• 1
    Blaurock, A. E. and W. Stoeckeneus (1971) Structure of the purple membrane. Nat. New. Biol. 233, 152155.
  • 2
    Baldwin, J. M., R. Henderson, E. Beckman and F. Zemlin (1988) Images of purple membrane at 2.8 Å resolution obtained by cryo-electron microscopy. J. Mol. Biol. 202, 586591.
  • 3
    Grigorieff, N., T. A. Ceska, K. H. Downing, J. M. Baldwin and R. Henderson (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259, 393421.
  • 4
    Pebay-Peyroula, E., G. Rummel, J. P. Rosenbusch and E. M. Landau (1997) X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277, 16761681.
  • 5
    Luecke, H., H. T. Richter and J. K. Lanyi (1998) Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution. Science 280, 19341937.
  • 6
    Essen, L., R. Siegert, W. D. Lehman and D. Oesterhelt (1998) Lipid patches in membrane protein oligomers: Crystal structure of the bacteriorhodopsin–lipid complex. Proc. Natl Acad. Sci. USA 95, 1167311678.
  • 7
    Sato, H., K. Takeda, K. Tani, T. Hino, T. Okada, M. Nakasako, N. Kamiya and T. Kouyama (1999) Specific lipid–protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin. Acta. Crystallogr. D 55, 12511256.
  • 8
    Havelka, W. A., R. Henderson, J. A. Heymann and D. Oesterhelt (1993) Projection structure of halorhodopsin from Halobacterium halobium at 6 Å resolution obtained by electron cryo-microscopy. J. Mol. Biol. 234, 837846.
  • 9
    Kolbe, M., H. Besier, L.-O. Essen and D. Oesterhelt (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution. Science 288, 13901396.
  • 10
    Kunji, E. R. S., E. N. Spudich, R. Grisshammer, R. Henderson and J. L. Spudich (2000) Electron crystallographic analysis of two-dimensional crystals of sensory rhodopsin II: A 6.9 Å projection structure. J. Mol. Biol. 308, 279293.
  • 11
    Luecke, H., B. Shobert, J. K. Lanyi, E. N. Spudich and J. L. Spudich (2001) Crystal structure of sensory rhodopsin II at 2.4 angstroms: Insights into color tuning and transducer interaction. Science 293, 14991503.
  • 12
    Royant, A., P. Nollert, K. Edman, R. Neutze, E. M. Landau, E. Pebay-Peyroula and J. Navaro (2001) X-ray structure of sensory rhodopsin II at 2.1-Å resolution. Proc. Natl Acad. Sci. USA 98, 1013110136.
  • 13
    Deisenhofer, J., O. Epp, K. Miki, R. Huber and H. Michel (1985) Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution. Nature 318, 618624.
  • 14
    Kuhlbrandt, W., D. N. Wang and Y. Fujiyoshi (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature 367, 614621.
  • 15
    McDermott, G., S. M. Prince, A. A. Freer, A. M. Hawthornthwaite-Lawless, M. Z. Papiz, R. J. Cogdell and N. W. Isaacs (1995) Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature 374, 517521.
  • 16
    Iwata, S., C. Ostermeier, B. Ludwig and H. Michel (1995) Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376, 660669.
  • 17
    Tsukihara, N., H. Aoyama, E. Yamashita, T. Tomizaki, H. Yamaguchi, K. Shinzawa-Itoh, R. Nakashima, R. Yano and S. Yoshikawa (1995) Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 Å. Science 269, 10691074.
  • 18
    Doyle, D. A., J. M. Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbiss, S. L. Cohen, B. T. Chait and R. MacKinnon (1998) The structure of the potassium channel: Molecular basis of K+ conduction and selectivity. Science 280, 6977.
  • 19
    Chang, G., R. H. Spencer, A.T. Lee, M.T. Barclay and D. C. Rees (1998) Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282, 22202226.
  • 20
    Palczewski, K., T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima, B. A. Fox, I. Le Trong, D. C. Teller, T. Okada, R. E. Stenkamp, M. Yamamoto and M. Miyano (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739745.
  • 21
    Toyoshima, C., M. Nakasako, H. Nomura and H. Ogawa (2000) Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 405, 647655.
  • 22
    Krebs, M. P. and T. A. Isenbarger (2000) Structural determinants of purple membrane assembly. Biochim. Biophys. Acta 1460, 1526.
  • 23
    Dencher, N. A. and M. P. Heyn (1983) Bacteriorhodopsin monomers pump protons. FEBS Lett. 108, 307310.
  • 24
    Dencher, N. A., K.-D. Kohl and M. P. Heyn (1983) Photochemical cycle and light-dark adaptation of monomeric and aggregated bacteriorhodopsin in various lipid environments. Biochemistry 22, 13231334.
  • 25
    Milder, S. J., T. E. Thorgeirsson, L. J. Mierke, R. M. Stroud and D. S. Kliger (1991) Effects of detergent environments on the photocycle of purified monomeric bacteriorhodopsin. Biochemistry 30, 17511761.
  • 26
    Dencher, N. A. and M. P. Heyn (1982) Preparation and properties of monomeric bacteriorhodopsin. Methods Enzymol. 88, 510.
  • 27
    Varo, G. and J. K. Lanyi (1991) Effects of the crystalline structure of purple membrane on the kinetics and energetics of the bacteriorhodopsin photocycle. Biochemistry 30, 71657171.
  • 28
    Saitô, H., S. Tuzi, S. Yamaguchi, M. Tanio and A. Naito (2000) Conformation and backbone dynamics of bacteriorhodopsin revealed by 13C-NMR. Biochim. Biophys. Acta 1460, 3948.
  • 29
    Saitô, H., S. Tuzi, M. Tanio and A. Naito (2002) Dynamic aspects of membrane proteins and membrane-associated peptides as revealed by 13C NMR: Lessons from bacteriorhodopsin as an intact protein. Annu. Rep. NMR Spectrosc. 47, 39108.
  • 30
    Saitô, H. (2004) Dynamic pictures of membrane proteins in two-dimensional crystal, lipid bilayer and detergent as revealed by site-directed solid-state 13C NMR. Chem. Phys. Lipids. 132, 101112.
  • 31
    Saitô, H. (2006) Site-directed solid-state NMR on membrane proteins. Annu. Rep. NMR Spectrosc. 57, 99175.
  • 32
    Saitô, H., I. Ando and A. Naito (2006) Solid State NMR Spectroscopy for Biopolymers: Principles and Applications, Chapter 13. Springer, Dordrecht, The Netherlands.
  • 33
    Heymann, J. B., D. J. Muller, E. M. Randau, J. P. Rosenbusch, E. Pebay-Peyroula, G. Büldt and A. Engel (1999) Charting the surfaces of the purple membrane. J. Struct. Biol. 128, 243249.
  • 34
    Müller, D. J., H.-J. Sass, S. A. Müller, G. Büldt and A. Engel (1999) Surface structures of native bacteriorhodopsin depend on the molecular packing arrangement in the membrane. J. Mol. Biol. 285, 19031909.
  • 35
    Tuzi, S., S. Yamaguchi, M. Tanio, H. Konishi, S. Inoue, A. Naito, R. Needleman, J. K. Lanyi and H. Saitô (1999) Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. Biophys. J. 76, 15231531.
  • 36
    Tuzi, S., A. Naito and H. Saitô (1993) A high-resolution solid-state 13C-NMR study on [1-13C]Ala and [3-13C]Ala and [1-13C]Leu and Val-labelled bacteriorhodopsin: Conformation and dynamics of transmembrane helices, loops and termini, and hydration-induced conformational change. Eur. J. Biochem. 218, 837844.
  • 37
    Fitter, J., R. E. Lechner and N. A. Dencher (1999) Interactions of hydration water and biological membranes studied by neutron scattering. J. Phys. Chem. B, 103, 80368050.
  • 38
    Dencher, N. A., H. J. Sass and G. Büldt (2000) Water and bacteriorhodopsin: Structure, dynamics and function. Biochim. Biophys. Acta 1460, 192203.
  • 39
    Yamaguchi, S., S. Tuzi, K. Yonebayashi, A. Naito, R. Needleman, J. K. Lanyi and H. Saitô (2001) Surface dynamics of bacteriorhodopsin as revealed by 13C NMR studies on [13C]Ala-labeled proteins: Detection of millisecond or microsecond motions in interhelical loops and C-terminal α-helix. J. Biochem. (Tokyo) 129, 373382.
  • 40
    Tuzi, S., A. Naito and H. Saitô (1996) Conformation and dynamics of [3-13C]Ala-labeled bacteriorhodopsin and bacterioopsin, induced by interaction with retinal and its analogs, as studied by 13C nuclear magnetic resonance. Biochemistry 35, 75207527.
  • 41
    Yamaguchi, S., S. Tuzi, M. Tanio, A. Naito, J. K. Lanyi, R. Needleman and H. Saitô (2000) Irreversible conformational change of bacterio-opsin induced by binding of retinal during its reconstitution to bacteriorhodopsin, as studied by 13C NMR. J. Biochem. 127, 861869.
  • 42
    Solomon, I. (1955) Relaxation processes in a system of two spins. Phys. Rev. 99, 559565.
  • 43
    Bloembergen, N. (1957) Proton relaxation times in paramagnetic solution. J. Chem. Phys. 27, 572573.
  • 44
    Tuzi, S., J. Hasegawa, R. Kawaminami, A. Naito and H. Saitô (2001) Regio-selective detection of dynamic structure of transmembrane α-helices as revealed from 13C NMR spectra of [3-13C]Ala-labeled bacteriorhodopsin in the presence of Mn2+ ion. Biophys. J. 81, 425434.
  • 45
    Saitô, H. (1986) Conformation-dependent 13C chemical shifts: A new means of conformational characterization as obtained by high-resolution solid-state NMR. Magn. Reson. Chem. 24, 835852.
  • 46
    Saitô, H. and I. Ando (1989) High-resolution solid-state NMR studies on synthetic and biological macromolecules. Annu. Rep. NMR Spectrosc. 21, 209290.
  • 47
    Krimm, S. and A. M. Dwivedi (1982) Infrared spectrum of the purple membrane: Clue to a proton conduction mechanism? Science 216, 407408.
  • 48
    Kawase, Y., M. Tanio, A. Kira, S. Yamaguchi, S. Tuzi, A. Naito, M. Kataoka, J. K. Lanyi, R. Needleman and H. Saitô (2000) Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation of Asp 85 and deprotonation of Schiff base as studied by 13C NMR. Biochemistry 39, 1447214480.
  • 49
    Kira, A., M. Tanio, S. Tuzi and H. Saitô (2004) Significance of low-frequency local fluctuation motions in the transmembrane B and C α-helices of bacteriorhodopsin, to facilitate efficient proton uptake from the cytoplasmic surface, as revealed by site-directed solid-state 13C NMR. Eur. J. Biophys. 33, 580588.
  • 50
    Suwelack, D., W. P. Rothwell and J. S. Waugh (1980) Slow molecular motion detected in the NMR spectra of rotating solids. J. Chem. Phys. 73, 25592569.
  • 51
    Saitô, H., J. Mikami, S. Yamaguchi, M. Tanio, A. Kira, T. Arakawa, K. Yamamoto and S. Tuzi (2004) Site-directed 13C solid-state NMR studies on membrane proteins: Strategy and goals toward revealing conformation and dynamics as illustrated for bacteriorhodopsin labeled with [1-13C]amino acid residues. Magn. Reson. Chem. 42, 218230.
  • 52
    Luecke, H., B. Schobert, H.-T. Richter, J.-P. Cartailler and J. K. Lanyi (1999) Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291, 899911.
  • 53
    Yamaguchi, S., K. Yonebayashi, H. Konishi, S. Tuzi, A. Naito, J. K. Lanyi, R. Needleman and H. Saitô (2001) Cytoplasmic surface structure of bacteriorhodopsin consisting of interhelical loops and C-terminal α helix, modified by a variety of environmental factors as studied by 13C-NMR. Eur. J. Biochem. 268, 22182228.
  • 54
    Yonebayashi, K., S. Yamaguchi, S. Tuzi and H. Saitô (2003) Cytoplasmic surface structures of bacteriorhodopsin modified by site-directed mutations and cation binding as revealed by 13C NMR. Eur. Biophys. J. 32, 111.
  • 55
    Riesle, J., D. Osterhelt, N. A. Dencher and J. Heberle (1996) D38 is an essential part of the proton translocation pathway in bacteriorhodopsin. Biochemistry 35, 66356643.
  • 56
    Checover, S., E. Nachliel, N. A. Dencher and M. Gutman (1997) Mechanism of proton entry into the cytoplasmic section of the proton-conducting channel of bacteriorhodopsin. Biochemistry 36, 1391913928.
  • 57
    Checover, S., YMarantz., E. L. Nachliel, M. Gutman, M. Pfeiffer, J. Tittor, D. Osterhelt and N. A. Dencher (2001) Dynamics of the proton transfer reaction on the cytoplasmic surface of bacteriorhodopsin. Biochemistry 40, 42814292.
  • 58
    Arakawa, T., K. Shimono, S. Yamaguchi, S. Tuzi, Y. Sudo, N. Kamo and H. Saitô (2003) Dynamic structure of pharaonis phoborhodopsin (sensory rhodopsin II) and complex with a cognate truncated transducer as revealed by site-directed 13C solid-state NMR. FEBS Lett. 536, 237240.
  • 59
    Yamaguchi, S., K. Shimono, Y. Sudo, S. Tuzi, A. Naito, N. Kamo and H. Saitô (2004) Conformation and dynamics of the [3-13C]Ala, [1-13C]Val-labeled truncated pharaonis transducer, pHtrII (1-159), as revealed by site-directed 13C solid-state NMR: Changes due to association with phoborhodopsin (sensory rhodopsin II). Biophys. J. 86, 31303140.
  • 60
    Gordeliy, V. I., J. Labahn, R. Moukhametzianov, R. Efremov, J. Granzin, R. Schlesinger, G. Buldt, T. Savopol, A. J. Scheidig, J. P. Klare and M. Engerhard (2002) Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex. Nature 419, 484487.
  • 61
    Rothwell, W. P. and J. S. Waugh (1981) Transverse relaxation of dipolar coupled spin systems under rf irradiation: Detecting motions in solid. J. Chem. Phys. 74, 27212732.
  • 62
    Barré, P., S. Yamaguchi, H. Saitô and D. Huster (2003) Backbone dynamics of bacteriorhodopsin as studied by 13C solid-state NMR spectroscopy. Eur. Biophys. J. 32, 578584.
  • 63
    Saitô, H., K. Yamamoto, S. Tuzi and S. Yamaguchi (2003) Backbone dynamics of membrane proteins in lipid bilayers: The effect of two-dimensional array formation as revealed by site-directed solid-state 13C NMR studies on [3-13C]Ala- and [1-13C]Val-labeled bacteriorhodopsin. Biochim. Biophys. Acta 1616, 127136.
  • 64
    Saitô, H., T. Tsuchida, K. Ogawa, T. Arakawa, S. Yamaguchi and S. Tuzi (2002) Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced by disrupted or disorganized two-dimensional crystalline lattice, through modified lipid–helix and helix–helix interactions, as revealed by 13C NMR. Biochim Biophys. Acta 1565, 97106.
  • 65
    Yamamoto, K., S. Tuzi, H. Saitô, I. Kawamura and A. Naito (2006) Conformation and dynamics changes of bacteriorhodopsin and its D85N mutant in the absence of 2D crystalline lattice as revealed by site-directed 13C NMR. Biochim. Biophys. Acta 1758, 181189.
  • 66
    Tuzi, S., A. Naito and H. Saitô (2003) Local protein structure and dynamics at kinked transmembrane α-helices of [1-13C]Pro-labeled bacteriorhodopsin as revealed by site-directed solid-state 13C NMR. J. Mol. Struct. 654, 205214.
  • 67
    Saitô, H., S. Yamaguchi, K. Ogawa, S. Tuzi, M. Márquez, C. Sanz and E. Padrós (2004) Glutamic acid residues of bacteriorhodopsin at the extracellular surface as determinants for conformation and dynamics as revealed by site-directed solid-state 13C NMR. Biophys. J. 86, 16731681.
  • 68
    Kawamura, I., Y. Ikeda, Y. Sudo, M. Iwamoto, K. Shimono, S. Yamaguci, S. Tuzi, H. Saitô, N. Kamo and A. Naito (2007) Participation of the surface structure of pharaonis phoborhodopsin, ppR and its A149S and A149 V mutants, consisting of the C-terminal α-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed 13C solid-state NMR. Photochem. Photobiol. 83, 339345.
  • 69
    Yamaguchi, S., S. Tuzi, J. U. Bowie and H. Saitô (2004) Secondary structure and backbone dynamics of Escherichia coli diacylglycerol kinase, as revealed by site-directed solid-state 13C NMR. Biochim. Biophys. Acta 1698, 97105.