Structural characterization of a zinc high-affinity binding site in rhodopsin

Photochemistry and Photobiology

Volumn 85, Issue 2, 2009, Pages 479-484

  Toledo, Darwin ^a   Cordomí, Arnau ^a   Proietti, Maria Grazia ^b   Benfatto, Maurizio ^c   Del Valle, Luis J ^a   Pérez, Juan J ^a   Garriga, Pere ^a   Sepulcre, Francesc ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b CSIC   (Spain)

^c INFN LABORATORI NAZIONALI DI FRASCATI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

RHODOPSIN; ZINC;

ANIMAL; BINDING SITE; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFERENCE PAPER; ENZYME SPECIFICITY; METABOLISM; PROTEIN TERTIARY STRUCTURE; SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

ANIMALS; BINDING SITES; CATTLE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; RHODOPSIN; SPECTRUM ANALYSIS; SUBSTRATE SPECIFICITY; ZINC;

INSECTIVORA;

EID: 60849102469     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1751-1097.2008.00529.x     Document Type: Conference Paper

References (41)

1. Palczewski, K. (2006) G protein-coupled receptor rhodopsin. Annu. Rev. Biochem. 75, 743 767.
2. Ridge, K. D. K. Palczewski (2007) Visual rhodopsin sees the light: Structure and mechanism of G protein signaling. J. Biol. Chem. 282 (13 9297 9301.
3. Shichida, Y. T. Morizumi (2007) Mechanism of G-protein activation by rhodopsin. Photochem. Photobiol. 83 (1 70 75.
4. Vallee, B. L. D. S. Auld (1990) Zinc coordination, function, and structure of zinc enzymes and other proteins. Biochemistry 29 (24 5647 5659.
5. Auld, D. S. (2001) Zinc coordination sphere in biochemical zinc sites. Biometals 14 (3-4 271 313.
6. Alberts, I. L., K. Nadassy S. J. Wodak (1998) Analysis of zinc binding sites in protein crystal structures. Protein Sci. 7 (8 1700 1716.
7. Shuster, T. A., A. K. Nagy, D. C. Conly D. B. Farber (1992) Direct zinc-binding to purified rhodopsin and disk membranes. Biochem. J. 282, 123 128.
8. del Valle, L. J., E. Ramon, X. Canavate, P. Dias P. Garriga (2003) Zinc-induced decrease of the thermal stability and regeneration of rhodopsin. J. Biol. Chem. 278 (7 4719 4724.
9. Stojanovic, A., J. Stitham J. Hwa (2004) Critical role of transmembrane segment zinc binding in the structure and function of rhodopsin. J. Biol. Chem. 279 (34 35932 35941.
10. + in native bovine rhodopsin. J. Biol. Chem. 282 (15 11377 11385.
11. Palczewski, K., T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima, B. A. Fox, I. L. Trong, D. C. Teller, T. Okada, R. E. Stenkamp, M. Yamamoto M. Miyano (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739 745.
12. Okada, T., Y. Fujiyoshi, M. Silow, J. Navarro, E. M. Landau Y. Shichida (2002) Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc. Natl Acad. Sci. USA 99 (9 5982 5987.
13. Okada, T., M. Sugihara, A. N. Bondar, M. Elstner, P. Entel V. Buss (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 angstrom crystal structure. J. Mol. Biol. 342 (2 571 583.
14. Patel, A. B., E. Crocker, P. J. Reeves, E. V. Getmanova, M. Eilers, H. G. Khorana S. O. Smith (2005) Changes in interhelical hydrogen bonding upon rhodopsin activation. J. Mol. Biol. 347 (4 803 812.
15. Strange, R. W. S. S. Hasnain (2005) Combined use of XAFS and crystallography for studying protein-ligand interactions in metalloproteins. In Protein-Ligand Interactions: Methods and Applications (Edited by G. U. Nienhaus Methods Mol. Biol. 305, 167 196.
16. Sepulcre, F., A. Cordomí, M. G. Proietti, J. J. Perez, J. Garcia, E. Querol E. Padros (2007) X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. Proteins 67 (2 360 374.
17. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov P. E. Bourne (2000) The Protein Data Bank. Nucleic Acids Res. 28 (1 235 242.
18. Li, J., P. C. Edwards, M. Burghammer, C. Villa G. F. X. Schertler (2004) Structure of bovine rhodopsin in a trigonal crystal form. J. Mol. Biol. 343 (5 1409 1438.
19. Molecular-Discovery (2003) GRID Version 21.0. Molecular Discovery Ltd., Oxford.
20. Goodford, P. J. (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28 (7 849 857.
21. Cordomí, A., O. Edholm J. J. Perez (2007) Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. J. Comput. Chem. 28 (6 1017 1030.
22. Cordomí, A. J. J. Perez (2007) Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers. J. Phys. Chem. B 111 (25 7052 7063.
23. Jorgensen, W. L., D. S. Maxwell J. Tirado-Rives (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118 (45 11225 11236.
24. Lindahl, E., B. Hess D. van der Spoel (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (8 306 317.
25. Berger, O., O. Edholm F. Jähnig (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72 (5 2002 2013.
26. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey M. L. Klein (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (2 926 935.
27. Babu, C. S. C. Lim (2006) Empirical force fields for biologically active divalent metal cations in water. J. Phys. Chem. A 110, 691 699.
28. Åqvist, J. A. Warshel (1992) Computer simulation of the initial proton-transfer step in human carbonic anhydrase I. J. Mol. Biol. 224 (1 7 14.
29. Pang, Y. P. (1999) Novel zinc protein molecular dynamics simulations: Steps toward antiangiogenesis for cancer treatment. J. Mol. Model. 5 (10 196 202.
30. Pang, Y. P. (2001) Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method. Proteins 45 (3 183 189.
31. Pang, Y. P., K. Xu, J. El Yazal F. G. Prendergast (2000) Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci. 9 (10 1857 1865.
32. Stephens, P. J., F. J. Devlin, C. F. Chabalowski M. J. Frisch (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98 (45 11623 11627.
33. Frisch, M. J., G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle J. A. Pople (1998) Gaussian 98, Revision A.11. Gaussian, Inc., Pittsburgh, PA.
34. Ankudinov, A., B. Ravle, J. J. Rehr S. D. Conradson (1998) Real-space multiple-scattering calculation and interpretation of X-ray-absorption near edge structure. Phys. Rev. B 58, 7565 7576.
35. Newville, M. (2001) IFEFFIT: Interactive XAFS analysis and FEFF fitting. J. Synchrotron Radiat. 8, 3.
36. Ravel B, N. M. (2005) ATHENA, ARTHEMIS, HEPHAESTUS: Data analysis for X-ray absorption spectroscopy using IFEFFIT. J. Synchrotron Radiat. 12, 5.
37. Galoisy, L., L. Cormier, G. Calas V. Briois (2001) Environment of Ni, Co and Zn in low alkali borate glasses: Information from EXAFS and XANES spectra. J. Non-Crystall. Sol. 293-295, 105 111.
38. Jacquamet, L., D. Aberdam, A. Adrait, J. L. Hazemann, J. M. Latour I. Michaud-Soret (1998) X-ray absorption spectroscopy of a new zinc site in the fur protein from Escherichia coli. Biochemistry 37 (8 2564 2571.
39. Meyer-Klaucke, W., R. Paul Soto, M. Hernandez Valladares, H. Adolph, H. Nolting, J. Frere M. Zeppezauer (1999) A comparison of Bacillus cereus and Aeromonas hydrophilia Zn-β-lactamases. J. Synchrotron Radiat. 6 (3 400 402.
40. Cordomi, A., O. Edholm J. J. Perez (2008) Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. A molecular dynamics simulation study. J. Phys. Chem. B 112 (5 1397 1408.
41. Diakun, G. P., L. Fairall A. Klug (1986) EXAFS study of the zinc-binding sites in the protein transcription factor IIIA. Nature 324, 698 699.