Molecular modelling studies on G protein-coupled receptors: From sequence to structure?

Journal of Receptor and Signal Transduction Research

Volumn 19, Issue 1-4, 1999, Pages 341-353

  Van Neuren, A S ^a   Muller G ^a   Klebe, G ^b   Moroder, L ^c  

^a BAYER AG   (Germany)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN; MEMBRANE PROTEIN; RECEPTOR PROTEIN;

AMINO ACID SEQUENCE; CONFERENCE PAPER; LIGAND BINDING; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

EID: 0032999956     PISSN: 10799893     EISSN: None     Source Type: Journal    
DOI: 10.3109/10799899909036656     Document Type: Conference Paper

References (35)

1. Schertler, G.F.; Villa, C. and Henderson, R. Projection structure of rhodopsin. Nature 362, 770-772, 1993.
2. Unger, V.M. and Schertier, G.F. Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy. Biophys.J. 68, 1776-1786, 1995.
3. Schertler, G.F. and Hargrave, P.A. Projection structure of frog rhodopsin in two crystal forms. Proc Natl Acad Sci U S A 92, 11578-11582, 1995.
4. Davies, A.; Schertler, G.F.; Gowen, B.E. and Saibil, H.R. Projection structure of an invertebrate rhodopsin. J Struct.Biol. 117, 36-44, 1996.
5. Pebay-Peyroula, E.; Rummel, G.; Rosenbusch, J.P. and Landau, E.M. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases [see comments]. Science 277, 1676-1681, 1997.
6. IJzerman, A.P.; Van Galen, P.J. and Jacobson, K.A. Molecular modeling of adenosine receptors. I. The ligand binding site on the A1 receptor. Drug Des Discov 9, 49-67, 1992.
7. Trumpp-Kallmeyer, S.; Hoflack, J.; Bruinvels, A. and Hibert, M. Modeling of G-protein-coupled receptors: application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors. J Med Chem 35, 3448-3462, 1992.
8. Cronet, P.; Sander, C. and Vriend, G. Modeling of transmembrane seven helix bundles. Protein Eng. 6, 59-64, 1993.
9. Lutz, J.; Romano-Gotsch, R.; Escrieut, C.; Fourmy, D.; Matha, B.; Muller, G.; Kessler, H. and Moroder, L. Mapping of ligand binding sites of the cholecystokinin-B/gastrin receptor with lipo-gastrin peptides and molecular modeling. Biopolymers 41, 799-817, 1997.
10. MaloneyHuss, K. and Lybrand, T.P. Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies. J Mol.Biol. 225, 859-871, 1992.
11. Herzyk, P. and Hubbard, R.E. Automated method for modeling seven-helix transmembrane receptors from experimental data [see comments]. Biophys J 69, 2419-2442, 1995.
12. Baldwin, J.M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J 12, 1693-1703, 1993.
13. Baldwin, J.M.; Schertler, G.F. and Unger, V.M. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J.Mol.Biol. 272, 144-164, 1997.
14. Kyte, J. and Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J Mol.Biol. 157, 105-132, 1982.
15. Crimi, M. and Degli Esposti, M. Structural predictions for membrane proteins: the dilemma of hydrophobicity scales. Trends.Biochem.Sci. 16, 119, 1991.
16. Rose, G.D. and Dworkin, J.E. in Prediction of Protein Structure and the Principles of Protein Conformation, edited by Fasman, G.D., p. 625-633,Plenum Press, New York, 1989.
17. Degli Esposti, M.; Crimi, M. and Venturoli, G. A critical evaluation of the hydropathy profile of membrane proteins. Eur.J Biochem. 190, 207-219, 1990.
18. Ballesteros, J. A. and Weinstein, H. Integrated Methods for the Construction of Three-Dimensional Models and Computational Probing of Structure-Function Relations in G Protein-Coupled Receptors. Meth.Neurosc. 25, 366-428, 1995.
19. Zhang, D. and Weinstein, H. Polarity conserved positions in transmembrane domains of G-protein coupled receptors and bacteriorhodopsin. FEBS Lett 337, 207-212, 1994.
20. Wolfenden, R.; Andersson, L.; Cullis, P.M. and Southgate, C.C. Affinities of amino acid side chains for solvent water. Biochemistry 20, 849-855, 1981.
21. Eisenberg, D.; Schwarz, E.; Komaromy, M. and Wall, R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol.Biol. 179, 125-142, 1984.
22. Hopp, T.P. and Woods, K.R. Prediction of protein antigenic determinants from amino acid sequences. Proc.Natl.Acad.Sci.U.S.A. 78, 3824-3828, 1981.
23. Zimmerman, J.M.; Eliezer, N. and Simha, R. The Characterization of Amino Acid Sequences in Proteins by Statistical Methods. J.Theoret.Biol. 21, 170-201, 1968.
24. von Heijne, G. The distribution of positvely charged residues in bacterial inner membrane proteins correlates with the transmembrane topology. EMBO J 5, 3021-3027, 1986.
25. Williams, K.A. and Deber, C.M. Proline residues in transmembrane helices: structural or dynamic role? Biochemistry 30, 8919-8923, 1991.
26. von Heijne, G. Proline kinks in transmembrane alpha-helices. J Mol.Biol. 218, 499-503, 1991.
27. Landolt-Marticorena, C.; Williams, K.A.; Deber, C.M. and Reithmeier, R.A. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J Mol.Biol. 229, 602-608, 1993.
28. Schiffer, M. and Edmundson, A.B. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J 7, 121-135, 1967.
29. Eisenberg, D.; Weiss, R.M. and Terwilliger, T.C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature 299, 371-374, 1982.
30. Eisenberg, D.; Wesson, M. and Wilcox, W. in Prediction of Protein Structure and the Principles of Protein Conformation, edited by Fasman, G.D., p. 635-646,Plenum Press, New York, 1989.
31. Eisenberg, D.; Weiss, R.M. and Terwilliger, T.C. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc.Natl.Acad.Sci.U.S.A. 81, 140-144, 1984.
32. Dunnill, P. The use of helical net-diagrams to represent protein structures. Biophys J 8, 865-875, 1968.
33. Donnelly, D.; Overington, J.P.; Ruffle, S.V.; Nugent, J.H. and Blundell, T.L. Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci. 2, 55-70, 1993.
34. Finer-Moore, J.; Bazan, J.F.; Rubin, J. and Stroud, R.M. in Prediction of Protein Structure and the Principles of Protein Conformation, edited by Fasman, G.D., p. 719-759,Plenum Press, New York, 1989.
35. Hecht, M.H.; Richardson, J.S.; Richardson, D.C. and Ogden, R.C. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 249, 884-891, 1990.