Exploring the active site structure of a photoreceptor protein by Raman optical activity

Journal of Physical Chemistry B

Volumn 117, Issue 5, 2013, Pages 1321-1325

  Unno, Masashi ^a,b   Kikukawa, Takashi ^c   Kumauchi, Masato ^d   Kamo, Naoki ^e  

^a SAGA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

^d OKLAHOMA STATE UNIVERSITY   (United States)

^e MATSUYAMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOPHORES; ISOMERS; OPTICAL MATERIALS; PROTEINS;

ACTIVE SITE STRUCTURE; FUTURE APPLICATIONS; NEAR INFRARED; NEAR-INFRARED EXCITATION; PHOTORECEPTOR PROTEINS; PROTON PUMP; RAMAN OPTICAL ACTIVITY; STRUCTURAL SENSITIVITY;

INFRARED DEVICES;

EID: 84873419054     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4001187     Document Type: Article

References (45)

1. Shelnutt, J. A.; Song, X.-Z.; Ma, J.-G.; Jia, S.-L.; Jentzenaand, W.; Medforth, C. J. Nonplanar Porphyrins and their Significance in Proteins Chem. Soc. Rev. 1998, 27, 31-41
2. Lim, L.; Molla, G.; Guinn, N.; Ghisla, S.; Pollegioni, L.; Vrielink, A. Structural and Kinetic Analyses of the H121A Mutant of Cholesterol Oxidase Biochem. J. 2006, 400, 13-22
3. Megley, C. M.; Dickson, L. A.; Maddalo, S. L.; Chandler, G. J.; Zimmer, M. Photophysics and Dihedral Freedom of the Chromophore in Yellow, Blue, and Green Fluorescent Protein J. Phys. Chem. B 2009, 113, 302-308
4. Liptak, M. D.; Wen, X.; Bren, K. L. NMR and DFT Investigation of Heme Ruffling: Functional Implications for Cytochrome c J. Am. Chem. Soc. 2010, 132, 9753-9763
5. Olea, C., Jr.; Kuriyan, J.; Marletta, M. A. Modulating Heme Redox Potential through Protein-Induced Porphyrin Distortion J. Am. Chem. Soc. 2010, 132, 12794-12795
6. Rocha-Rinza, T.; Sneskov, K.; Christiansen, O.; Ryde, U.; Kongsted, J. Unraveling the Similarity of the Photoabsorption of Deprotonated p -Coumaric Acid in the Gas Phase and within the Photoactive Yellow Protein Phys. Chem. Chem. Phys. 2011, 13, 1585-1589
7. Kukura, P.; McCamant, D. W.; Yoon, S.; Wadschneider, D. B.; Mathies, R. A. Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman Science 2005, 310, 1006-1009
8. Ihee, H.; Rajagopal, S.; Srajer, V.; Pahl, R.; Anderson, S.; Schmidt, M.; Schotte, F.; Anfinrud, P. A.; Wulff, M.; Moffat, K. Visualizing Reaction Pathways in Photoactive Yellow Protein from Nanoseconds to Seconds Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7145-7150
9. Sudo, Y.; Furutani, Y.; Wada, A.; Ito, M.; Kamo, N.; Kandori, H. Steric Constraint in the Primary Photoproduct of an Archaeal Rhodopsin from Regiospecific Perturbation of C-D Stretching Vibration of the Retinyl Chromophore J. Am. Chem. Soc. 2005, 127, 16036-16037
10. Nafie, L. A. Infrared and Raman Vibrational Optical Activity: Theoretical and Experimental Aspects Annu. Rev. Phys. Chem. 1997, 48, 357-386
11. Hug, W. Raman Optical Activity Spectroscopy. In Handbook of Vibrational Spectroscopy; Chalmers, J. M.; Griffiths, P. R., Eds.; Chichester, John Wiley & Sons, Inc.: Chichester, UK, 2002; Vol. 1, pp 745-758.
12. Blanch, E. W.; Hecht, K.; Barron, L. D. Vibrational Raman Optical Activity of Proteins, Nucleic Acids, and Viruses Methods 2003, 29, 196-209
13. Nafie, L. A.; Brinson, B. E.; Cao, X.; Rice, D. A.; Rahim, O. M.; Dukor, R. K.; Halas, N. J. Near-Infrared Excited Raman Optical Activity Appl. Spectrosc. 2007, 61, 1103-1106
14. Johannessen, C.; White, P. C.; Abdali, S. Resonance Raman Optical Activity and Surface Enhanced Resonance Raman Optical Activity Analysis of Cytochrome c J. Phys. Chem. A 2007, 111, 7771-7776
15. Abdali, S.; Johannessen, C.; Nygaard, J.; Nørbygaard, T. Resonance Surface Enhanced Raman Optical Activity of Myoglobin as a Result of Optimized Resonance Surface Enhanced Raman Scattering Conditions J. Phys.: Condens. Matter 2007, 19, 285205
16. Johnson, C. K.; Rubinovitz, R. Fourier Transform Raman Spectroscopy of Photoactive Proteins with Near-Infrared Excitation Appl. Spectrosc. 1990, 44, 1103-1106
17. Schulte, A.; Bradley, L., II; Williams, C. Equilibrium Composition of Retinal Isomers in Dark-Adapted Bacteriorhodopsin and Effect of High Pressure Probed by Near-Infrared Raman Spectroscopy Appl. Spectrosc. 1995, 49, 80-83
18. Unno, M.; Tsukiji, Y.; Kubota, K.; Masuda, S. N-Terminal Truncation Does Not Affect the Location of a Conserved Tryptophan in the BLUF Domain of AppA from Rhodobacter Sphaeroides J. Phys. Chem. B 2012, 116, 8974-8980
19. Lanyi, J. K. Bacteriorhodopsin Annu. Rev. Physiol. 2004, 66, 665-688
20. Harbison, G. S.; Smith, S. O.; Padoen, J. A.; Winkel, C.; Lugtenburg, J.; Herzfeld, J.; Mathies, R.; Griffin, R. G. Dark-Adapted Bacteriorhodopsin Contains 13- cis,15- syn and all- trans,15- anti Retinal Schiff Bases Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 1706-1709
21. Borshchevskiy, V. I.; Round, E. S.; Popov, A. N.; Buldt, G.; Gordeliy, V. I. X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure J. Mol. Biol. 2011, 409, 813-825
22. Lanyi, J. K.; Schobert, B. Structural Changes in the L Photointermediate of Bacteriorhodopsin J. Mol. Biol. 2007, 365, 1379-1392
23. Faham, S.; Yang, D.; Bare, E.; Yohannan, S.; Whitelegge, J. P.; Bowie, J. U. Side-chain Contributions to Membrane Protein Structure and Stability J. Mol. Biol. 2004, 335, 297-305
24. Schobert, B.; Cupp-Vickery, J.; Hornak, V.; Smith, S.; Lanyi, J. K. Crystallographic Structure of the K Intermediate of Bacteriorhodopsin: Conservation of Free Energy after Photoisomerization of the Retinal J. Mol. Biol. 2002, 321, 715-726
25. Facciotti, M. T.; Rouhani, S.; Burkard, F. T.; Betancourt, F. M.; Downing, K. H.; Rose, R. B.; McDermott, G.; Glaeser, R. M. Structure of an Early Intermediate in the M-State Phase of the Bacteriorhodopsin Photocycle Biophys. J. 2001, 81, 3442-3455
26. Belrhali, H.; Nollert, P.; Royant, A.; Menzel, C.; Rosenbusch, J. P.; Landau, E. M.; Pebay-Peyroula, E. Protein, Lipid and Water Organization in Bacteriorhodopsin Crystals: A Molecular View of the Purple Membrane at 1.9 Å Resolution Structure Fold Des 1999, 7, 909-917
27. Luecke, H.; Schobert, B.; Richter, H. T.; Cartailler, J. P.; Lanyi, J. K. Structure of Bacteriorhodopsin at 1.55 Å Resolution J. Mol. Biol. 1999, 291, 899-911
28. Matsui, Y.; Sakai, K.; Murakami, M.; Shiro, Y.; Adachi, S.; Okumura, H.; Kouyama, T. Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin J. Mol. Biol. 2002, 324, 469-481
29. Nishikawa, T.; Murakami, M.; Kouyama, T. Crystal Structure of the 13- cis Isomer of Bacteriorhodopsin in the Dark-adapted State J. Mol. Biol. 2005, 352, 319-328
30. Patzelt, H.; Simon, B.; terLaak, A.; Kessler, B.; Kühne, R.; Schmieder, P.; Oesterhelt, D.; Oschkinat, H. The Structures of the Active Center in Dark-Adapted Bacteriorhodopsin by Solution-State NMR Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9765-9770
31. Sato, M.; Kubo, M.; Aizawa, T.; Kamo, N.; Kikukawa, T.; Nitta, K.; Demura, M. Role of Putative Anion-Binding Sites in Cytoplasmic and Extracellular Channels of Natronomonas pharaonis Halorhodopsin Biochemistry 2005, 44, 4775-4784
32. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A., Gaussian 09, Revision A.2; Gaussian, Inc.: Wallingford, CT.
33. Merrick, J. P.; Moran, D.; Radom, L. An Evaluation of Harmonic Vibrational Frequency Scale Factors J. Phys. Chem. A 2007, 111, 11683-11700
34. Smith, S. O.; Braiman, M. S.; Myers, A. B.; Pardoen, J. A.; Courtin, J. M. L.; Winkel, C.; Lugtenburg, J.; Mathies, R. A. Vibrational Analysis of the all- trans -Retinal Chromophore in Light-Adapted Bacteriorhodopsin J. Am. Chem. Soc. 1987, 109, 3108-3125
35. Smith, S. O.; Pardoen, J. A.; Lugtenburg, J.; Mathies, R. A. Vibrational Analysis of the 13- cis -Retinal Chromophore in Dark-Adapted Bacteriorhodopsin J. Phys. Chem. 1987, 91, 804-819
36. Barron, L. D.; Bogaard, M. P.; Buckingham, A. D. Raman Scattering of Circularly Polarized Light by Optically Active Molecules J. Am. Chem. Soc. 1973, 95, 603-605
37. Essen, L.-O. Halorhodopsin: Light-Driven Ion Pumping Made Simple? Curr. Opin. Struct. Biol. 2002, 12, 516-522
38. Kolbe, M.; Besir, H.; Essen, L.-O.; Oesterhelt, D. Halorhodopsin at 1.8 Å Resolution Structure of the Light-Driven Chloride Pump Science 2000, 288, 1390-1396
39. Kouyama, T.; Kanada, S.; Takeguchi, Y.; Narusawa, A.; Murakami, M.; Ihara, K. Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis J. Mol. Biol. 2010, 396, 564-579
40. Zimányi, L.; Lanyi, J. K. Fourier Transform Raman Study of Retinal Isomeric Composition and Equilibration in Halorhodopsin J. Phys. Chem. B 1997, 101, 1930-1933
41. 578 Form of Halorhodopsin J. Biol. Chem. 1984, 259, 12326-12329
42. Ruud, K.; Thorvaldsen, A. J. Theoretical Approaches to the Calculation of Raman Optical Activity Spectra Chirality 2009, 21, E54-E67
43. He, Y.; Wang, B.; Dukor, R. K.; Nafie, L. A. Determination of Absolute Configuration of Chiral Molecules Using Vibrational Optical Activity: A Review Appl. Spectrosc. 2011, 65, 699-723
44. Cheeseman, J. R.; Shaik, M. S.; Popelier, P. L. A.; Blanch, E. W. Calculation of Raman Optical Activity Spectra of Methyl-β-D-Glucose Incorporating a Full Molecular Dynamics Simulation of Hydration Effects J. Am. Chem. Soc. 2011, 133, 4991-4997
45. Hopmann, K. H.; Ruud, K.; Pecul, M.; Kudrzej, A.; Dračí nský, M.; Bouř, P. Explicit versus Implicit Solvent Modeling of Raman Optical Activity Spectra J. Phys. Chem. B 2012, 116, 2554-2563