Hydrogen-bonding alterations of the protonated Schiff base and water molecule in the chloride pump of Natronobacterium pharaonis

Biochemistry

Volumn 44, Issue 37, 2005, Pages 12279-12286

  Shibata, Mikihiro ^a   Muneda, Norikazu ^a   Sasaki, Takanori ^b   Shimono, Kazumi ^b   Kamo, Naoki ^b   Demura, Makoto ^b   Kandori, Hideki ^a  

^a NAGOYA INSTITUTE OF TECHNOLOGY   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CHROMOPHORES; FOURIER TRANSFORM INFRARED SPECTROSCOPY; HYDROGEN BONDS; ISOMERIZATION; MOLECULAR VIBRATIONS;

HALORHODOPSIN; PHOTOISOMERIZATION; SCHIFF BASE; WATER MOLECULES;

CHLORINE COMPOUNDS;

CHLORIDE ION; HALIDE; HALORHODOPSIN; HYDROGEN; NITROGEN 15; PROTON; SCHIFF BASE; WATER;

ARTICLE; BINDING SITE; CHLORIDE PUMP; ESCHERICHIA COLI; FOURIER TRANSFORMATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; ISOTOPE LABELING; LOW TEMPERATURE PROCEDURES; NATRONOBACTERIUM PHARAONIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN PURIFICATION;

CHLORIDES; DEUTERIUM OXIDE; HALORHODOPSINS; HYDROGEN BONDING; NATRONOBACTERIUM; SCHIFF BASES; SPECTROPHOTOMETRY, INFRARED; WATER;

NATRONOMONAS PHARAONIS;

EID: 24944531254     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050726d     Document Type: Article

References (34)

1. Haupts, U., Tittor, J., and Oesterhelt, D. (1999) Closing in on bucleriorhodopsin: progress in understanding the molecules, Annu. Rev. Biophys. Biomol. Struct. 28, 367-399.
2. Lanyi, J. K. (2004) Bacteriorhodopsin. Annu. Rev. Physiol. 66, 665-688.
3. Váró, G. (2000) Analogies between halorhodopsin and bacteriorhodopsin. Biodim. Biophys. Acta. 1460, 220-229.
4. Essen, L.-O. (2002) Halorhodopsin: light-driven ion pumping made simple?. Curr. Opin. Struct. Biol. 12, 516-522.
5. Kolbe, M., Besir, H., Essen, L.-O., and Oesterhelt, D. (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution, Science 288, 1390-1396.
6. Luecke, H., Schobert, B., Richter, H.-T., Cartailler, J. P., and Lanyi, J. K. (1999) Structure of bacteriorhodopsin at 1.55 A resolution. J. Mol. Biol. 291, 899-911.
7. Aton, B., Doukas, A. G., Callender, R. H., Becher, B., and Ebrey, T. G. (1977) Resonance Raman studies of the purple membrane, Biochemistry 16, 2995-2999.
8. Baasov, T., Friedman, N., and Sheves, M. (1987) Factors affecting the C=N stretching in protonated retinal Schiff base: a model study for bacteriorhodopsin and visual pigments, Biochemistry 26, 3210-3217.
9. Smith, S. O., Marvin, M. J., Bogomolni, R. A., and Mathies, R. A. (1984) Structure of the retinal chromophore in the hR578 form of the halorhodopsin. J. Biol. Chem. 259, 12326-12329.
10. L intermedeiate of halorhodopsin from resonance spectroscopy, Biochemistry 26, 6775-6778.
11. Gerscher, S., Mylrajan, M., Hildebrandt, P., Baron, M.-H., Müller, R., and Engelhard, M. (1997) Chromophore-anion interactions in halorhodopsin form Natronobacterium pharaonis probed by time-resolved resonance Raman spectroscopy. Biochemistry 36, 11012-11020.
12. Walter, T. J., and Braiman, M. S. (1994) Anion-protein interactions during halorhodopsin pumping: halide binding at the protonated Schiff base. Biochemistry 33, 1724-1733.
13. Lussier, L. S., Sandorfy, C., Le-Thanh, H., and Vocelle, D. (1987) Effect of acids on the infrared spectra of the Schiff base of transretinal. J. Phys. Chem. 91, 2282-2287.
14. Kandori, H., Kinoshita, N., Shichida, Y., and Maeda, A. (1998) Protein structural changes in bacteriorhodopsin upon photoisomerization as revealed by polarized FTlR spectroscopy, J. Phys. Chem., B 102, 7899-7905.
15. Kandori, H., Belenky, M., and Herzfeld, J. (2002) Vibrational frequency and dipolar orientation of the protonated Schiff base in bacteriorhodopsin before and after photoisomerization, Biochemistry 41, 6026-6031.
16. Kandori, H., and Shichida, Y. (2000) Direct observation of the bridged water stretching vibrations inside a protein. J. Am. Chem. Soc. 122, 11745-11746.
17. Shibata, M., Tanimoto, T., and Kandori, H. (2003) Water molecules in the Schiff base region of bacteriorhodopsin, J. Am. Chem. Soc. 125, 13312-13313.
18. Tanimoto, T., Furutani, Y., and Kandori, H. (2003) Structural changes of water in the Schiff base region of bacteriorhodopsin: proposal of a hydration switch model, Biochemistry 42, 2300-2306.
19. Furutani, Y., Shichida, Y., and Kandori, H. (2003) Structural changes of water molecules during the photoactivation processes in bovine rhodopsin, Biochemistry 42, 9619-9625.
20. Furutani, Y., Bezerra, A. G., Jr., Waschuk, S., Sumii, M., Brown, L. S., and Kandori, H. (2004) FTIR spectroscopy of the K photointermediate of Neurospore rhodopsin: structural changes of the retinal, protein, and water molecules after photoisomerization, Biochemistry 43, 9636-9646.
21. Shibata, M., Muneda, N., Ihara, K., Sasaki, T., Demura, M., and Kandori, H. (2004) Internal water molecules of light-driven chloride pump proteins, Chem. Phys. Lett. 392, 330-333.
22. Sato, M., Kanamori, T., Kamo, N., Demura, M., and Nitta, K. (2002) Stopped-flow analysis on anion binding to blue-form halorhodopsin from Natronobacterium pharaonis: comparison with the anion-uptake process during the photocycle, Biochemistry 41, 2452-2458.
23. Kandori, H., Shimono, K., Sudo, Y., Iwamoto, M., Shichida, Y., and Kamo, N. (2001) Structural change of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: infrared spectral comparison with bacteriorhodopsin, Biochemistry 40, 9238-9246.
24. Shimono, K., Furutani, Y., Kamo, N., and Kandori, H. (2003) Vibrational modes of the protonated Schiff base in pharaonis phoborhodopsin, Biochemistry 42, 7801-7806.
25. Hackmann, C., Guijarro, J., Chizhov, I., Engelhard, M., Rödig, C., and Siebert, F. (2001) Static and time-resolved step-scan Fourier transform infrared investigations of the photoreaction of halorhodopsin from Natronobacterium pharaonis: consequences for models of the anion translocation mechanism, Biophys. J. 81, 394-406.
26. Chon, Y.-S., Kandori, H., Sasaki, J., Lanyi, J. K., Needleman, R., and Maeda, A. (1999) Existence of two L photointermediates of halorhodopsin from Halobacterium salinarum, differing in their protein and water FTIR bands. Biochemistry 38, 9449-9455.
27. Edman, K., Nollert, P., Royant, A., Belrhali, H., Pebay-Peyroula, E., Hajdu, J., Neutze, R., and Landau, E. M. (1999) High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle, Nature 401, 822-826.
28. Schobert, B., Cupp-Vickery, J., Hornak, V., Smith, S. O., and Lanyi, J. K. (2002) Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal, J. Mol. Biol. 321, 715-726.
29. Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., and Kouyama, T. (2002) Specific damage induced by X-ray radiation and structural changes in the primary photo-reaction of bacteriorhodopsin, J. Mol. Biol. 324, 469-481.
30. Edman, K., Royant, A., Nollert, P., Maxwell, C. A., Pebay-Peyroula, E.. Navarro, J., Neutze, R., and Landau, E. M. (2002) Early structural rearrangements in the photocycle of an integral membrane sensory receptor. Structure 10, 473-482.
31. Hayashi, S., Tajkhorshid, E., and Schulten, K. (2002) Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle, Biophys. J. 83, 1281-1297.
32. Sato, M., Kubo, M., Aizawa, T., Kamo, N., Kikukawa, T., Nitta, K.. and Demura, M. (2005) Role of putative anion-binding sites in cytoplasmic and extracellular channels of Natronomonas pharaonis halorhodopsin, Biochemistry 44, 4775-4784.
33. Ohtomo, N., and Arakawa, K. (1980) Neutron diffraction of aqueous ionic solutions. II. aqueous solutions of sodium chloride and potassium chloride, Bull. Chem. Soc. Jpn. 53, 1789-1794.
34. Ohtomo, N., Arakawa, K., Takeuchi, M., Yamaguchi, T., and Ohtaki, H. (1981) Neutron diffraction study of aqueous hydrochloric and hydrobromic acid solutions, Bull. Chem. Soc. Jpn. 54, 1314-1319.