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PMID: 19176531 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Location of the retinal chromophore in the activated state of rhodopsin*.

The Journal of biological chemistry ·Vol. 284 ·No. 15 ·2009-04-10 ·Pages 10190-201

Ahuja S, Crocker E, Eilers M, Hornak V, Hirshfeld A, Ziliox M, Syrett N, Reeves PJ, Khorana HG, Sheves M, Smith SO

Abstract

Rhodopsin is a highly specialized G protein-coupled receptor (GPCR) that is activated by the rapid photochemical isomerization of its covalently bound 11-cis-retinal chromophore. Using two-dimensional solid-state NMR spectroscopy, we defined the position of the retinal in the active metarhodopsin II intermediate. Distance constraints were obtained between amino acids in the retinal binding site and specific (13)C-labeled sites located on the beta-ionone ring, polyene chain, and Schiff base end of the retinal. We show that the retinal C20 methyl group rotates toward the second extracellular loop (EL2), which forms a cap on the retinal binding site in the inactive receptor. Despite the trajectory of the methyl group, we observed an increase in the C20-Gly(188) (EL2) distance consistent with an increase in separation between the retinal and EL2 upon activation. NMR distance constraints showed that the beta-ionone ring moves to a position between Met(207) and Phe(208) on transmembrane helix H5. Movement of the ring toward H5 was also reflected in increased separation between the Cepsilon carbons of Lys(296) (H7) and Met(44) (H1) and between Gly(121) (H3) and the retinal C18 methyl group. Helix-helix interactions involving the H3-H5 and H4-H5 interfaces were also found to change in the formation of metarhodopsin II reflecting increased retinal-protein interactions in the region of Glu(122) (H3) and His(211) (H5). We discuss the location of the retinal in metarhodopsin II and its interaction with sequence motifs, which are highly conserved across the pharmaceutically important class A GPCR family, with respect to the mechanism of receptor activation.

MeSH Terms
Binding Sites Cell Line Humans Magnetic Resonance Spectroscopy Molecular Conformation Polyenes/chemistry Protein Conformation Receptors, G-Protein-Coupled/chemistry Retina/metabolism Rhodopsin/chemistry,metabolism Rod Cell Outer Segment/metabolism Schiff Bases/chemistry
Chemicals
Polyenes Receptors, G-Protein-Coupled Schiff Bases metarhodopsins Rhodopsin
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Ahuja Shivani
Departments of Physics & Astronomy and Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215.
Crocker Evan
Eilers Markus
Hornak Viktor
Hirshfeld Amiram
Ziliox Martine
Syrett Natalie
Reeves Philip J
Khorana H Gobind
Sheves Mordechai
Smith Steven O
References (70)
70 references, click to expand
  1. Identification of two serine residues involved in agonist activation of the beta-adrenergic receptor.
    J Biol Chem. 1989 Aug 15;264(23):13572-8 PMID: 2547766
  2. Quantum mechanical studies on the crystallographic model of bathorhodopsin.
    Angew Chem Int Ed Engl. 2006 Jun 26;45(26):4274-7 PMID: 16729349
  3. Receptor activation: what does the rhodopsin structure tell us?
    Trends Pharmacol Sci. 2001 Nov;22(11):587-93 PMID: 11698103
  4. Crystallographic analysis of primary visual photochemistry.
    Angew Chem Int Ed Engl. 2006 Jun 26;45(26):4270-3 PMID: 16586416
  5. Photoacoustic calorimetric study of the conversion of rhodopsin and isorhodopsin to lumirhodopsin.
    Biochemistry. 1991 Feb 5;30(5):1254-8 PMID: 1991105
  6. Residues in the fifth membrane-spanning segment of the dopamine D2 receptor exposed in the binding-site crevice.
    Biochemistry. 1995 Dec 19;34(50):16433-9 PMID: 8845371
  7. Structural analysis and dynamics of retinal chromophore in dark and meta I states of rhodopsin from 2H NMR of aligned membranes.
    J Mol Biol. 2007 Sep 7;372(1):50-66 PMID: 17640664
  8. The ring of the rhodopsin chromophore in a hydrophobic activation switch within the binding pocket.
    J Mol Biol. 2004 Oct 22;343(3):719-30 PMID: 15465057
  9. Structure and function in rhodopsin: a tetracycline-inducible system in stable mammalian cell lines for high-level expression of opsin mutants.
    Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13413-8 PMID: 12370422
  10. Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study.
    Biochemistry. 1996 Sep 24;35(38):12470-8 PMID: 8823182
  11. Function of extracellular loop 2 in rhodopsin: glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II.
    Biochemistry. 2002 Mar 19;41(11):3620-7 PMID: 11888278
  12. Dipolar assisted rotational resonance NMR of tryptophan and tyrosine in rhodopsin.
    J Biomol NMR. 2004 May;29(1):11-20 PMID: 15017136
  13. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.
    J Mol Biol. 2007 Sep 28;372(4):906-917 PMID: 17719606
  14. Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch.
    J Biol Chem. 2002 Oct 25;277(43):40989-96 PMID: 12167654
  15. Relative orientation between the beta-ionone ring and the polyene chain for the chromophore of rhodopsin in native membranes.
    Biochemistry. 2002 Jun 18;41(24):7549-55 PMID: 12056885
  16. Crystal structure of the ligand-free G-protein-coupled receptor opsin.
    Nature. 2008 Jul 10;454(7201):183-7 PMID: 18563085
  17. Differential modes of agonist binding to 5-hydroxytryptamine(2A) serotonin receptors revealed by mutation and molecular modeling of conserved residues in transmembrane region 5.
    Mol Pharmacol. 2000 Nov;58(5):877-86 PMID: 11040033
  18. Single amino acid residue as a functional determinant of rod and cone visual pigments.
    Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2322-6 PMID: 9122193
  19. Rhodopsin: structural basis of molecular physiology.
    Physiol Rev. 2001 Oct;81(4):1659-88 PMID: 11581499
  20. NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light activation.
    Biochemistry. 2004 Feb 3;43(4):1126-33 PMID: 14744159
  21. Mapping of the amino acids in membrane-embedded helices that interact with the retinal chromophore in bovine rhodopsin.
    J Biol Chem. 1991 Mar 5;266(7):4269-75 PMID: 1999419
  22. Local peptide movement in the photoreaction intermediate of rhodopsin.
    Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12729-34 PMID: 16908857
  23. Role of the C9 methyl group in rhodopsin activation: characterization of mutant opsins with the artificial chromophore 11-cis-9-demethylretinal.
    Biochemistry. 1998 Jan 13;37(2):538-45 PMID: 9425074
  24. Recognition of opsin to the longitudinal length of retinal isomers in the formation of rhodopsin.
    Vision Res. 1978;18(5):607-9 PMID: 664347
  25. Magic angle spinning NMR of the protonated retinylidene Schiff base nitrogen in rhodopsin: expression of 15N-lysine- and 13C-glycine-labeled opsin in a stable cell line.
    Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):487-92 PMID: 9892660
  26. Cis-trans isomers of vitamin A and retinene in the rhodopsin system.
    J Gen Physiol. 1952 Nov;36(2):269-315 PMID: 13011282
  27. Orientation of aromatic residues in rhodopsin. Rotation of one tryptophan upon the meta I to meta II transition afer illumination.
    Photochem Photobiol. 1979 Aug;30(2):295-9 PMID: 504353
  28. Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation.
    Nat Struct Mol Biol. 2009 Feb;16(2):168-75 PMID: 19182802
  29. Volume and enthalpy changes after photoexcitation of bovine rhodopsin: laser-induced optoacoustic studies.
    Biophys J. 1997 May;72(5):2294-303 PMID: 9129833
  30. Lipid headgroup and acyl chain composition modulate the MI-MII equilibrium of rhodopsin in recombinant membranes.
    Biochemistry. 1993 Mar 9;32(9):2438-54 PMID: 8443184
  31. The functional microdomain in transmembrane helices 2 and 7 regulates expression, activation, and coupling pathways of the gonadotropin-releasing hormone receptor.
    J Biol Chem. 1999 Oct 8;274(41):28880-6 PMID: 10506131
  32. Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions.
    J Biol Chem. 2004 Feb 27;279(9):8126-32 PMID: 14660595
  33. Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin.
    J Mol Biol. 2006 Mar 17;357(1):163-72 PMID: 16414074
  34. Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations.
    Biochemistry. 2002 Sep 3;41(35):10799-809 PMID: 12196019
  35. Two different forms of metarhodopsin II: Schiff base deprotonation precedes proton uptake and signaling state.
    Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7849-53 PMID: 8356093
  36. An improved broadband decoupling sequence for liquid crystals and solids.
    J Magn Reson. 2000 Jan;142(1):97-101 PMID: 10617439
  37. Coupling of retinal isomerization to the activation of rhodopsin.
    Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10048-53 PMID: 15220479
  38. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin.
    Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16123-8 PMID: 17060607
  39. Energy uptake in the first step of visual excitation.
    Nature. 1979 Nov 29;282(5738):531-3 PMID: 503236
  40. (1)H and (13)C MAS NMR evidence for pronounced ligand-protein interactions involving the ionone ring of the retinylidene chromophore in rhodopsin.
    Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9101-6 PMID: 12093898
  41. Changes in interhelical hydrogen bonding upon rhodopsin activation.
    J Mol Biol. 2005 Apr 8;347(4):803-12 PMID: 15769471
  42. Transducin activation by rhodopsin without a covalent bond to the 11-cis-retinal chromophore.
    Science. 1991 Feb 1;251(4993):558-60 PMID: 1990431
  43. Helix packing moments reveal diversity and conservation in membrane protein structure.
    J Mol Biol. 2004 Mar 26;337(3):713-29 PMID: 15019789
  44. The forgotten serine. A critical role for Ser-2035.42 in ligand binding to and activation of the beta 2-adrenergic receptor.
    J Biol Chem. 2000 Dec 1;275(48):37779-88 PMID: 10964911
  45. High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation.
    Proc Natl Acad Sci U S A. 2008 May 27;105(21):7439-44 PMID: 18490656
  46. Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy.
    Nature. 2002 Nov 7;420(6911):98-102 PMID: 12422222
  47. 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. 1996 Dec 13;271(50):32337-42 PMID: 8943296
  48. Agonists and partial agonists of rhodopsin: retinals with ring modifications.
    Biochemistry. 2005 Sep 6;44(35):11684-99 PMID: 16128569
  49. Evidence for the specific interaction of a lipid molecule with rhodopsin which is altered in the transition to the active state metarhodopsin II.
    FEBS Lett. 1998 Oct 9;436(3):304-8 PMID: 9801137
  50. Mechanism of activation and inactivation of opsin: role of Glu113 and Lys296.
    Biochemistry. 1992 Dec 22;31(50):12592-601 PMID: 1472495
  51. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin.
    Science. 1996 Nov 1;274(5288):768-70 PMID: 8864113
  52. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure.
    J Mol Biol. 2004 Sep 10;342(2):571-83 PMID: 15327956
  53. Movement of retinal along the visual transduction path.
    Science. 2000 Jun 23;288(5474):2209-12 PMID: 10864869
  54. Signaling states of rhodopsin. Formation of the storage form, metarhodopsin III, from active metarhodopsin II.
    J Biol Chem. 2003 Jan 31;278(5):3162-9 PMID: 12427735
  55. Deuterium NMR structure of retinal in the ground state of rhodopsin.
    Biochemistry. 2004 Oct 12;43(40):12819-28 PMID: 15461454
  56. Constitutive activation of opsin by mutation of methionine 257 on transmembrane helix 6.
    Biochemistry. 1998 Jun 2;37(22):8253-61 PMID: 9609722
  57. Protonation states of membrane-embedded carboxylic acid groups in rhodopsin and metarhodopsin II: a Fourier-transform infrared spectroscopy study of site-directed mutants.
    Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):10206-10 PMID: 7901852
  58. Structure and function in rhodopsin: high level expression of a synthetic bovine opsin gene and its mutants in stable mammalian cell lines.
    Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11487-92 PMID: 8876162
  59. Chloroethylclonidine binds irreversibly to exposed cysteines in the fifth membrane-spanning domain of the human alpha2A-adrenergic receptor.
    Mol Pharmacol. 1998 Mar;53(3):370-6 PMID: 9495800
  60. Functional microdomains in G-protein-coupled receptors. The conserved arginine-cage motif in the gonadotropin-releasing hormone receptor.
    J Biol Chem. 1998 Apr 24;273(17):10445-53 PMID: 9553103
  61. Structure and function in rhodopsin. Studies of the interaction between the rhodopsin cytoplasmic domain and transducin.
    J Biol Chem. 1992 Jul 25;267(21):14767-74 PMID: 1634520
  62. Magic angle spinning nuclear magnetic resonance of isotopically labeled rhodopsin.
    Methods Enzymol. 2002;343:212-22 PMID: 11675791
  63. Assignment and interpretation of hydrogen out-of-plane vibrations in the resonance Raman spectra of rhodopsin and bathorhodopsin.
    Biochemistry. 1982 Jan 19;21(2):384-93 PMID: 7074022
  64. Plaque production by the polyoma virus.
    Virology. 1959 Jul;8(3):396-7 PMID: 13669362
  65. Constitutive activation of opsin: influence of charge at position 134 and size at position 296.
    Biochemistry. 1993 Jun 15;32(23):6111-5 PMID: 8099498
  66. Specific tryptophan UV-absorbance changes are probes of the transition of rhodopsin to its active state.
    Biochemistry. 1996 Aug 27;35(34):11149-59 PMID: 8780519
  67. Crystal structure of opsin in its G-protein-interacting conformation.
    Nature. 2008 Sep 25;455(7212):497-502 PMID: 18818650
  68. Constitutively active mutants of rhodopsin.
    Neuron. 1992 Oct;9(4):719-25 PMID: 1356370
  69. Conformational states and dynamics of rhodopsin in micelles and bilayers.
    Biochemistry. 2006 May 2;45(17):5538-50 PMID: 16634635
  70. The effects of amino acid replacements of glycine 121 on transmembrane helix 3 of rhodopsin.
    J Biol Chem. 1996 Dec 13;271(50):32330-6 PMID: 8943295
Article Info
Journal
The Journal of biological chemistry
Abbr.
J Biol Chem
ISSN
0021-9258
DOI
10.1074/jbc.M805725200
Published
2009-04-10
Epub
2009-00-28
Pages
10190-201
Language
English
Region
United States
NLM ID
2985121R
PMCID
PMC2665073
Subset
IM
Grants
NIGMS NIH HHS · R01 GM041412 · United States
NEI NIH HHS · EY-11716 · United States
NIGMS NIH HHS · GM-41412 · United States
NCRR NIH HHS · S10 RR13889 · United States
External Links
PubMed source DOI: 10.1074/jbc.M805725200 PMC Full Text View journal details
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