Dark and photoactivated rhodopsin share common binding modes to transducin

FEBS Letters

Volumn 582, Issue 6, 2008, Pages 991-996

  Fanelli, Francesca ^a   Dell'Orco, Daniele ^a  

^a DULBECCO TELETHON INSTITUTE   (Italy)

Author keywords

Computational modeling; G protein; GPCRs; Molecular recognition; Protein protein docking

Indexed keywords

DOCKING PROTEIN; GT PROTEIN; RHO FACTOR; RHODOPSIN; TRANSDUCIN; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER MODEL; HUMAN; INTERMETHOD COMPARISON; MOLECULAR MODEL; MOLECULAR RECOGNITION; PHOTOACTIVATION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTON TRANSPORT; STRUCTURE ANALYSIS;

EID: 40349088696     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2008.02.041     Document Type: Article

References (34)

1. K. Palczewski G protein-coupled receptor rhodopsin Annu. Rev. Biochem. 75 2006 743 767
2. [2] B. Knierim K.P. Hofmann O.P. Ernst W.L. Hubbell Sequence of late molecular events in the activation of rhodopsin Proc. Natl. Acad. Sci. USA 2007
3. D.L. Farrens C. Altenbach K. Yang W.L. Hubbell H.G. Khorana Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin Science 274 1996 768 770
4. S.P. Sheikh T.A. Zvyaga O. Lichtarge T.P. Sakmar H.R. Bourne Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F Nature 383 1996 347 350
5. L. Aris A. Gilchrist S. Rens-Domiano C. Meyer P.J. Schatz E.A. Dratz H.E. Hamm Structural requirements for the stabilization of metarhodopsin II by the C terminus of the alpha subunit of transducin J. Biol. Chem. 276 2001 2333 2339
6. D.C. Teller T. Okada C.A. Behnke K. Palczewski R.E. Stenkamp Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs) Biochemistry 40 2001 7761 7772
7. W.M. Oldham H.E. Hamm Structural basis of function in heterotrimeric G proteins Quart. Rev. Biophys. 39 2006 117 166
8. F. Fanelli D. Dell’Orco Rhodopsin activation follows pre-coupling with transducin: inferences from computational analysis Biochemistry 44 2005 14695 14700
9. D. Dell’Orco M. Seeber F. Fanelli Monomeric dark rhodopsin holds the molecular determinants for transducin recognition: insights from computational analysis FEBS Lett. 581 2007 944 948
10. B. Jastrzebska T. Maeda L. Zhu D. Fotiadis S. Filipek A. Engel R.E. Stenkamp K. Palczewski Functional characterization of rhodopsin monomers and dimers in detergents J. Biol. Chem. 279 2004 54663 54675
11. M. Chabre M. le Maire Monomeric G-protein-coupled receptor as a functional unit Biochemistry 44 2005 9395 9403
12. O.P. Ernst V. Gramse M. Kolbe K.P. Hofmann M. Heck Monomeric G protein-coupled receptor rhodopsin in solution activates its G protein transducin at the diffusion limit Proc. Natl. Acad. Sci. USA 104 2007 10859 10864
13. T.H. Bayburt A.J. Leitz G. Xie D.D. Oprian S.G. Sligar Transducin activation by nanoscale lipid bilayers containing one and two rhodopsins J. Biol. Chem. 282 2007 14875 14881
14. M.R. Whorton B. Jastrzebska P.S. Park D. Fotiadis A. Engel K. Palczewski R.K. Sunahara Efficient coupling of transducin to monomeric rhodopsin in a phospholipid bilayer J. Biol. Chem. 2007
15. D. Salom Crystal structure of a photoactivated deprotonated intermediate of rhodopsin Proc. Natl. Acad. Sci. USA 103 2006 16123 16128
16. A.K. Kusnetzow C. Altenbach W.L. Hubbell Conformational states and dynamics of rhodopsin in micelles and bilayers Biochemistry 45 2006 5538 5550
17. P.S. Park D.T. Lodowski K. Palczewski Activation of G protein-coupled receptors: beyond two-state models and tertiary conformational changes Annu. Rev. Pharmacol. Toxicol. 2007
18. T. Okada M. Sugihara A.N. Bondar M. Elstner P. Entel V. Buss The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure J. Mol. Biol. 342 2004 571 583
19. R. Chen Z. Weng A novel shape complementarity scoring function for protein–protein docking Proteins 51 2003 397 408
20. D.G. Lambright J. Sondek A. Bohm N.P. Skiba H.E. Hamm P.B. Sigler The 2.0 Å crystal structure of a heterotrimeric G protein Nature 379 1996 311 319
21. O.G. Kisselev J. Kao J.W. Ponder Y.C. Fann N. Gautam G.R. Marshall Light-activated rhodopsin induces structural binding motif in G protein alpha subunit Proc. Natl. Acad. Sci. USA 95 1998 4270 4275
22. A. Loew Y.K. Ho T. Blundell B. Bax Phosducin induces a structural change in transducin beta gamma Structure 6 1998 1007 1019
23. O.G. Kisselev M.A. Downs Rhodopsin controls a conformational switch on the transducin gamma subunit Structure (Camb.) 11 2003 367 373
24. F. Fanelli P.G. De Benedetti Computational modeling approaches to structure–function analysis of G protein-coupled receptors Chem. Rev. 105 2005 3297 3351
25. D. Casciari M. Seeber F. Fanelli Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach BMC Bioinform. 7 2006 340
26. B.R. Brooks R.E. Bruccoleri B.D. Olafson D.J. States S. Swaminathan M. Karplus Charmm: a program for macromolecular energy, minimization and dynamics calculations J. Comput. Chem. 4 1983 187 217
27. W. Im M. Feig C.L. Brooks 3rd. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins Biophys. J. 85 2003 2900 2918
28. F. Fanelli P.G. De Benedetti Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling J. Comput. Aided Mol. Des. 2006
29. J.M. Janz D.L. Farrens Rhodopsin activation exposes a key hydrophobic binding site for the transducin alpha-subunit C terminus J. Biol. Chem. 279 2004 29767 29773
30. N. Lehmann U. Alexiev K. Fahmy Linkage between the intramembrane H-bond network around aspartic acid 83 and the cytosolic environment of helix 8 in photoactivated rhodopsin J. Mol. Biol. 366 2007 1129 1141
31. F. Fanelli C. Menziani A. Scheer S. Cotecchia P.G. De Benedetti Theoretical study of the electrostatically driven step of receptor-G protein recognition Proteins 37 1999 145 156
32. I.D. Alves G.F. Salgado Z. Salamon M.F. Brown G. Tollin V.J. Hruby Phosphatidylethanolamine enhances rhodopsin photoactivation and transducin binding in a solid supported lipid bilayer as determined using plasmon-waveguide resonance spectroscopy Biophys. J. 88 2005 198 210
33. D. Fotiadis Y. Liang S. Filipek D.A. Saperstein A. Engel K. Palczewski Atomic-force microscopy: rhodopsin dimers in native disc membranes Nature 421 2003 127 128
34. R. Vogel S. Martell M. Mahalingam M. Engelhard F. Siebert Interaction of a G protein-coupled receptor with a G protein-derived peptide induces structural changes in both peptide and receptor: a Fourier-transform infrared study using isotopically labeled peptides J. Mol. Biol. 366 2007 1580 1588