3EML [ 1 ] ZM241385 Human chemokine receptor ( CXCR4 ) 3ODU, 3OE0, 3OE6, 3OE8, 3OE9 [ 5 ] IT1t, CVX15 Human dopamine D3 receptor ( D3R ) 3PBL [ 1 ] Eticlopride Summary of structural information available on GPCRs as of January 2011.
Structure of the agonist-bound neurotensin receptor.
(2012) Nature 490
PubMed: 23051748 | PubMedCentral: PMC3482300 | DOI: 10.1038/nature11558
(c) Alignment of the inactive state of β 2 AR 40 (pale mauve, PDB code 2RH1) and its active state 32 (pale grey, PDB code 3SN6) and NTS1-GW5 (green).
(c) The same comparison for inactive β 2 AR 40 (pale mauve, PDB code 2RH1) and active β 2 AR 32 (pale grey, PDB code 3SN6) (residues E130, R131 and Y219).
Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists.
PubMed: 23185482 | PubMedCentral: PMC3503826 | DOI: 10.1371/journal.pone.0049910
The docking spheres used as anchor points in the binding site to position the database molecules in the orthosteric pocket were calculated based on the heavy-atom positions of carazolol and 1 when sup... rimposing the backbone atoms of the β 2 -adrenergic receptor (PDB code 2RH1) and A 2A AR, respectively, with the A 1 AR model.
The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations.
PubMed: 23189124 | PubMedCentral: PMC3506623 | DOI: 10.1371/journal.pone.0047114
Since the region corresponding to helix H8 at cytoplasmic side of CXCR4 is unfolded in the crystal, the crystal structure of human β 2 -adrenergic receptor  (PDB id 2RH1) was used as the s... cond template for the H8 regions of FPR1.
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
[ 152 ] constructed homology model of human D 3 receptor using the X-ray crystal structure of the human β 2 AD receptor (PDB entry: 2RH1, resolution 2.4 Ε) as the template structure.
Recently, the appearance of crystal structures of four new GPCRs (Opsin, 3cap; β 2 adrenergic (β 2 -AR), 2rh1; turkey b1 adrenergic (β 1 -AR), 2vt4; human A2A adenosine receptor, 3eml) brings a broader template diversity for in silico modeling.
Analyzing the bovine rhodopsin structure with the human β 2 -adrenergic receptor (2rh1) gives basis for understanding some facts and drawbacks of the modeling techniques used earlier for GPCR's[ 123 ].
Novel homodimer model of the ?-adrenergic receptor in complex with free fatty acids and cholesterol: first-principles calculation studies.
PubMed: 23275728 | PubMedCentral: PMC3532008 | DOI: 10.6026/97320630081245
βAR-cholesterol complex : We superimposed a cholesterol molecule, which is contained in the crystal structure of the inactive form of human β2AR (PDB ID: 2RH1 [ 5 ]), onto the β... AR structure.
This calculation result is in good agreement with the experimental thermal stability of the structure of the inactive form of human β2AR (PDB ID: 2RH1 [ 5 ]) due to cholesterol binding to the β2AR.
Identifying ligand binding conformations of the ?2-adrenergic receptor by using its agonists as computational probes.
PubMed: 23300522 | PubMedCentral: PMC3534076 | DOI: 10.1371/journal.pone.0050186
Materials and Methods In addition to the carazolol bound inactive crystal structure (2RH1.
The superimpositions of these snapshots to the crystal structure of the inactive form of β 2 AR (2RH1.
Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.
(2013) PLoS One 8
PubMed: 23468878 | PubMedCentral: PMC3585245 | DOI: 10.1371/journal.pone.0056742
Here, we superposed crystal structures of three GPCRs of varied loop conformations: chemokine CXCR4 (PDB id: 3ODU), adrenergic β2AR (2RH1) and adenosine A2AR receptors (2YDV).
In some cases, given a quite accurate alignment in which nearly 90% of residues are correctly aligned (β1AR (2VT4) and β2AR (2RH1) - see Figure 3 ), it may be beneficial to skip the loop refinement step and rely only on a template structure.
Publication Year: 2013
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.
The role of Cysteine 6.47 in class A GPCRs.
(2013) BMC Struct Biol 13
PubMed: 23497259 | PubMedCentral: PMC3610275 | DOI: 10.1186/1472-6807-13-3
Figure 2 A shows a detailed view centered at C6.47 for β 2 AR INV structure (PDB:2RH1) taken as representative.
The results revealed that the conformer present in β 2 AR INV (PDB:2RH1) is the most favorable in all structures.
Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.
(2013) J Comput Aided Mol Des 27
PubMed: 23553533 | PubMedCentral: PMC3639355 | DOI: 10.1007/s10822-013-9640-z
The model RMSD for C α in the TM region relative to the template structure (β 2 AR, pdb code 2rh1 [ 19 ]) was 1.9 Å and 1.5 Å for the D 1 and D 2 receptor model... , respectively.
Common and distinct mechanisms of activation of rhodopsin and other G protein-coupled receptors.
(2013) Sci Rep 3
PubMed: 23677071 | PubMedCentral: PMC3654499 | DOI: 10.1038/srep01844
Briefly, all the polypeptides from PDB entries were superimposed onto the inactive-like state of β 2 receptor (2RH1) by secondary structure matching 18 , and 7 helices consisting of 200 residu... s were isolated based on unambiguous sequence alignment.
Table 1 PDB entries used for this study PDB ID receptor Inactive-like Active-like rhodopsin 1GZM-A 2X72 1U19-A 3PQR 3PXO 4A4M β 2 receptor 2RH1 3P0G 3D4S 3SN6 3NY8 3NY9 A 2A receptor 3EML 2YDO 3VG9 2YDV 4EIY 3QAK
All of these structures contain the same sequence ranges of the transmembrane domains superimposed onto the same reference coordinates—the inactive state of β 2 receptor (2RH1)—by secondary structure matching 18 .
Efficacy of the ??-adrenergic receptor is determined by conformational equilibrium in the transmembrane region.
(2012) Nat Commun 3
PubMed: 22948827 | PubMedCentral: PMC3658005 | DOI: 10.1038/ncomms2046
The crystal structure of β 2 AR with an inverse agonist, carazolol (PDB accession code: 2RH1 ) 7 , is shown in grey ribbons.
The crystal structures of β 2 AR have been solved in the forms bound to inverse agonists 6 7 8 9 10 , a neutral antagonist 10 , a full agonist 11 and a full agonist with a G-protein 12 or a G-protein-mimicking nanobody 13 (PDB accession codes: 3D4S , 2RH1 , 3PDS , 3SN6 , and 3P0G ).
Conformation guides molecular efficacy in docking screens of activated ?-2 adrenergic G protein coupled receptor.
(2013) ACS Chem Biol 8
PubMed: 23485065 | PubMedCentral: PMC3658555 | DOI: 10.1021/cb400103f
Using the same set of agonists and inverse-agonists with the same decoys, the inactive carazolol-bound β2AR crystal structure (PDB ID 2RH1) found no agonists in the top 1% of the database and ... 3% (4/30 agonists) in the top 10% of the database.
A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor.
PubMed: 23799068 | PubMedCentral: PMC3682944 | DOI: 10.1371/journal.pone.0066009
Materials and Methods Comparative Modeling Bovine rhodopsin (UniProtKB accession number P35372; PDB accession code: 1U19)  and the β 2 adrenergic receptor (UniProtKB: P02699; PDB: 2RH1) [1... ] were used as templates in the creation of models of the human MUR transmembrane domain (UniProtKB: P07550)  .
Active-state models of ternary GPCR complexes: determinants of selective receptor-G-protein coupling.
PubMed: 23826246 | PubMedCentral: PMC3691126 | DOI: 10.1371/journal.pone.0067244
(A) Intracellular view of the superposition of active-state models of D2 Down R (green) and D2 Up R (dark-red) and the crystal structures of D3R (PDB-ID 3PBL, grey) and β2AR in complex with di... ferent binding partners (violet: carazolol, PDB-ID 2RH1; dark-blue: FAUC50, PDB-ID 3PDS; blue: BI167107 and the G s protein, PDB-ID 3SN6).
On homology modeling of the M? muscarinic acetylcholine receptor subtype.
PubMed: 23812908 | PubMedCentral: PMC3717152 | DOI: 10.1007/s10822-013-9660-8
Eleven homology modeling templates were chosen due to the high resolution and high homology with the M 2 muscarinic receptor: bovine rhodopsin (PDB:1U19) [ 8 ], human β 2 -adrenergic receptor ... 4-lysozyme chimera (PDB:2RH1 and PDB:3D4S) [ 14 , 15 ], turkey β 1 -adrenergic receptor with stabilizing mutations (PDB:2VT4) [ 16 ], CXCR4 chemokine receptor (PDB:3ODU) [ 33 ], human dopamine D 3 receptor (PDB:3PBL) [ 34 ], adenosine A 2A receptor (PDB:3RFM) [ 35 ], human histamine H 1 receptor (PDB:3RZE) [ 36 ], sphingosine 1-phosphate receptor 1 (PDB:3V2Y) [ 37 ], M 3 muscarinic receptor (PDB:4DAJ) [ 6 ], and human κ-opioid receptor (PDB:4DJH) [ 38 ].
Table 2 Quality checks of templates and target structure Homology Homology Resolution Prime YASARA 1D [%] 2D [%] [Å] G-factor (+) Z-score (+) Templates 1U19 24 74 2.2 −7.935 −0.733 2RH1 31 89 2.4 −7.313 0.589 2VT4 31 91 2.7 −7.154 0.413 3D4S 31 86 2.8 −7.436 0.788 3ODU 25 73 2.5 −7.808 0.236 3PBL 34 85 2.9 −7.299 0.044 3RFM 29 84 3.6 −7.246 0.086 3RZE 39 89 3.1 −8.043 −0.472 3V2Y 29 73 2.8 −7.365 −0.262 4DAJ 71 97 3.4 −7.778 −0.156 4DJH 31 78 2.9 −7.309 0.118 Target 3UON 100 100 3.0 −7.585 0.052 Qualities of the templates per cent of sequence (1D) and secondary structure (2D) homology of the templates to the target structure (3UON), resolution of the crystalographic structures in Å, Prime geometry factor (G-factor), and YASARA quality check score (Z-score) are shown.
2 upper right), which is based on the human β 2 -adrenergic receptor structure (2RH1), though the β 2 -adrenergic receptor is structurally closer to the muscarinic receptor than to rhodopsin.
RMSDs of the models to the target structure (3UON) are listed in Table 4 Table 1 List of models, their templates and the modeling programs that were used Model Procedure Template (s) [PDB codes] ver01 Prime 1U19 ver02 Prime 2RH1 ver03 Prime 2VT4 ver04 YASARA 1U19, 2RH1, 2VT4, 3D4S ver05 Modeller 1U19, 2RH1, 2VT4, 3D4S ver06 YASARA Hybrid model of ver07 and ver08 ver07 Prime 4DAJ ver08 YASARA 4DAJ ver09 YASARA 1U19, 2RH1, 2VT4, 3D4S, 4DAJ ver10 YASARA 1U19, 2RH1, 2VT4, 3D4S, 3ODU, 3PBL, 3RFM, 3RZE, 3V2Y, 4DAJ, 4DJH ver11 Prime 1U19, 2RH1, 2VT4, 3D4S, 4DAJ ver12 Prime 1U19, 2RH1, 2VT4, 3D4S, 3ODU, 3PBL, 3RFM, 3RZE, 3V2Y, 4DAJ, 4DJH Templates used for first six models (ver01–ver06) share from 24 to 31 % of sequence homology and from 74 to 91 % of secondary structure homology, have 2.8 Å or better resolution.
Orthosteric binding of ?-Da1a, a natural peptide of snake venom interacting selectively with the ?1A-adrenoceptor.
PubMed: 23935897 | PubMedCentral: PMC3723878 | DOI: 10.1371/journal.pone.0068841
Nine β 2 -AR structures are available (2RH1, 3D4S, 3KJ6, 3NY8, 3NY9, 3NYA, 3PDS, 3P0G, 3SN6) and are very similar (Cα RMSDs<1.5 Å for 253 residues).
We used the X-ray structure with the highest resolution (2RH1) as a template  .
Simulations of biased agonists in the ?(2) adrenergic receptor with accelerated molecular dynamics.
(2013) Biochemistry 52
PubMed: 23879802 | PubMedCentral: PMC3763781 | DOI: 10.1021/bi400499n
The available crystal structures of the β 2 AR with PDB codes 2RH1, 3D4S, 3NY8, 3NY9, 3NYA, 3PDS, 3P0G, and 3SN6 were used to monitor whether the simulated conformational space samples the pro... ection of available experimental structures.
GOMoDo: A GPCRs online modeling and docking webserver.
PubMed: 24058518 | PubMedCentral: PMC3772745 | DOI: 10.1371/journal.pone.0074092
We docked the ligand carazolol to the hβ2AR model with fast VINA and compared our results against the experimentally determined X-ray structure (PDB code: 2RH1 [ 46 ]).
( A ) VINA docking of carazolol to the hβ2AR model and compared to the crystal structure (PDB: 2RH1).
Membrane driven spatial organization of GPCRs.
PubMed: 24105260 | PubMedCentral: PMC3793225 | DOI: 10.1038/srep02909
A model of the inactive β 2 AR was constructed based on the PDB entry 2RH1 6 .
(c) The relative frequency with which the different regions of the protein participate in protein-protein interactions during the last 1.4 μs, shown in a color-coded heatmap projected onto a X-ray structure of β 2 AR (PDB 2RH1 6 ).
The MD simulations of the diffusion-interaction of β 2 AR molecules in the lipid bilayer were performed with a system of 9 β 2 AR molecules constructed from the starting structure obtained from the CGMD simulation of the monomeric β 2 AR based on the X-ray structure 2RH1 (see previous subsection).
A molecular and chemical perspective in defining melatonin receptor subtype selectivity.
PubMed: 24018885 | PubMedCentral: PMC3794785 | DOI: 10.3390/ijms140918385
The model of the MT 2 receptor was created by using homology modeling from the published crystal structure of the human β2 adrenergic receptor solved at 2.4 Å resolution (PDB access co... e 2RH1) [ 111 ].
Applications of molecular replacement to G protein-coupled receptors.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 24189241 | PubMedCentral: PMC3817703 | DOI: 10.1107/S090744491301322X
One inactive conformation structure of each unique GPCR published to date was aligned with that of β 2 AR (PDB entry 2rh1 ; Cherezov et al. , 2007 ▶ ).
Adrenaline-activated structure of ?2-adrenoceptor stabilized by an engineered nanobody.
(2013) Nature 502
PubMed: 24056936 | PubMedCentral: PMC3822040 | DOI: 10.1038/nature12572
Diffraction data were processed in HKL2000 24 , and the structure was solved using molecular replacement with the structures of active β 2 AR, Nb80 (PDB ID: 3P0G), and T4 lysozyme (PDB ID: 2RH... ) used as search models in Phaser 25 .
Molecular interactions between fenoterol stereoisomers and derivatives and the ??-adrenergic receptor binding site studied by docking and molecular dynamics simulations.
(2013) J Mol Model 19
PubMed: 24043542 | PubMedCentral: PMC3825559 | DOI: 10.1007/s00894-013-1981-y
Molecules of fenoterol and its derivatives, in all possible stereochemical configurations (94 structures, Table 1 ) were docked to the receptor into two forms: (i) a high resolution structure... of carazolol-bound receptor (an inactive form of β 2 -AR, In_β 2 -AR, PDB: 2RH1) and (ii) a structure stabilized with Nb80 nanobody (an active form of β 2 -AR; Ac_β 2 -AR, PDB: 3P0G).
Molecular models of β 2 -AR have been developed by using the crystal structure of the human β 2 -AR T4 lysozyme fusion protein with bound ( S )-carazolol (PDB ID: 2RH1) and more recently reported structure of a nanobody-stabilized active state of the β 2 -AR with the bound full agonist BI-167107 (PDB ID: 3P0G).
The flexible, optimized ligands were docked into the binding pocket of two high resolution X-ray crystal structures of β 2 -AR (PDB IDs: 2RH1 and 3P0G).
At first, the human β 2 -AR was crystallized in complex with an inverse agonist, ( S )-carazolol (PDB ID: 2RH1) [ 8 ].
Two systems under consideration consisted of receptor protein, 125 POPC lipid molecules, 16271 water molecules (including 16 water molecules seen in the β 2 -AR crystal structure; PDB ID: 2RH1 in the case of In_β 2 -AR model) and two sodium ions.
Fig. 2 The comparison of the positions of ligands co-crystallized with β 2 -AR (gray), ( S )-carazolol (PDB ID: 2RH1) ( a ) and BI-167107 (PDB ID: 3P0G) ( b ) with ( R , R ’)-1 docked to In_β 2 -AR ( a ) and Ac_β 2 -AR model ( b ).
Effect of intracellular loop 3 on intrinsic dynamics of human ?2-adrenergic receptor.
PubMed: 24206668 | PubMedCentral: PMC3834532 | DOI: 10.1186/1472-6807-13-29
The conformational change of ICL3 gives rise to a “very inactive” state of the receptor Figure 4 A shows the RMSD profiles of the sixth transmembrane helix (TM6) from its inac... ive (PDB:2RH1) and its active states (PDB:3SN6) in reported crystal structures.
Methods Preparation of the receptor models The X-ray crystallographic structure of human β 2 AR in complex with T4 lysozyme (T4L) (PDB:2RH1) at 2.40 Å resolution [ 3 ] was used as the initial conformation.
The docking site was selected based on the location of the partial inverse agonist carazolol in the complex structure (PDB:2RH1).
[ 9 ] is found to be identical to the inactive state of the receptor (PDB:2RH1).
Both models were generated from the inactive state of the receptor (PDB:2RH1) after removal of T4L.
Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure.
PubMed: 24044607 | PubMedCentral: PMC3848830 | DOI: 10.1186/1472-6807-13-15
Table 1 Sequence alignments in GPCR-ModSim indicate squid rhodopsin has the greatest identity to Tre1 + and Tre1 sctt Template Tre1 + Tre1 sctt Total % identities Total % identities 1U19 – bov... ne rhodopsin 14.3 14.1 2RH1 – human β 2 -adrenergic receptor 15.1 14.6 2VT4 – turkey β 1 -adrenergic receptor 14.8 14.3 2Z73 – squid rhodopsin * 17.4 16.7 3EML – human A 2A -adenosine receptor 14.0 13.5 3ODU – human chemokine receptor 4 16.3 14.8 3PBL – human D 3 dopamine receptor 16.1 15.9 * Denotes the template chosen for homology modeling.
Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis.
PubMed: 24144388 | PubMedCentral: PMC3880013 | DOI: 10.1021/bi401119m
Sequences of human OX1 (O43613) and human OX2 (O43614) were retrieved from Swiss-Prot database and aligned with four published crystal structures of GPCR receptors [bovine rhodopsin (PDB entry 1U19), ... 3 human dopamine D3 receptor (D3, PDB entry 3PBL), 64 human A 2A adenosine receptor (A 2A , PDB entry 3EML), 65 and the β2-adrenergic receptor (β2AR, PDB entry 2RH1)], 66 using MOE (version 2010.10, Chemical Computing Group).
Human ? Opioid Receptor Models with Evaluation of the Accuracy Using the Crystal Structure of the Murine ? Opioid Receptor.
(2012) J Anesth Clin Res 3
PubMed: 24527268 | PubMedCentral: PMC3920553 | DOI: 10.4172/2155-6148.1000218
Methods Two different homology models were constructed in our group before the crystal structure of murine μ opioid receptor was disclosed: (i) The first model, named as 2T-hMOP-R, used the X-... ay crystallographic structures of human β 2 adrenergic receptor at 2.4 Å resolution (PDB accession code: 2RH1) [ 17 ] and bovine rhodopsin at 2.2 Å resolution (PDB accession code: 1U19) [ 18 ] as templates.
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
(2014) Nat Chem 6
PubMed: 24345941 | PubMedCentral: PMC3923464 | DOI: 10.1038/nchem.1821
Both the inactive (PDB 2RH1) and the active (PDB 3P0G) crystal structure were simulated as ligand-free apo structure as well as receptor bound to the partial inverse agonist carazolol and the full ago... ist BI-167107( 1 , 2 ).
Simulations were initiated from both an inactive (PDB 2RH1) ( 1 ) and active (PDB 3P0G) ( 2 ) crystal structure of β 2 AR.
Methods Simulation systems Membrane-aligned crystal structures for PDB IDs 2RH1 and 3P0G were extracted from the OPM database ( 29 ).
Residues in grey are the aligned inactive crystal (2RH1) conformations; residues in yellow are from the active crystal structure (3P0G).
We also dock to both the active (3P0G) and inactive (2RH1) crystal structures, and to 20 randomly selected snapshots from previously performed long-timescale agonist bound GPCR deactivation simulations( 5 ).
Figure 4 Examples of GPCR Ligand Chemotypes Enriched at MSM States Along Activation Pathways MSM states from high flux activation pathways were assigned a progress score ξ based on structural metrics in Figure 1 and range from the inactive crystal structure (2RH1) at ξ=0 to the active crystal structure (3P0G) at ξ=1.
These results are a statistically significant improvement over results from docking to the active (3P0G) and inactive (2RH1) crystal structures and to randomly selected snapshots from long-timescale, agonist bound β 2 AR deactivation simulations( 5 ).
Publication Year: 2014
BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.
PubMed: 24330655 | PubMedCentral: PMC3924234 | DOI: 10.1186/1472-6807-13-32
Figure 2 Examples of the three superimposition types available in the BioSuper web server ( http://ablab.ucsd.edu/BioSuper ): a) standard superimposition of the angiogenin protein; PDB IDs: 1agi, chai... A (green) and 1gio, chain A from first NMR model (lilac), b) weighted superimposition of the estrogen receptor alpha in different conformations; PDB IDs: 3ert, chain A (green) and 3erd, chain A (lilac), c) structural superimposition of the β 2 adrenergic receptor and the adenosine A 2A receptor; PDB IDs: 2rh1, chain A (green), and 3EML, chain A (lilac).
Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.
(2013) Comput Struct Biotechnol J 5
PubMed: 24688704 | PubMedCentral: PMC3962124 | DOI: 10.5936/csbj.201302011
Illustration of GPCR plasticity is given with: ( b ) zoomed side view of X-ray structure of 2AR in complex with the antagonist (S)-Carazolol (2AR inactive state, PDB entry 2rh1); ( c ) X-ray structure... of 2AR in complex with a high affinity agonist (BI-167107) (2AR-Gs protein active complex, PDB entry 3sn6); ( d ) overlay of the side views ( b ) and ( c ) showing residues in close contact (< 5 Å) with the antagonist (cyanide blue) and the agonist (brown).
In silico analysis reveals sequential interactions and protein conformational changes during the binding of chemokine CXCL-8 to its receptor CXCR1.
(2014) PLoS One 9
PubMed: 24705928 | PubMedCentral: PMC3976404 | DOI: 10.1371/journal.pone.0094178
Materials and Methods Full-length CXCR1 structure modeling Since the N- and C-terminal domains of rhodopsin-like GPCRs are known to be highly flexible, to date, only the bovine rhodopsin structure was... resolved including N- and C-terminal domain (PDB code: 1U19), whereas others, such as CXCR1 (PDB code: 2LNL), β2AR (PDB code: 2RH1), A2AR (PDB code: 3EML) and CXCR4 (PDB code: 3ODU) lacked N- or C-terminal part.
Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.
(2014) Chem Rev 114
PubMed: 24364740 | PubMedCentral: PMC3979449 | DOI: 10.1021/cr4003769
The antagonist bound structure is the carazolol bound β 2 AR-T4L fusion (PDB ID: 2RH1), and the agonist bound structure is the nanobody stabilized, BI-167107 high affinity agonist bound struct... re (PDB ID: 3POG).
Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor.
(2014) J Phys Chem B 118
PubMed: 24579769 | PubMedCentral: PMC3983344 | DOI: 10.1021/jp411618h
We also calculated the root-mean-square deviations (RMSDs) in coordinates of the corresponding residues in the fully active G-protein-coupled state of the β 2 -adrenergic receptor (pdb ID: 3SN... ) and the inactive state of the β 2 -adrenergic receptor (pdb ID: 2RH1).
Design, synthesis and biological evaluation of bivalent ligands against A(1)-D(1) receptor heteromers.
(2013) Acta Pharmacol Sin 34
PubMed: 23334237 | PubMedCentral: PMC4002486 | DOI: 10.1038/aps.2012.151
The model of the D 1 receptor was constructed using multiple templates from the crystal structures of Rhodopsin (PDB code: 1U19) 23 , the β 2 adrenergic receptor (PDB code: 2RH1) 24 , the hist... mine H 1 receptor (PDB code: 3RZE) 25 , the S1P1 receptor (PDB code: 3V2Y) 26 , and the dopamine D 3 receptor (PDB code: 3PBL) 27 .
High-resolution modeling of transmembrane helical protein structures from distant homologues.
(2014) PLoS Comput Biol 10
PubMed: 24854015 | PubMedCentral: PMC4031050 | DOI: 10.1371/journal.pcbi.1003636
Importantly, as shown for 3ODU from 2RH1 ( Fig. 3A–C ) and for 3EML from 1U19 ( Fig. 3D–F ) and in Table S2 , the precise conformation of the kinked regions that were rebuilt de novo w... s also improved as measured by the differences in dihedral angles between template or model and native structures.
Similar improvements of starting templates leading to close to atomic accuracy backbone and near-native side-chain conformation predictions in the TM region were observed for other distant homolog pairs such as 2RH1 from CXCR4 (Cα RMSD of 1.7 Å, Fig. 2D ) and 1U7G from 3B9W (Cα RMSD of 1.1 Å, Fig. 2E ).
The following X-ray structures and corresponding pdb codes were selected from the protein database: GPCRs: Bovine rhodopsin (1U19), Squid rhodopsin (2Z73), Beta2 adrenergic receptor (2RH1), Beta1 adrenergic receptor (2Y00), Adenosine A2A receptor (3EML), Dopamine D3 receptor (3PBL), Chemokine receptor CXCR4 (3ODU), Kappa opioid receptor (4DJH), M2 muscarinic acetylcholine receptor (3UON), Histamine H1 receptor (3RZE), Sphingosine 1-phosphate receptor 1 (3V2Y), Delta opioid receptor (4EJ4), M3 Muscarinic Acetylcholine Receptor (4DAJ), human glucagon receptor (4L6R), corticotropin-releasing factor receptor 1 (4K5Y).
Structural probing of off-target G protein-coupled receptor activities within a series of adenosine/adenine congeners.
PubMed: 24859150 | PubMedCentral: PMC4032265 | DOI: 10.1371/journal.pone.0097858
(A) Side view and (B) top view of the superposition of turkey β 1 adrenergic receptor (PDB ID: 4AMJ) (green carbons), human β 2 adrenergic receptor (PDB ID: 2RH1) (cyan carbons) and hu... an β 3 adrenergic receptor model (pink carbons).
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.
(2014) Database (Oxford) 2014
PubMed: 24857970 | PubMedCentral: PMC4038255 | DOI: 10.1093/database/bau041
The extraction of sequence from PDB could be difficult for many reasons: numbering in PDB may not be continuous because of the insertion of residue (numbering for example 100-100A-100B-103) or inserti... n of protein fragment (like lysozyme in PDB structure 2RH1), the structure could contain missing residues, gaps (but not necessarily along with gaps in numbering), mutations could be present and the residue names could be different from the 20 standard amino acids.
PubMed ID is not available.
Published in 2010
Rhodopsin (PDB ID 1F88) [ 93 ], the β2-adrenoceptor (PDB ID 2RH1) [ 110 ], the β1-adrenoceptor (PDB ID 2VT4) [ 15 ] and the adenosine A2a receptor (PDB ID 3EML) [ 16 ] have 30 complete... y conserved amino acids (8.9-12.2% identity).
Table 2 Amino acids conserved at both the primary and tertiary (mainchain RMSD < 2 Å) structure levels among the transmembrane segments of rhodopsin (PDB ID 1f88) [ 93 ], the β2- (PDB ID 2RH1) [ 110 ], and β1-adrenoceptors(PDB ID 2VT4) [ 15 ] and the adenosine A2a receptor (PDB ID 3EML) [ 16 ].
Seven additional years were required before the first crystal structures were reported by two different research groups of a GPCR activated by a noncovalently-bound ligand, the β2-aderenoceptor (PDB ID 2R4R, 2R4S, 2RH1) [ 12 , 14 , 33 , 94 ].
Colors used are coded by GPCR and method; red (β2 fragment, 1DEP [ 121 ]), green (CB1 fragment 2B0Y [ 141 ]), orange (alpha factor receptor fragment from S. cerevisiae , 1PJD [ 144 ]), blue (β2-aderenoceptor crystal structure, 2RH1 [ 110 ]), cyan (rhodopsin crystallographic structure, 1F88 [ 93 ]), blue-green (rhodopsin fragment, 1EDS [ 139 ]), purple (S1P 4 engineered fragment, 2DCO [ 149 ]), yellow (α2A-adrenoceptor fragment, 1HLL [ 142 ]), gold (DRY to IRY mutant α2A-adrenoceptor fragment, 1HOD [ 142 ]).
Published in 2011
DRD3 Case Since it has the highest similarity to the dopamine D3 receptor, the ADRB2 structure [ 11 ] (PDB code 2RH1) was chosen as the modeling template.
The structural alignment was performed with MOE2009.10 [ 40 ] and consisted of the structures of the human adenosine A2A Receptor [ 8 ] (PDB: 3EML), human adrenergic Beta 1 Receptor [ 12 ] (PDB: 2VT4), human Adrenergic Beta 2 receptor [ 11 ] (PDB: 2RH1) and the bovine opsin structure [ 29 ] (PDB: 3DQB).
The recombinant expression systems for structure determination of eukaryotic membrane proteins.
(2014) Protein Cell 5
PubMed: 25119489 | PubMedCentral: PMC4145085 | DOI: 10.1007/s13238-014-0086-4
Protein Species PDB code Reference Insect cell S. frugiperda 1 β 2 AR (Fab) Homo sapiens 2R4R 2R4S Rasmussen et al., 2007 2 β 2 AR (T4L) Homo sapiens 2RH1 Cherezov et al., 2007 3 ... b2; 2 AR-agonist complex Homo sapiens 3PDS Rosenbaum et al., 2011 4 β 2 AR-GS complex Homo sapiens 3SN6 Rasmussen et al., 2011a , b 5 A 2A adenosine receptor Homo sapiens 3EML Jaakola et al., 2008 6 CXCR4 Homo sapiens 3ODU 3OE8 Wu et al., 2010 7 Dopamine D3 receptor Homo sapiens 3PBL Chien et al., 2010 8 Sphingosine 1-phosphate receptor subtype 1 Homo sapiens 3V2 W 3V3Y Hanson et al., 2012 9 M2 muscarinic acetylcholine receptor Homo sapiens 3UON Haga et al., 2012 10 M3 muscarinic acetylcholine receptor Rattus norvegicus 4DAJ Kruse et al., 2012 11 κ-Opioid receptor Homo sapiens 4DJH Wu et al., 2012 12 μ-Opioid receptor Mus musculus 4DKL Manglik et al., 2012 13 δ-Opioid receptor Mus musculus 4EJ4 Granier et al., 2012 14 N/OFQ receptor Homo sapiens 4EA3 Thompson et al., 2012 15 CCR5 Homo sapiens 4MBS Tan et al., 2013 16 PAR1 Homo sapiens 3VW7 Zhang et al., 2012 17 5-HT 1B/2B serotonin receptor Homo sapiens 4IAR 4IB4 Wang et al., 2013a , b ; Wacker et al., 2013 18 Smoothened receptor Homo sapiens 4JKV Wang et al., 2013a , b 19 Glucagon receptor Homo sapiens 4L6R Siu et al., 2013 20 Metabotropic glutamate receptor1 Homo sapiens 4OR2 Wu et al., 2014 21 P2X 4 Danio rerio (Zebra fish) 3I5D 3H9 V 4DW1 Kawate et al., 2009 ; Hattori and Gouaux, 2012 22 ASIC1 Gallus gallus 2QTS 3HGC Jasti et al., 2007 ; Gonzales et al., 2009 23 GluA2 Rat 3KG2 3KGC Sobolevsky et al., 2009 24 GLuClα Caenorhabditis elegans 3RHW, 3RIF, 3RI5 3RIA Hibbs and Gouaux, 2011 25 CX26 Homo sapiens 2ZW3 Maeda et al., 2009 26 UT-B Bos taurus 4EZC 4EZD Levin et al., 2012 27 ZMPSTE24 Homo sapiens 4AW6 Quigley et al., 2013 28 ABCB10 Homo sapiens 4AYT Shintre et al., 2013 29 Caludin-15 Mus Musculus 4P79 Suzuki et al., 2014 30 NRT1.1 Arabidopsis thaliana 4OH3 Sun et al., 2014 Trichoplusia ni 31 β1 adrenergic receptor Meleagris gallopavo 2VT4 Warne et al., 2008 32 NTS1 Neurotensin Receptor Rattus norvegicus 4GRV White et al., 2012 33 CmClC Cyanidioschyzonmerolae 3ORG Feng et al., 2010 34 Corticotropin-releasing factor receptor Homo sapiens 4K5Y Hollenstein et al., 2013 35 GLUT1 Homo sapiens 4PYP Deng et al., 2014 * For some proteins like GPCR and potassium channel, only the representative ones are listed After the protein IL-2 was first expressed in large scale with the baculovirus-infected insect cells in 1985, this system has been quickly accepted and widely used (Smith et al., 1983 ; Maeda et al., 1985 ).
Deformable elastic network refinement for low-resolution macromolecular crystallography.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 25195739 | PubMedCentral: PMC4157441 | DOI: 10.1107/S1399004714016496
The final deposited crystal structure of activated β 2 AR (gray; PDB entry 3p0g ) is superimposed with ( a ) the crystal structure of the inactive form (blue; PDB entry 2rh1 ) that was used as... a molecular-replacement search model, ( b ) a model (green) obtained by a ‘standard’ refinement procedure (ten macrocycles with phenix.refine ) and ( c ) a model (red) obtained from DEN refinement.
The phases were originally determined by molecular replacement using the inactive β 2 AR structure (Cherezov et al. , 2007 ▶ ; PDB entry 2rh1 ) as a search model.
Published in 2014
Table 1 Information of 10 Crystal Structures of GPCRs Used in the Present Work a SMO bovine rhodopsin CXCR4 M2MAR D3R β2AR A 2A AR H1R S1P β1AR PDB entry 4JKV 1F88 3ODU 3UON ... PBL 2RH1 2YDO 3RZE 3V2W 2Y00 resolution (Å) 2.45 2.40 2.50 3.00 2.89 2.40 3.00 3.10 3.35 2.50 whole sequence identity (±2%) 14.4 17.4 19.1 20.9 23.5 24.4 25.1 25.2 28.5 28.5 sequence identity in TM (±2%) 18 25 21 27 28 28 29 30 34 35 proSA-web Z-score –2.80 –2.82 –3.54 –3.24 –2.72 –4.21 –4.87 –3.36 –3.49 –4.33 ref ( 35 ) ( 19 ) ( 37 ) ( 31 ) ( 38 ) ( 30 ) ( 33 ) ( 34 ) ( 32 ) ( 36 ) a We listed the information on 10 GPCRs used in the present work, including PDB entry, resolution, sequence identity to CB2, and the related references.
A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.
PubMed: 25313636 | PubMedCentral: PMC4196896 | DOI: 10.1371/journal.pone.0109312
In contrast, in the 5-HT 2B R, this residue is located nearer to helix 7 ( Figure 1B (right) inactive F 6.44 state) and, therefore, is closer to the position of F 6.44 in the carazolol-bound inactive ... orm of the β2-adrenergic receptor (PDB ID: 2RH1  ).
Profiling the interaction mechanism of quinoline/quinazoline derivatives as MCHR1 antagonists: an in silico method.
(2014) Int J Mol Sci 15
PubMed: 25257526 | PubMedCentral: PMC4200842 | DOI: 10.3390/ijms150915475
The recently reported X-ray structure of β-adrenergic receptor (PDB: 2RH1) [ 61 ] taken from RCSB Protein Data Bank (Brookhaven National Laboratory, New York, NY, USA) [ 29 ] was selected as t... e homology modeling template due to its high sequence similarity to MCHR1.
The recently reported X-ray crystal structure of β-adrenergic receptor (PDB:2RH1) was utilized as template in homology modeling due to its high sequence similarity to MCHR1.
The best hit, Compound 42 , in their work, which is linear with a terminal nitrogen, was subjected to a full flexible ligand docking study with the X-ray structure of β2-adrenergic receptor (PDB:2RH1) utilized as template in homology modeling.
The model of the inactive-state NOP receptor was constructed by a multiple template approach using the crystal structures of the antagonist-bound inactive β2 adrenergic receptor (AR) (PDB code... 2RH1) and rhodopsin structure (PDB code: 1F88) as templates.
A molecular fragment cheminformatics roadmap for mesoscopic simulation.
(2014) J Cheminform 6
PubMed: 25383098 | PubMedCentral: PMC4212157 | DOI: 10.1186/s13321-014-0045-3
As an example, the start geometry of a simulation box with a “squeezed” G-protein sphere compartment (PDB ID: 2RH1 [ 35 ], colored green) in a sphere compartment below a phosphatidylet... anolamine membrane compartment (right side) is shown in Figure 8 .
Graph analysis of ?2 adrenergic receptor structures: a "social network" of GPCR residues.
(2013) In Silico Pharmacol 1
PubMed: 25505660 | PubMedCentral: PMC4230308 | DOI: 10.1186/2193-9616-1-16
Figure 1 Five interconnected residues in the carazolol-bound structure of the β 2 AR (PDB ID: 2RH1).
A key residue in the activation of the receptor, namely Phe 282 6.44 , is shown with its non-hydrogen atoms represented as spheres and colored in red for the 2RH1 structure and green for the 3P0G structure.
Figure 5 View of the “knot region” of the β 2 AR, with the P-I-F motif highlighted: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G).
The backbone of the receptor is schematically portrayed as a ribbon for the 2RH1 structure and as a tube for the 3P0G structure and is colored with a continuous spectrum ranging from red at the N-terminus to purple at the C-terminus, with TM1 in red/orange, TM2 in orange, TM3 in yellow, TM4 in yellow/green, TM5 in green, TM6 in blue and TM7 in purple.
In particular, the analyzed structures, identified through their PDB ID, with their respective resolution indicated in parentheses, are: a) 2RH1 (2.40 Å) (Cherezov et al.
Figure 3 Interhelical hydrogen bonds within the “knot region” of the β 2 AR: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G).
Figure 2 Three alternative views of two of the experimentally solved structures of the β 2 AR, one solved in the inactive state (2RH1) and one in an activated state (3P0G).
Figure 4 View of the “knot region” of the β 2 AR, with the cluster of interconnected aromatic residues highlighted: a) the carazolol-bound inactive structure (2RH1); b) the active structure (3P0G).
A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2.
(2014) J Am Chem Soc 136
PubMed: 25314362 | PubMedCentral: PMC4235374 | DOI: 10.1021/ja508394x
The coordinates for the palmitoyl chain were obtained from the crystal structure of the β 2 adrenergic receptor (PDB accession code, 2RH1).
Structural Alignment For the structural analyses, all the structures were aligned to the structure of the β 2 adrenergic receptor (PDB accession code, 2RH1) oriented with respect to the lipid bilayer according to the OPM database 26 by using the Cα atoms of the TM helices (for details about the segments considered in the structural alignment see Figure S3A in SI ).
16 Briefly, the 5-HT 2A R model was created with homology modeling using as templates, the high-resolution X-ray crystal structures of the β 2 adrenergic receptor (PDB accession code, 2RH1) and bovine rhodopsin (PDB accession code, 1U19).
A palmitoyl moiety was attached at position C397 based on the structural information on the β 2 adrenergic receptor (PDB accession code, 2RH1).
Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach.
(2014) Malar J 13
PubMed: 25407998 | PubMedCentral: PMC4253978 | DOI: 10.1186/1475-2875-13-434
For the inactive conformation, a structure was obtained that was built based on many GPCR antagonist-bound and inverse agonist-bound conformations, primarily a crystal structure of β 2 -adrene... gic receptor with partial inverse agonist carazolol bound [PDB:2RH1].
To obtain initial ligand poses used in grid generation, each of the conformations were first overlapped in PyMOL [ 39 ] with the top templates used by I-TASSER for their creation (2RH1 for the inactive conformation and 3SN6 for the active conformation) and the positions of the ligands found in each of the templates were first saved as a PDB file, then added using Schrodinger Suite 2011’s Maestro to their respective AgOAR45B conformation (2RH1 partial inverse agonist CAU was used for the inactive conformation and 3SN6 agonist 30G was used for the active conformation) to denote the active site of the protein.
Sequence alignments of sstr2 and the known crystal structure of GPCR revealed that sstr2 has a moderate sequence identity similarity: ∼40% to nociceptin/orphanin FQ receptor (NOP, PDB entry: 4... A3, resolution: 3.01), ∼44% to μ-opioid receptor (MOR, PDB entry: 4DKL, resolution: 2.80), ∼41% to κ-opioid receptor (KOR, PDB entry: 4DJH, resolution: 3.01), 42% to δ-opioid receptor (DOR, PDB entry: 4EJ4, resolution: 3.40), ∼34% to chemokine receptor CXCR4 (PDB entry: 3ODU, resolution: 2.50), ∼28% todopamine D3 receptor (D3R, PDB entry: 3PBL, resolution: 2.89), 27% to human beta2-adrenergic receptor (PDB entry: 2RH1, resolution: 2.40), ∼28% to chemokine receptor CXCR1 (PDB entry: 2LNL, solid-state NMR), ∼22% to human A2A receptor (A2AAR, PDB entry: 2YDO, resolution: 3.00), ∼26% to human histamine H1 receptor (H1R, PDB entry: 3RZE, resolution: 3.10), ∼25% to sphingosine 1-phosphate receptor (S1P, PDB entry: 3V2W, resolution: 3.35), and ∼31% to human beta1-adrenergic receptor (PDB entry: 2Y00, resolution: 2.50).
Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human ?2-adrenergic receptor.
PubMed: 25501358 | PubMedCentral: PMC4263363 | DOI: 10.1371/journal.pcbi.1004006
The crystal structure PDB ID:2RH1 was chosen as the reference structure for the coordinates from residue 29 to 342.
In the crystal structure (2RH1), the binding site cleft is entirely open and a salt bridge is seen to be formed between residues Asp 192 and Lys 305.
A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.
(2015) Acta Crystallogr F Struct Biol Commun 71
PubMed: 25615961 | PubMedCentral: PMC4304740 | DOI: 10.1107/S2053230X14026843
As much as possible, the dimensions of the lipid (tan oval with tail), detergent (pink oval with tail), cholesterol (purple), protein (blue and green; β 2 -adrenergic receptor-T4 lysozyme fusi... n; PDB entry 2rh1 ), bilayer and aqueous channels (dark blue) have been drawn to scale.
Type Name (PDB record count) Organism Function Host and additive lipids PDB entry (resolution, ) -Helical GPCR (54) Homo sapiens , Rattus norvegicus , Mus musculus , Meleagris gallopavo G protein-coupled receptor 9.9 MAG + cholesterol; 7.7 MAG + cholesterol; 9.9 MAG 4phu (2.33), 3eml (2.60), 4eiy (1.80), 3qak (2.70), 4gbr (3.99), 2rh1 (2.40), 3d4s (2.80), 3ny9 (2.84), 3ny8 (2.84), 3nya (3.16), 3pds (3.50), 3p0g (3.50), 3odu (2.50), 3oe0 (2.90), 3oe6 (3.20), 3oe8 (3.10), 3oe9 (3.10), 4k5y (2.98), 3pbl (2.89), 4oo9 (2.60), 3rze (3.10), 3uon (3.00), 4mqs (3.50), 4mqt (3.70), 3vw7 (2.20), 4jkv (2.45), 4o9r (3.20), 4n4w (2.80), 4qim (2.61), 4qin (2.06), 3v2w (3.35), 3v2y (2.80), 4djh (2.90), 4lde (2.79), 4ldl (3.10), 4ldo (3.20), 4qkx (3.30), 4iaq (2.80), 4iar (2.70), 4ib4 (2.70), 4nc3 (2.80), 4n6h (1.80), 4l6r (3.30), 4ntj (2.62), 4pxz (2.50), 4py0 (3.10), 4ea3 (3.01), 4or2 (2.80), 4mbs (2.71), 4daj (3.40), 4grv (2.80), 4dkl (2.80), 4ej4 (3.40), 4bvn (2.10) Bacteriorhodopsin (39) Halobacterium salinarum Rhodopsin, nonvisual 9.9 MAG; -XylOC 16+4 ; 95% monomethyl-DOPE, 5% DOPE-mPEG350 1ap9 (2.35), 1brx (2.30), 1qhj (1.90), 1c3w (1.55), 1c8r (1.80), 1c8s (2.00), 1cwq (2.25), 1qko (2.10), 1qkp (2.10), 1f4z (1.80), 1f50 (1.70), 1e0p (2.10), 1jv6 (2.00), 1jv7 (2.25), 1kg8 (2.00), 1kg9 (1.81), 1kgb (1.65), 1m0k (1.43), 1m0l (1.47), 1m0m (1.43), 1o0a (1.62), 1mgy (2.00), 1p8h (1.52), 1p8i (1.86), 1p8u (1.62), 1vjm (2.30), 1s8j (2.30), 1s8l (2.30), 2i1x (2.00), 2i20 (2.08), 2i21 (1.84), 2ntu (1.53), 2ntw (1.53), 2wjk (2.30), 2wjl (2.15), 3mbv (2.00), 3ns0 (1.78), 3nsb (1.78), 4fpd (2.65) Cytochrome ba 3 oxidase (13) Thermus thermophilus Cytochrome oxidase 9.9 MAG 3s8f (1.80), 3s8g (1.80), 4fa7 (2.50), 4faa (2.80), 4gp4 (2.80), 4gp5 (2.70), 4gp8 (2.80), 4g7r (3.05), 4g70 (2.60), 4g71 (2.90), 4g72 (3.19), 4g7q (2.60), 4g7s (2.00) Diacylglycerol kinase (7) Escherichia coli K-12 Enzyme 7.8 MAG; 7.9 MAG 3ze3 (2.05), 3ze4 (3.70), 3ze5 (3.10), 4bpd (3.30), 4brb (2.55), 4brr (2.44), 4d2e (2.28) MATE transporters (7) Pyrococcus furiosus Transporter 9.9 MAG 3vvn (2.40), 3vvo (2.50), 3vvp (2.91), 3vvr (3.00), 3vvs (2.60), 3w4t (2.10), 3wbn (2.45) Photosynthetic reaction centre (6) Blastochloris viridis Reaction centre 9.9 MAG 2wjm (1.95), 2wjn (1.86), 2x5u (3.00), 2x5v (3.00), 4ac5 (8.2), 4cas (3.50) Sensory rhodopsin II (6) Natronomonas pharaonis Rhodopsin, nonvisual 9.9 MAG 1jgj (2.40), 1gu8 (2.27), 1gue (2.27), 1h68 (2.10), 3qap (1.90), 3qdc (2.50) Photosynthetic reaction centre (5) Rhodobacter sphaeroides Reaction centre 9.9 MAG 1ogv (2.35), 2bnp (2.70), 2bns (2.50), 2gnu (2.00), 4tqq (2.50) Peptide (POT) transporter (5) Geobacillus kaustophilus Transporter 9.9 MAG 4ikv (1.90), 4ikw (2.00), 4ikx (2.30), 4iky (2.10), 4ikz (2.40) CDP-alcohol phosphotranspherase (4) Archaeoglobus fulgidus Enzyme 9.9 MAG 4o6m (1.90), 4o6n (2.10), 4q7c (3.10), 4mnd (2.66) Sensory rhodopsin IItransducer complex (4) Natronomonas pharaonis Rhodopsin, nonvisual 11.7 MAG 1h2s (1.93), 2f93 (2.00), 2f95 (2.20), 4gyc (2.05) Halorhodopsin (3) Halobacterium salinarum Rhodopsin, nonvisual 9.9 MAG 1e12 (1.80), 2jag (1.93), 2jaf (1.70) Peptide (POT) transporter (3) Streptococcus thermophilus Transporter 7.8 MAG 4d2b (2.35), 4d2c (2.47), 4d2d (2.52) Na + /bile acid symporter (2) Yersinia frederiksenii Transporter 9.9 MAG 4n7w (2.80), 4n7x (1.95) Sugar (SWEET) transporter (2) Leptospira biflexa , Vibrio sp.
Publication Year: 2015
Published in 2015
2011a ) and inactive conformational states (β 2 -AR co-crystallized with the inverse agonist (carazolol) PDB: 2RH1) (Cherezov et al.
The ligand position in the global minimum is very similar to that observed in the crystal structure of the carazolol–β 2 -AR complex (PDB: 2RH1); the average RMSD was 0.21 Å (Fig.
Methods Modeling of the ligand–receptor complexes β 2 -AR in its inactive and active states was modeled on the basis of the crystal structure of human β 2 –AR–T4 lysozyme fusion protein (PDB: 2RH1) (Cherezov et al.
The FEP profiles reported by González et al. ( 2011 ) were obtained on the basis of the crystal structure of β 2 -AR (PDB: 2RH1) which did not contain the uncrystallized region of the N-terminus which, according to our US simulations, can be of crucial importance in the initial stages of the ligand-binding process.
For fenoterol, the calculations were performed separately for the two conformational forms of β 2 -AR, i.e. the inverse agonist-bound (inactive form, PDB: 2RH1) and the agonist-bound (active form, PDB 3POG) to elucidate potential similarities and differences.
The two different conformational forms of β 2 -AR, i.e. active β 2 -AR–PDB: 3P0G and inactive β 2 -AR–PDB: 2RH1 were included in this stage of the study.
The initial position of the carazolol molecule corresponded to the crystal structure of β 2 -AR co-crystallized with carazolol (PDB: 2RH1).
One was co-crystalized in the complex with an inverse agonist, ( S )-carazolol (PDB: 2RH1) (Cherezov et al.
In addition, the positions of fenoterol in the global minima are very similar to the positions of the ligand co-crystallized with β 2 -AR (PDB: 2RH1 and 3P0G) (Fig.
For comparison, the α group member β 2 -adrenergic receptor with the partial inverse agonist carazolol (PDB code 2RH1) is shown.
The OR is the top-ranked model of OR85b (see Fig. 1c ); the GPCR is the crystal structure of the β2-adrenergic receptor (PDB 2RH1 55 ); the AR1 structure is the top-ranked model described prev... ously 28 .
Hereafter B2I refers to the simulations starting with the inactive conformation (PDB: 2RH1) and B2A to simulations starting with the active conformation (PDB: 3P0G).
These ligands were docked into both the active (PDB: 3P0G) and inactive (PDB: 2RH1) structures of β 2 AR using Autodock Vina, 57 and differences in scores of the top ranked conformations were calculated as Δ E dock = | E dock act | – | E dock inact |, where E dock act and E dock inact are scores from top ranked poses in the active and inactive structures, respectively.
35 Figure 4 A) GFE FragMaps from the B2A (left) and B2I (center) simulations overlaid on the active (PDB: 3P0G) and inactive (PDB: 2RH1) states of the β 2 AR with ligands BI-167107 and carazolol, respectively; receptors atoms occluding the view of binding pocket were removed.
For instance, a cholesterol binding pocket was identified in a groove characterized by highly conserved residues (so-called “consensus-motif” residues) between the intracellular ends o... helices TM2 and TM4 in two B2AR crystal structures, i.e., the carazolol-bound 2RH1 [ 32 ] and the timolol-bound 3D4S [ 33 ].
The putative helix dimensions and loop regions are assigned according to observable properties in the crystal structure of the inactivated β 2 -adrenergic receptor conformation (pdb entry code... 2RH1).
Finally, 342 residues of target sequence was aligned with ten top-ranked BLAST search, 2Y00 (297 residues), 2VT4, 2R4R, 3KJ6, 2R4S, 3SN6, 4GBR, 3P0G, 2RH1 and 3PDS The average alignment score for manu... lly edited multiple sequence alignment is better (76.47) than the score obtained by raw multiple sequence alignment (74.89).
These models were based initially upon the 2.4Å crystal structure of the β 2 -AR (PDB Name: 2RH1; Cherezov et al., 2007 ) and then modified to reflect sequence dictated conformational ... ifferences in TMHs 1,2,5,6 and 7 [please see a complete discussion in the paper ( Kotsikorou et al., 2011 )].
Fig 3 shows the volume occupied by peptide ligands in peptide-binding GPCRs (PDB IDs 3OE0 [ 9 ] and 4GRV [ 18 ]) and by organic ligands in small molecule-binding GPCRs (PDB IDs 2YCW [ 6 ], 3EML [ 7 ],... 3PBL [ 8 ], 3RZE [ 10 ], 3V2Y [ 11 ], 3UON [ 12 ], 4DAJ [ 13 ], 4IAR [ 21 ], 4IB4 [ 21 ], 4NTY [ 27 ], 1U19 [ 36 ], and 2RH1 [ 37 ]) after superposition of their 7TM helices.
In case that several crystal structures were available for one receptor, we chose the one with highest available resolution for data analysis [respective PDB IDs: rhodopsin (OPSD): 1U19 [ 36 ]; β 2 adrenergic receptor (ADBR2): 2RH1 [ 37 ]; β 1 adrenergic receptor (ADBR1): 2YCW [ 6 ]; A 2A adenosine receptor (AA2AR): 4EIY [ 20 ]; D3 dopamine receptor (D3DR): 3PBL [ 8 ]; H1 histamine receptor (H1HR): 3RZE [ 10 ]; (S1PR1): 3V2Y [ 11 ]; chemokine receptor CXCR4 (CXCR4): 3OE0 [ 9 ]; chemokine receptor CCR5 (CCR5): 4MBS [ 26 ]; δ-opioid receptor (OPRD): 4EJ4 [ 17 ]; μ-opioid (OPRM): 4DKL [ 14 ]; κ-opioid (OPRK): 4DJH [ 15 ]; N/OFQ opioid (OPRX): 4EA3 [ 16 ]; M2 muscarinic receptor (ACM2): 3UON [ 12 ]; M3 muscarinic receptor (ACM3): 4DAJ [ 13 ],; neurotensin receptor 1 (NTR1): 4GRV [ 18 ]; protease-activated receptor 1 (PAR1): 3VW7 [ 19 ]; serotonine receptor 1B (5HT1B): 4IAR [ 21 ]; serotonine receptor 2B (5HT2B): 4IB4 [ 21 ]; purine receptor P2Y12 (P2Y12): 2PXZ [ 27 ]; glucagon receptor (GLR): 4L6R [ 23 ]; smoothened receptor (SMO): 4JKV [ 24 ]; corticotropin-releasing factor receptor 1 (CRFR1): 4K5Y [ 25 ]; metabotropic glutamate receptor 1 (GRM1): 4OR2 [ 28 ]].
Table 4 Compound counts for retrospective screening scenarios Group of compounds Total number of compounds Number of compounds after Ligprep actives 271 550 Inactives 324 601 DUDs 2000 2526 ZINC 2000 ... 557 Table 5 Crystal structures of beta-2 adrenergic receptor used in the study PDB ID Resolution [Å] 2RH1 2.40 3D4S 2.80 3NY8 2.84 3NY9 2.84 3NYA 3.16 3KJ6 3.40 2R4R 3.40 2R4S 3.40 3P0G 3.50 3PDS 3.50 After this initial models evaluation, all compounds from a particular group of molecules (actives, true inactives, DUDs, and ZINC) were docked into the constructed homology models and crystal structures.
The dataset consists of 18 Class A GPCR structures in their inactive state: rhodopsin (PDB id: 1GZM), adenosine A2A receptor (PDB id: 3PWH), β2-adrenergic receptor (PDB id: 2RH1), β1-a... renergic receptor (PDB id: 2VT4), squid rhodopsin (PDB id: 2Z73), histamine H1 receptor (PDB id: 3RZE), sphingosine1-phosphate receptor 1 (PDB id: 3V2Y), dopamine D3 receptor (PDB id: 3PBL), CXCR4 chemokine receptor (PDB id: 3ODU), M2 muscarinic acetylcholine receptor (PDB id: 3UON), M3 muscarinic acetylcholine Receptor (PDB id: 4DAJ), protease-activated receptor 1 (PDB id: 3VW7), kappa opioid receptor (PDB id: 4DJH), mu-opioid receptor (PDB id: 4DKL), nociceptin/orphanin FQ opioid receptor (PDB id: 4EA3), delta opioid receptor (PDB id: 4N6H), CCR5 chemokine receptor (PDB id: 4MBS), P2Y12 receptor (PDB id: 4NTJ); and 7 Class A GPCR structures in their active state: β2-adrenergic receptor (PDB id: 4LDE), metarhodopsin II (PDB id: 3PQR), adenosine A2A receptor (PDB id: 3QAK), neurotensin NTS1 receptor (PDB id: 4GRV), M2 muscarinic acetylcholine receptor (PDB id: 4MQT), serotonin 5-HT2B receptor (PDB id: 4IB4), P2Y12 receptor (PDB id: 4PY0).
Using homology modeling of the β 2 -adrenergic receptor (pdb: 2RH1; Cherezov et al., 2007 ), a 3D model of the h5-HT 7 receptor was built and stabilized by large scale simulation in membrane b... layers.
The homology model of the h5-HT 7 receptor was kindly supplied by Prof. Ingebrigt Sylte’s group (unpublished data) and built from the crystal structure of the β 2 -adrenergic receptor (pdb: 2RH1; Cherezov et al., 2007 ) by SwissModel server.
As illustrated in Fig 2 , the deviations between the experimental C α positions and the model are barely discernible for the protein structures ranging from ultra-high resolution (pdbid 1EJG, ... .46Å), to medium resolution (pdbid 2RH1, 2.6Å), and to low resolution structures (pdbid 3ZC1, 3.3Å, S1 Fig in the Supporting Information (SI)).
The spatial differences between the backbone atoms and their closest points on the helix ribbon diagram generated by the model are barely visible (indicated by the arrows) for either (a) an ultra-high resolution protein structure (pdbid 1EJG) or (b) a medium-resolution structure (pdbid 2RH1).
In (a) the three GPCR structures (pdbid 1U19, 2RH1 and 3EML) are overlayed based on their sequence similarity [ 26 ].
The helix ribbon diagrams are colored as in Fig 2 except that the residues in 1U19, 2RH1 and 3EML with a helix score < 20.0 are colored respectively in green, classic rose and bright azure.
TMs 5 and 6 of rhodopsin (light brown, 1GZM) [ 2 ], the β 2 -adrenergic receptor (yellow, 2RH1) [ 3 ], and the β 2 -adrenergic receptor in complex with Gs (orange, 3SN6) [ 4 ] are supe... imposed on the 5-HT 2A R.
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