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Research Article

Modeling of G-Protein Coupled Receptors with Bacteriorhodopsin as a Template. A Novel Approach Based on Interaction Energy Differences

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Pages 167-186 | Published online: 26 Sep 2008

References

  • Schertler G. F. X., Villa C., Henderson R. Projection structure of rhodopsin. Nature 1993; 362: 770–772
  • Ovchinnikov Y. A. Rhodopsin and bacteriorhodopsin: structure‐function relationships. FEBS Lett. 1982; 148: 179–191
  • Fryxell K. J., Meyerowitz E. M. The Evolution of Rhodopsins and Neurotransmitter Receptors. J. Mol. Evol. 1991; 33: 367–378
  • Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the Structure of Bacteriorhodopsin Based on High‐resolution electron Cryo‐microscopy. J. Mol. Biol. 1990; 213: 899–929
  • Findlay J. B. C., Pappin D. J.C. The opsin family of proteins. Biochem. J. 1986; 238: 625–642
  • Findlay J., Eliopoulos E. Three‐dimensional modeling of G protein‐linked receptors. Trends Pharmacol. Sci. 1990; 11: 492–499
  • Grötzinger J., Engels M., Jacoby E., Wollmer A., Straßburger W. A model for the C5a receptor and for its interaction with the ligand. Prot. Eng. 1991; 4: 767–771
  • Höltje H. ‐D., Briem H. Molecular modeling studies in the mechanism of action of agonists and antagonists at G‐protein coupled membrane receptors. PharmacoChem. Libr. 1991; 16: 245–252
  • Dahl S. G., Edvardsen Ø., Sylte I. Molecular dynamics of dopamine at the D2‐receptor. Proc. Natl. Acad. Sci. USA 1991; 88: 8111–8115
  • MaloneyHuss K., Lybrand T. P. Three‐dimensional structure for the ß2‐adrenergic receptor protein based on computer modeling studies. J. Mol. Biol. 1992; 225: 859–871
  • Baldwin J. M. The probable arrangement of the helices in G protein‐coupled receptors. EMBO J. 1993; 12: 1693–1703
  • Hibert M. F., Trumpp‐Kallmeyer S., Bruinvels A., Hoflack. Three‐dimensional Models of Neurotransmitter GTP‐Binding Protein‐Coupled Receptors. Mol. Pharmacol. 1991; 40: 8–15
  • Trumpp‐Kallmeyer S., Hoflack J., Bruinvels A., Hibert M. Modeling of G‐protein‐coupled receptors: Application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors. J. Med. Chem. 1992; 35: 3448–3462
  • Lewell W. Q. A model of the adrenergic beta‐2 receptor and binding sites for agonist and antagonist. Drug Design Discov. 1992; 9: 29–48
  • Ijzerman A. P., van Galen P. J. M., Jacobson K. A. Molecular Modeling of Adenosine Receptors. I. The Ligand Binding Site on the Al‐Receptor. Drug Design Discov. 1992; 9: 49–67
  • Nordvall G., Hacksell U. Binding‐Site Modeling of the Muscarinic m1‐Receptor: A Combination of Homology‐Based and Indirect Approaches. J. Med. Chem. 1993; 36: 967–976
  • Brann M. R., Klimkowski V. J., Ellis J. Structure/Function Relationships of Muscarinic Acetylcholine Receptors. Life Sciences 1993; 52: 405–412
  • Yamamoto Y., Kamiya K., Terao S. Modeling of Human Thromboxane A2‐Receptor and Analysis of the Receptor‐Ligand Interaction. J. Med. Chem. 1993; 36: 820–825
  • Cronet P., Sander C., Vriend G. Modeling of trans‐membrane seven helix bundles. Prot. Eng. 1993; 6: 59–64
  • Hoflack J., Hibert M. F., Trumpp‐Kallmeyer S. Three‐dimensional models of Gonado‐Thyrotropin Hormone Receptor Transmembrane Domain. Drug Design Discov. 1993; 10: 157–171
  • Donnelly D., Overington J. P., Ruffle S. V., Nugent J. H. A., Blundell T. L. Modeling α‐helical transmembrane domains: The calculation and use of substitution tables for lipid‐facing residues. Prot. Sci. 1993; 2: 55–70
  • Bowie J. U., Eisenberg D. Inverted protein structure prediction. Curr. Opin. struct. Biol. 1993; 3: 437–444
  • Dunn R., McCoy J., Simsek M., Majumdar A., Chang S. H., Rajbhandary U. L., Khorana H. G. The bacteriorhodopsin gene. Proc. Natl. Acad. Sci. USA 1981; 78: 6744–6748
  • Probst W. C., Snyder L. A., Schuster D. I., Brosius J., Sealfon S. C. Sequence alignment of the G‐protein coupled receptor superfamily. DNA and Cell Biologie 1992; 11: 1–20
  • Henderson R., personal communication
  • Greenhalgh D. A., Altenbach C., Hubbell W. L., Khorana H. G. Locations of Arg‐82, Asp‐85, and Asp‐96 in helix C of bacteriorhodopsin relative to the aqueous boundaries. Proc. Natl. Acad. Sci. USA 1991; 88: 8626–8630
  • Popot J. ‐L., Gerchman S. ‐E., Engelman D. M. Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two‐stage process. J. Mol. Biol. 1987; 198: 655–676
  • Popot J. ‐L., Engelman D. M. Membrane protein folding and oligomerization: the two‐stage model. Biochemistry 1990; 29: 4031–4037
  • Kahn T. W., Engelman D. M. Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five‐helix fragment. Biochemistry 1992; 31: 6144–6151
  • Sharp K. A., Nicholls A., Friedman R., Honig B. Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models. Biochemistry 1991; 30: 9686–9697
  • CHEMX. Chemical Design Ltd., OxfordEngland, developed and distributed by
  • Vriend G. WHATIF: a molecular modeling and drug design program. J. Mol. Graph. 1990; 8: 52–56
  • , GROMOS program library (W.F. van Gunsteren program system GROMOS, distributed by BIOMOS biomolecular software b.v., Laboratory of Physical Chemistry, University of Groningen, NL)
  • Kobilka B. K., Dixon R. A. F., Frielle T., Dohlman H. G., Bolanowski M. A., Sigal I. S., Yang‐Feng T. L., Franke U. A., Caron M. G., Lefkowitz R. J. cDNA for the human beta 2‐adrenergic receptor: a protein with multiple membrane‐spanning domains and encoded by a gene whose chromosomal location is shared with that of the receptor for platelet‐derived growth factor. Proc. Natl. Acad. Sci. USA 1987; 84: 46–50
  • Gerard N. P., Gerard C. The chemotactic receptor for human C5a anaphylatoxin. Nature 1991; 349: 614–617
  • Ovchinnikov Y. A., Abdulaev N. G., Feigina M. Y., Artamonov I. D., Zolotarev A. S., Kostina M. B., Bogachuck A. S., Moroshinikov A. I., Martinov V. I., Kudelin A. B. The complete amino acid sequence of visual rhodopsin. Bioorg. Khim. 1982; 8: 1011–1014
  • Nathans J., Hogness D. S. Isolation sequence analysis, and intron‐exon arrangement of the gene encoding bovine rhodopsin. Cell 1983; 34: 807–814
  • Hargrave P. A., McDowell J. H., Curtis D. R., Wang J. K., Juszczak E., Fong S. ‐L., Rao J. K. M., Argos P. The structure of bovine rhodopsin. Biophys. Struct. Mechn. 1983; 9: 235–244
  • Dixon R. A. F., Sigal I. S., Candelore M. R., Register R. B., Scattergood W., Rands E., Strader C. D. Structural features required for ligand binding to the beta‐adrenergic receptor. EMBO J. 1987; 6: 3269–3275
  • Dixon R. A. F., Sigal I. S., Strader C. D. Structure‐Function Analysis of the ß‐Adrenergic Receptor. Cold spring Harbor Symposia on Quantitative Biology 1988; LIII: 487–497
  • Strader C. D., Sigal I. S., Register R. B., Candelore M. R., Rands E., Dixon R. A.F. Identification of residues required for ligand binding to the ß‐adrenergic receptor. Proc. Natl. Acad. Sci. USA 1987; 84: 4384–4388
  • Strader C. D., Sigal I. S., Candelore M. R., Rands E., Hill W. S., Dixon R. A.F. Conserved aspartic residues 79 and 113 of the ß‐adrenergic receptor have different roles in receptor function. J. Biol. Chem. 1988; 263: 10267–10271
  • Zhukovsky E. A., Oprian D. D. Effect of Carboxylic Acid Side Chains on the Absorption Maximum of Visual Pigments. Science 1989; 246: 928–930
  • Franke R. R., Koenig B., Sakmar T. P., Khorana H. G., Hofmann K. P. Rhodopsin mutants that bind but fail to activate transducin. Science 1990; 250: 123–125
  • Wess J., Nanavati S., Vogel Z., Maggio R. Functional role of proline and tryptophan residues highly conserved among G protein‐coupled receptors studied by mutational analysis of the m3‐muscarinic receptor. EMBO J. 1993; 12: 331–338
  • Strader C. D., Candelore M. R., Hill W. S., Sigal I. S., Dixon R. A.F. Identification of two serine residues involved in agonist activation of the beta‐adrenergic receptor. J. Biol. Chem. 1989; 264: 13572–13578
  • Fong T. M., Cascieri M. A., Yu H., Bansal A., Swain C., Strader C. D. Amino‐aromatic interaction between histidine 197 of the neurokinin‐1 receptor and CP 96345. Nature 1993; 362: 350–353
  • Doi T., Molday R. S., Korana H. G. Role of the intra‐discal domain in rhodopsin assembly and function. Proc. Natl. Acad. Sci. USA 1990; 87: 4991–4995
  • Nathans J. Rhodopsin: Structure, Function and Genetics. Biochemistry 1992; 31: 4923–4931
  • Suryanarayana S., Daunt D. A., Von Zastrow M., Kobilka B. K. A Point Mutation in the seventh hydrophobic Domain of the α2‐Adrenergic Receptor Increases Its Affinity for a Family of ß‐Receptor Antagonists. J. Biol. Chem. 1991; 266: 15488–15492
  • Sachais B. S., Snider R. M., Lowe J. A., III, Krause J. E. Molecular Basis for the Species Selectivity of the Substance P Antagonist CP‐96, 345. J. Biol. Chem. 1993; 268: 2319–2323
  • Henderson R., Unwin P. N.T. Three‐dimensional model of purple membrane obtained by electron microscopy. Nature 1975; 257: 28–32
  • Mollison K. W., Mandecki W., Zuiderweg E. R. P., Fayer L., Fey T. A., Krause R. A., Conway R. G., Miller L., Edalji R. P., Shallcross M. A., Lane B., Fox J. L., Greer J., Carter G. W. Identification of receptor‐binding residues in the inflammatory complement protein C5a by site‐directed mutagenesis. Proc. Natl. Acad. Sci. USA 1989; 86: 292–296
  • Bautsch W., Raffetseder U., unpublished data
  • Cowan S. W., Schirmer T., Rummel G., Steiert M., Ghosh R., Pauptit R. A., Jansonius J. N., Rosenbusch J. P. Crystal structures explain functional properties of two E. coli porins. Nature 1992; 358: 727–733
  • Schiffer M., Chang C. ‐H., Stevens F. J. The functions of tryptophan residues in membrane proteins. Prot. Eng. 1992; 5: 213–214
  • Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982; 157: 105–132
  • Allen J. P., Feher G., Yeates T. O., Komiya H., Rees D. C. Structure of the reaction center from Rhodobacter spaeroides R‐26: The protein subunits. Proc. Natl. Acad. Sci. USA 1987; 84: 6162–6166
  • Yeates T. O., Komiya H., Rees D. C., Allen J. P., Feher G. Structure of the reaction center from Rhodobacter sphaeroides R‐26: Membrane‐protein interactions. Proc. Natl. Acad. Sci. USA 1987; 84: 6438–6442

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