Evidence of α-Helix Slidings during Bacteriorhodopsin Photocycle-Energetics Coupling

Tohoku Journal of Experimental Medicine

Volumn 182, Issue 1, 1997, Pages 15-33

  Goto, Kunihiko ^a   Iwamoto, Masatoshi ^b  

^a TOHOKU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b TOHOKU GAKUIN UNIVERSITY   (Japan)

Author keywords

Bacteriorhodopsin; Hydrophobic interaction; Photocycle; Retinal; Thermodynamics

Indexed keywords

BACTERIORHODOPSIN; RETINAL;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENERGY TRANSFER; METABOLISM; MOLECULAR GENETICS; PHOTOCHEMISTRY; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; RADIATION EXPOSURE; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTERIORHODOPSINS; CRYSTALLOGRAPHY, X-RAY; ENERGY TRANSFER; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOTOCHEMISTRY; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; RETINALDEHYDE; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0031137988     PISSN: 00408727     EISSN: None     Source Type: Journal    
DOI: 10.1620/tjem.182.15     Document Type: Article

References (39)

1. Ballesteros, J.A. & Weinstein, H. (1992) Analysis and refinement of criteria for predicting the structure and relative orientations of transmembranal helical domains. Biophys. J., 62, 107-109.
2. Brown, L.S., Yamazaki, Y., Maeda, M., Sun, L., Needleman, R. & Lanyi, J.K. (1994) The proton transfers in the cytoplasmic domain of bacteriorhodopsin are facilitated by a cluster of interacting residues. J. Mol. Biol., 239, 401-414.
3. Brünger, A.T. (1992) X-PLOR. Version 3.1, A System for X-Ray Crystallography and NMR. Yale Univ. Press, New Haven, London.
4. Chothia, C. (1974) Hydrophobie bonding and accessible surface area in proteins. Nature, 248, 338-339.
5. DeGrip, W.J., Bonting, S.L. & Daemen, F.J.M. (1975) Biochemical aspects of the visual process XXVIII. Classification of sulfhydryl groups in rhodopsin and other photoreceptor membrane proteins. Biochim. Biophys. Acta, 396, 104-115.
6. Deng, H., Huang, L., Callender, R. & Ebrey, T. (1994) Evidence for a bound water molecule next to the retinal Schiff base in bacteriorhodopsin and rhodopsin: A resonance raman study of the Schiff base hydrogen/deuterium exchange. Biophys. J., 66, 1129-1136.
7. Fodor, S.P.A., Ames, J.B., Gebhard, R., van den Berg, E.M.M., Stoeckenius, W., Lugtenburg, J. & Mathies, R.A. (1988) Chromophore structure in bacteriorhodopsin's N intermediate: Implications for the proton-pumping mechanism. Biochemistry, 27, 7097-7101.
8. Fukuda, K. & Kouyama, T. (1992) Formation and decay kinetics of bacteriorhodopsin's N intermediate: Softening the protein conformation with alcohols affects intraprotein proton transfer and retinal isomerization. Photochem. Photobiol., 56, 1057-1062.
9. Furosis-Corbin, S. & Pullman, A. (1989) A possible model of the inner wall of the acetylcholine receptor channel. Biochim. Biophys. Acta, 984, 339-350.
10. Galzi, J.-L., Revah, F., Bessis, A. & Changeux, J.-P. (1991) Functional architecture of the nicotinic acetylcholine receptor: From electric organ to brain. Annu. Rev. Pharmacol., 31, 37-72.
11. Goto, K. (1994) The on-off mechanisms of the nicotinic acetylcholine receptor ion channel are performed by thermodynamic forces. J. Theoret. Biol., 170, 267-272.
12. Goto, K. (1995) Hydrophobie accessible surface areas are proportional to binding energies of serine protease-protein inhibitor complexes. Biochem. Biophys. Res. Commun., 206, 497-501.
13. Goto, K. (1996) Rotation model: The oil-in-water and water-in-oil thermodynamic mechanisms explain various phenomena containing ion channel and molecular recognition and predict various yet-unobserved phenomena. Mebio, 13(12), 88-96. (in Japanese)
14. Goto, K. (1997a) Rotation model - Molecular hypothesis not only explaining various phenomena without contradiction, but also predicting various yetunobserved phenomena - . Membrane, 22, 96-104.
15. Goto, K. (1997b) Rotation model: A molecular mechanism driven by hydrophobic and hydrophilic interactions, and underlying molecular recognition and ion channels. Progr. Anesth. Mech. in press.
16. Grigorieff, N., Ceska, T.A., Doning, K.H., Baldwin, J.M. & Henderson, R. (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol., 259, 393-421.
17. Henderson, R., Baldwin, J.M. & Ceska, T.A. (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol., 213, 899-929.
18. Honig, B.H. (1986) Electrostatic interactions in membranes and proteins. Ann. Rev. Biophys. Biophys. Chem., 15, 163-193.
19. Kataoka, M., Kamikubo, H., Tokunaga, F., Brown, L.S., Yamazaki, Y., Maeda, A., Sheves, M., Needleman, R. & Lanyi, J.K. (1994) Energy coupling in an ion pump. The reprotonation switch of bacteriorhodpsin. J. Mol. Biol., 243, 621-638.
20. Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation. Adv. Prot. Chem., 14, 1-63.
21. Koch, M.H.J., Dencher, N.A, Oesterhelt, D., Plöhn, H.-J., Rapp, G. & Büldt, G. (1991) Time-resolved x-ray diffraction study of structural changes associated with the photocycle of bacteriorhodopsin. EMBO J., 10, 521-526.
22. Kouyama, T., Nasuda-Kouyama, A., Ikegami, A., Mathew, M.K. & Stoeckenius, W. (1988) Bacteriorhodopsin photoreaction: Identification of a long-lived intermediate N(P, R350) at high pH and M-like photoproduct. Biochemistry, 27, 5855-6863.
23. Lanyi, J.K. (1995) Bacteriorhodopsin as a model for proton pumps. Nature, 375, 461-463.
24. Lin, S.W. & Mathies, R.A. (1989) Orientation of the protonated retinal Schiff base group in bacteriorhodopsin from absorption linear dichroism. Biophys. J., 56, 653-660.
25. Mukhopadhyay, A.K., Bose, S. & Hendlerr, R.W. (1994) Membrane-mediated control of the bacteriorhodopsin photocycle. Biochemistry, 33, 10889-10895.
26. Nakagawa, T., Hamanaka, T., Nishimura, S., Uruga, T. & Kito, Y. (1994) The specific binding site of the volatile anesthetic diiodomethane to purple membrane by X-ray diffraction. J. Mol. Biol., 238, 297-301.
27. Nakasako, M., Kataoka, M., Amemiya, Y. & Tokunaga, F. (1991) Crystallographic characterization by x-ray diffraction of the M-intermediate from the photo-cycle of bacteriorhodopsin at room temperature. FEBS Lett., 292, 73-75.
28. Némethy, G. & Scheraga, A. (1962) Structure of water and hydrophobic bonding in proteins. 1. A model for the thermodynamic properties of liquid water. J. Chem. Phys., 36, 3382-3400.
29. Nozaki, Y. & Tanford, J. (1971) The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J. Biol. Chem., 246, 2211-2217.
30. Piela, L., Némethy, G. & Scheraga, H.A. (1987) Proline-induced constraints in α-helices. Biopolymers, 26, 1587-1600.
31. Rath, P., Bovee-Geurts, P.H.M., DeGrip, W.J. & Rothschild, K.J. (1994) Photoactivation of rhodopsin involves alterations in cysteine side chains: Detection of an S-H band in the meta I→meta FTIR difference spectrum. Biophys. J., 66, 2085-2091.
32. Rothschild, K.J., He, Y.-W., Sonar, S., Marti, T. & Khorana, H.G. (1992) Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence that Thr-46 and Thr-89 form part of a transient network of hydrogen bonds. J. Biol. Chem., 267, 1615-1622.
33. Schulenberg, P.L., Rohr, M., Gartner, W. & Braslavsky, S.E. (1994) Photoinduced volume changes associated with the early transformations of bacteriorhodopsin: A laser-induced optoacoustic spectroscopy study. Biophys. J., 66, 838-843.
34. Schulz, G.E. & Schirmer, R.H. (eds.) (1979) Principles of Protein Structure, Springer-Verlag, New York.
35. Smith, S.O., Myers, A.B., Pardoen, J.A., Winkel, C., Mulder, P.P.J., Lugtenburg, J. & Mathies, R. (1984) Determination of retinal Schiff base configuration in bacteriorhodopsin. Proc. Natl. Acad. Sci. USA, 81, 2055-2059.
36. Subramaniam, S., Gerstein, M., Oesterhelt, D. & Henderson, R. (1993) Electron diffracton analysis of structural changes in the photocycle of bacteriorhodopsin. EMBO J., 12, 1-8.
37. Unwin, P.N.T. & Zampighi, G. (1980) Structure of the junction between communicating cells. Nature, 283, 545-549.
38. Váró, G. & Lanyi, J.K. (1991) Thermodynamics and energy coupling in the bacteriorhodopsin photocycle. Biochemistry, 30, 5016-5022.
39. Warshel, A. (1979) Bicycle-pedal model for the first step in the vision process. Nature, 260, 679-683.