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Dimerization and domain swapping in g-protein-coupled receptors: a computational study
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A new approach to docking in the beta(2)-adrenergic receptor that exploits the domain structure of G-protein-coupled receptors
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Dimerization of G-protein-coupled receptors
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Dean M.K., Higgs C., Smith R.E., Bywater R.P., Snell C.R., Scott P.D., Upton G.J., Howe T.J., and Reynolds C.A. Dimerization of G-protein-coupled receptors. J Med Chem 44 (2001) 4595-4614
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6
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34548188312
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Computational studies of Family A and Family B GPCRs
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A personal perspective of the relationship between early GPCR dimerization calculations and current knowledge.
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Vohra S., Chintapalli S.V., Illingworth C.J., Reeves P.J., Mullineaux P.M., Clark H.S., Dean M.K., Upton G.J., and Reynolds C.A. Computational studies of Family A and Family B GPCRs. Biochem Soc Trans 35 (2007) 749-754. A personal perspective of the relationship between early GPCR dimerization calculations and current knowledge.
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Biochem Soc Trans
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7
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34347385221
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Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base
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An excellent review of key issues in GPCR dimerization and potentially an extremely useful resource.
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Skrabanek L., Murcia M., Bouvier M., Devi L., George S.R., Lohse M.J., Milligan G., Neubig R., Palczewski K., Parmentier M., et al. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinformatics 8 (2007) 177. An excellent review of key issues in GPCR dimerization and potentially an extremely useful resource.
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BMC Bioinformatics
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Skrabanek, L.1
Murcia, M.2
Bouvier, M.3
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Neubig, R.8
Palczewski, K.9
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8
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gpDB: a database of GPCRs, G-proteins, effectors and their interactions
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Theodoropoulou M.C., Bagos P.G., Spyropoulos I.C., and Hamodrakas S.J. gpDB: a database of GPCRs, G-proteins, effectors and their interactions. Bioinformatics 24 (2008) 1471-1472
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9
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The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics
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Filizola M., and Weinstein H. The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics. FEBS J 272 (2005) 2926-2938
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Filizola, M.1
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Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones
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Kobayashi H., Ogawa K., Yao R., Lichtarge O., and Bouvier M. Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones. Traffic 10 (2009) 1019-1033
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Traffic
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The fourth transmembrane segment forms the interface of the dopamine D2 receptor homodimer
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Guo W., Shi L., and Javitch J.A. The fourth transmembrane segment forms the interface of the dopamine D2 receptor homodimer. J Biol Chem 278 (2003) 4385-4388
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Guo, W.1
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10744223537
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Identification of amino acid residues crucial for chemokine receptor dimerization
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Hernanz-Falcon P., Rodriguez-Frade J.M., Serrano A., Juan D., del Sol A., Soriano S.F., Roncal F., Gomez L., Valencia A., Martinez A., and Mellado M. Identification of amino acid residues crucial for chemokine receptor dimerization. Nat Immunol 5 (2004) 216-223
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Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation
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An article that lays the foundation for current studies on the activation of TM4-TM4 dimers.
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Guo W., Shi L., Filizola M., Weinstein H., and Javitch J.A. Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. Proc Natl Acad Sci U S A 102 (2005) 17495-17500. An article that lays the foundation for current studies on the activation of TM4-TM4 dimers.
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Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation
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Primarily interesting as a functional complementation study that shows the active complex has two receptors and a single G-protein activated by agonist binding to a single protomer; the computational interest arises because of the use of experimentally assisted docking to address the nature of the active dimer.
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Han Y., Moreira I.S., Urizar E., Weinstein H., and Javitch J.A. Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation. Nat Chem Biol 5 (2009) 688-695. Primarily interesting as a functional complementation study that shows the active complex has two receptors and a single G-protein activated by agonist binding to a single protomer; the computational interest arises because of the use of experimentally assisted docking to address the nature of the active dimer.
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Nat Chem Biol
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Han, Y.1
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15
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Ligand-regulated oligomerization of beta(2)-adrenoceptors in a model lipid bilayer
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Fung J.J., Deupi X., Pardo L., Yao X.J., Velez-Ruiz G.A., Devree B.T., Sunahara R.K., and Kobilka B.K. Ligand-regulated oligomerization of beta(2)-adrenoceptors in a model lipid bilayer. EMBO J 28 (2009) 3315-3328
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Liang Y., Fotiadis D., Filipek S., Saperstein D.A., Palczewski K., and Engel A. Organization of the G protein-coupled receptors rhodopsin and opsin in native membranes. J Biol Chem 278 (2003) 21655-21662
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Kobilka B., and Schertler G.F. New G-protein-coupled receptor crystal structures: insights and limitations. Trends Pharmacol Sci 29 (2008) 79-83
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Inference of macromolecular assemblies from crystalline state
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Useful software for examining alternative (GPCR) X-ray dimer interfaces.
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Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 372 (2007) 774-797. Useful software for examining alternative (GPCR) X-ray dimer interfaces.
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Krissinel, E.1
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Davies A., Gowen B.E., Krebs A.M., Schertler G.F., and Saibil H.R. Three-dimensional structure of an invertebrate rhodopsin and basis for ordered alignment in the photoreceptor membrane. J Mol Biol 314 (2001) 455-463
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20
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Guo W., Urizar E., Kralikova M., Mobarec J.C., Shi L., Filizola M., and Javitch J.A. Dopamine D2 receptors form higher order oligomers at physiological expression levels. EMBO J 27 (2008) 2293-2304
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21
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33749578426
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Benchmark studies on oligomerization from the docking of membrane proteins.
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Casciari D., Seeber M., and Fanelli F. Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinformatics 7 (2006) 340. Benchmark studies on oligomerization from the docking of membrane proteins.
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Casciari, D.1
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Fanelli F. Dimerization of the lutropin receptor: insights from computational modeling. Mol Cell Endocrinol 260-262 (2007) 59-64
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Casciari D., Dell'Orco D., and Fanelli F. Homodimerization of neurotensin 1 receptor involves helices 1, 2, and 4: insights from quaternary structure predictions and dimerization free energy estimations. J Chem Inf Model 48 (2008) 1669-1678
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24
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Design and synthesis of specific probes for human 5-HT4 receptor dimerization studies
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Soulier J.L., Russo O., Giner M., Rivail L., Berthouze M., Ongeri S., Maigret B., Fischmeister R., Lezoualc'h F., Sicsic S., and Berque-Bestel I. Design and synthesis of specific probes for human 5-HT4 receptor dimerization studies. J Med Chem 48 (2005) 6220-6228
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25
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34548487956
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Synthesis of specific bivalent probes that functionally interact with 5-HT(4) receptor dimers
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An interesting application to bivalent ligand drug design.
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Russo O., Berthouze M., Giner M., Soulier J.L., Rivail L., Sicsic S., Lezoualc'h F., Jockers R., and Berque-Bestel I. Synthesis of specific bivalent probes that functionally interact with 5-HT(4) receptor dimers. J Med Chem 50 (2007) 4482-4492. An interesting application to bivalent ligand drug design.
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J Med Chem
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Russo, O.1
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Lezoualc'h, F.7
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26
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67650089750
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Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions
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A study of the conformational changes induced by heterodimerization that has been partially validated by ligand docking studies.
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Bruno A., Guadix A.E., and Costantino G. Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions. J Chem Inf Model 49 (2009) 1602-1616. A study of the conformational changes induced by heterodimerization that has been partially validated by ligand docking studies.
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J Chem Inf Model
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Bruno, A.1
Guadix, A.E.2
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Computational study of the heterodimerization between mu and delta receptors
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Liu X., Kai M., Jin L., and Wang R. Computational study of the heterodimerization between mu and delta receptors. J Comput-Aided Mol Des 23 (2009) 321-332
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Liu, X.1
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Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer
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Filizola M., Wang S.X., and Weinstein H. Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. J Comput-Aided Mol Des 20 (2006) 405-416
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Witt M., Slusarz M.J., and Ciarkowski J. Molecular modeling of vasopressin V2 receptor tetramer in hydrated lipid membrane. QSAR Comb Sci 27 (2008) 684-693
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Niv M.Y., and Filizola M. Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis. Proteins 71 (2008) 575-586
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Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework
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Taylor M.S., Fung H.K., Rajgaria R., Filizola M., Weinstein H., and Floudas C.A. Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophys J 94 (2008) 2470-2481
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A coarse-grained simulation of GPCR assembly that introduces the concept of hydrophobic mismatch into the GPCR dimerization debate.
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Periole X., Huber T., Marrink S.J., and Sakmar T.P. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J Am Chem Soc 129 (2007) 10126-10132. A coarse-grained simulation of GPCR assembly that introduces the concept of hydrophobic mismatch into the GPCR dimerization debate.
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J Am Chem Soc
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Periole, X.1
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