Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin

Journal of Molecular Biology

Volumn 281, Issue 4, 1998, Pages 741-754

  Herzyk, Pawel ^a   Hubbard, Roderick E ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Conformational search; G protein coupled receptor; Membrane protein; Rhodopsin; Simulated annealing

Indexed keywords

MEMBRANE PROTEIN; RHODOPSIN;

ALPHA HELIX; ARTICLE; BIOPHYSICS; FROG; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION;

ANURA;

EID: 0032575763     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1981     Document Type: Article

References (47)

1. Altenbach C., Yang K., Ferrens D.L., Farahbakhsh Z.T., Khorana H.G., Hubbell W.L. Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin a site-directed spin-labeling study. Biochemistry. 35:1996;12470-12478
2. Arnis S., Fahmy K., Hofmann K.P., Sakmar T.P. A conserved carboxylic acid group mediates light-dependent proton uptake and signaling by rhodopsin. J. Biol. Chem. 269:1994;23879-23881
3. Baldwin J.M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 12:1993;1693-1703
4. Baldwin J.M., Schertler G.F.X., Unger V.M. An alpha-carbon template for the transmembrane helices in rhodopsin family of G-protein-coupled receptors. J. Mol. Biol. 272:1997;144-164
5. Ballesteros J.A., Weinstein H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci. 25:1995;366-428
6. Beck M., Sakmar T.P., Siebert F. Spectroscopic evidence for interaction between transmembrane helices 3 and 5 in rhodopsin. Biochemistry. 37:1998;7630-7639
7. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217
8. Brünger A.T. X-PLOR (version 3.1). A system for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven
9. Chan T., Lee M., Sakmar T.P. Introduction of hydroxyl-bearing amino acids causes bathochromic spectral shifts in rhodopsin. J. Biol. Chem. 267:1992;9478-9480
10. Dratz E.A., Hargrave P.A. The structure of rhodopsin and the rod outer segment disk membrane. Trends Biochem. Sci. 8:1983;128-131
11. Dryja T.P., Berson E.L., Rao V.R., Oprian D.D. Heterozygous missense mutation in the rhodopsin gene as a cause of congenital stationary night blindness. Nature Genet. 4:1993;280-283
12. Farahbakhsh Z.T., Ridge K.D., Khorana H.G., Hubbell W.L. Mapping light-dependent structural changes in the cytoplasmic loop connecting helices C and D in rhodopsin a site-directed spi labelling study. Biochemistry. 34:1995;8812-8819
13. Gröbner G., Choi G., Burnett I.J., Glaubitz C., Verdegem P.J.E., Lugtenburg J., Watts A. Photoreceptor rhodopsin structural and conformational study of its chromphore 11-cis retinal in oriented membranes by deuterium solid-state NMR. FEBS Letters. 422:1998;201-204
14. Han M., Smith S.O. NMR constraints on the location of the retinal chromophore in rhodopsin and bathorhodopsin. Biochemistry. 34:1995;1425-1432
15. Han M., DeDecker B.S., Smith S.O. Localization of the retinal protonated Schiff base counterion in rhodopsin. Biophys. J. 65:1993;899-906
16. Han M., Lin S.W., Minkova M., Smith S.O., Sakmar T.P. Functional interaction of transmembrane helices 3 and 6 in rhodopsin replacement of phenylalanine 261 by alanine causes reversion of phenotype of a glycine 121 replacement mutant. J. Biol. Chem. 271:1996;32337-32342
17. Han M., Lin S.W., Smith S.O., Sakmar T.P. The effects of amino acid replacements of glycine 121 on transmembrane helix 3 of rhodopsin. J. Biol. Chem. 271:1996;32330-32336
18. Herzyk P., Hubbard R.E. An automated method for modelling seven-helix transmembrane receptors from experimental data. Biophys. J. 69:1995;2419-2442
19. Herzyk P., Hubbard R.E. Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban. Biophys. J. 74:1998;1203-1214
20. Kaushal S., Khorana H.G. Structure and function in rhodopsin. 7. Point mutations associated with autosomal dominant retinis pigmentosa. Biochemistry. 33:1994;6121-6128
21. Kerr I.D., Sankararamakrishnan R., Smart O.S., Sansom M.S.P. Parallel helix bundles and ion channels molecular modelling via simulated annealing and restrained molecular dynamics. Biophys. J. 67:1994;1501-1515
22. Kirkpatrick S.C.D., Gellat J., Vecchi M.P. Optimization by simulated annealing. Science. 220:1983;671-680
23. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291
24. Liebman P.A. In situ microspectrophotometric studies on the pigments of single retinal rods. Biophys. J. 2:1962;161-178
25. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., Teller E. Equation of state calculation by fast computing machines. J. Chem. Phys. 21:1953;1087-1092
26. Nakayama T.A., Khorana H.G. Mapping of the amino acids in membrane-embedded helices that interact with the retinal chromophore in bovine rhodopsin. J. Biol. Chem. 266:1991;4269-4275
27. Neitz M., Neitz J., Jacobs G.H. Spectral tuning of pigments underlying red-green color vision. Science. 252:1991;971-974
28. Neria E., Fisher S., Karplus M. Simulation of activation free-energies in molecular-systems. J. Chem. Phys. 105:1996;1902-1921
29. Nilges M., Brünger A.T. Automated modeling of coiled coils application to the GCN4 dimerization region. Protein Eng. 4:1991;649-659
30. Nina M., Roux B., Smith J.C. Functional interpretations in bacteriorhodopsin-a theoretical-analysis of retinal hydrogen-bonding with water. Biophys. J. 68:1995;25-39
31. Oldfield T.J. SQUID a program for the analysis and display of data from crystallography and molecular dynamics. J. Mol. Graph. 10:1992;247-252
32. Oliveira L., Paiva A.C.M., Vriend G. A common motif in G-protein-coupled seven transmembrane helix receptors. J. Comput. Aided Mol. Des. 7:1993;649-658
33. Oprian D.D. The ligand-binding domain of rhodopsin and other G protein-linked receptors. J. Bioenerg. Biomembr. 24:1992;211-217
34. Pogozheva I.D., Lomize A.L., Mosberg H.I. The transmembrane 7-α-bundle of rhodopsin distance geometry calculations with hydrogen bonding constraints. Biophys. J. 72:1997;1963-1985
35. Prusis P., Schioth H.-B., Muceniece R., Herzyk P., Afshar M., Hubbard R.E., Wikberg J.E.S. Modeling of the three-dimensional structure of the human melanocortin-1 receptor using an automated method and docking of a rigid cyclic MSH core peptide. J. Mol. Graphics Mod. 15:1997;307-317
36. Rao V.R., Cohen G.B., Oprian D.D. Rhodopsin mutation G90D and a molecular mechanism for congenital night blindness. Nature. 367:1994;639-642
37. Sankararamakrishnan R., Vishveshwara S. Geometry of proline-containing alpha-helices in proteins. Int. J. Pept. Protein Res. 39:1992;356-363
38. Schertler G.F.X., Hargrave P.A. Projection structure of frog rhodopsin in two crystal forms. Proc. Natl Acad. Sci. USA. 92:1995;11578-11582
39. Schertler G.F.X., Villa C., Henderson R. Projection structure of rhodopsin. Nature. 362:1993;770-772
40. 1B-adrenergic receptor role of the highly conserved polar amino-acids in receptor activation. EMBO. J. 15:1996;3566-3578
41. Sheikh S.P., Zvyaga T.A., Lichtarge O., Sakmar T.P., Bourne H.R. Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature. 383:1996;347-350
42. Unger V.M., Hargrave P.A., Baldwin J.M., Schertler G.F.X. Arrangement of rhodopsin transmembrane helices. Nature. 389:1997;203-206
43. Weitz C.J., Nathans J. Histidine residues regulate the transition of photoexcited rhodopsin to its active conformation, metharhodopsin-II. Neuron. 8:1992;465-472
44. Zhang H., Lerro K.A., Yamamoto T., Lien T.H., Sastry L., Gawinowicz M.A., Nakanishi K. The location of the chromophore in rhodopsin a photoaffinity study. J. Am. Chem. Soc. 116:1994;10165-10173
45. Zhukovsky E.A., Robinson P.R., Oprian D.D. Changing the location od the Schiff base counterion in rhodopsin. Biochemistry. 31:1992;10400-10405
46. Zvyaga T.A., Min K.C., Beck M., Sakmar T.P. Movement of the retinylidine Schiff base counterion in rhodopsin by one helix turn reverses the pH dependence of the metarhodopsin I to metarhodopsin II transition. J. Biol. Chem. 268:1993;4661-4667
47. Zvyaga T.A., Fahmy K., Sakmar T.P. Characterisation of rhodopsin-transducin interaction a mutant rhodopsin photoproduct with a protonated Schiff base activates transducin. Biochemistry. 33:1994;9753-9761