Structural genomics of membrane proteins

Accounts of Chemical Research

Volumn 36, Issue 3, 2003, Pages 199-206

  Kyogoku, Yoshimasa ^a   Fujiyoshi, Yoshinori ^a,b   Shimada, Ichio ^a,c   Nakamura, Haruki ^a,d   Tsukihara, Tomitake ^a,d   Akutsu, Hideo ^a,d   Odahara, Takayuki ^a   Okada, Tetsuji ^a   Nomura, Nobuo ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; COLLAGEN; COMPLEMENTARY DNA; ENDOTHELIN B RECEPTOR; G PROTEIN COUPLED RECEPTOR; LIGAND; MASTOPARAN; MEMBRANE PROTEIN; RECEPTOR; RECEPTOR PROTEIN; VON WILLEBRAND FACTOR;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CRYSTALLIZATION; ELECTRON MICROSCOPY; GENE EXPRESSION SYSTEM; GENOMICS; INSTRUMENTATION; LIGAND BINDING; MEDICAL GENETICS; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; SYNCHROTRON; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

BACTERIORHODOPSINS; CRYSTALLOGRAPHY, X-RAY; GENOMICS; HUMAN GENOME PROJECT; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 0037351720     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar0101279     Document Type: Article

References (39)

1. Drews, J. Drug Discovery: A Historical Perspective. Science 2000, 287, 1960-1964.
2. Sato, C.; Ueno, Y.; Asai, K.; Takahashi, K.; Sato, M.; Engel, A.; Fujiyoshi, Y. The Voltage-sensitive Sodium Channel is a Bellshaped Molecule with Several Cavities. Nature 2001, 409, 1047-1051.
3. 2+ Channel. Biochem. Biophys. Res. Commun. 2001, 282, 284-291.
4. Doi, T.; Hiroaki, Y.; Arimono, I.; Fujiyoshi, Y.; Okamoto, T.; Satoh, M.; Furuichi, Y. Characterization of Human Endothelin B Receptor and Mutant Receptors Expressed in Insect Cells. Eur. J. Biochem. 1997, 248, 139-148.
5. Kuehlbrandt, W. Two-dimensional Crystallization of Membrane Proteins. Q. Rev. Biophys. 1992, 25, 1-49
6. Oesterhelt D.; Stoeckenius, W. Isolation of the Cell Membrane of Halobacterium halobium and Its Fractionation into Red and Purple Membrane. Methods Enzymol. 1974, 31, 667-678.
7. Fujiyoshi, Y. The Structural Study of Membrane Proteins by Electron Crystallography. Adv. Biophys. 1998, 35, 25-80.
8. Fujiyoshi, Y.; Mizusaki, T.; Morikawa, K.; Yamagishi, H.; Aoki, Y.; Kihara, H.; Harada, Y. Development of a Superfluid Helium Stage for High-Resolution Electron Microscopy. Ultramicroscopy 1991, 38, 241-251.
9. Henderson, R.; Baldwin, J. M.; Ceska, T. A.; Zemlin, F.; Beckmann, E.; Downing, K. H. Model for the Structure of Bacteriorhodopsin Based on High-resolution Electron Cryo-microscopy. J. Mol. Biol. 1990, 213, 899-929.
10. Kimura, Y.; Vassylyev, D. G.; Miyazawa, A.; Kidera, A.; Matsushima, M.; Mitsuoka, K.; Murata, K.; Hirai, T.; Fujiyoshi, Y. Surface of Bacteriorhodopsin Revealed by High-resolution Electron Crystallography. Nature 1997, 389, 206-211.
11. Mitsuoka, K.; Hirai, T.; Murata, K.; Miyazawa, A.; Kidera, A.; Kimura, Y.; Fujiyoshi, Y. The Structure of Bacteriorhodopsin at 3.0 Å Resolution Based on Electron Crystallography: Implication of the Charge Distribution. J. Mol. Biol. 1999, 286, 861-882.
12. Murata, K.; Mitsuoka, K.; Hirai, T.; Walz, T.; Agre, P.; Heymann, J. B.; Engel, A.; Fujiyoshi, Y. Structure Determinants of Water Permeation through Aquaporin-1. Nature 2000, 407, 599-605.
13. Michel, H. Crystallization of Membrane Proteins. Trends Biochem. Sci. 1983, 8, 56-59.
14. Yoshikawa, S.; Tera, T.; Takahashi, Y.; Tsukihara, T.; Caughey, W. S. Crystalline Cytochrome c Oxidase of Bovine Heart Mitochondrial Membrane: Composition and X-ray Diffraction Studies. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 1354-1358.
15. Shinzawa-Itoh, K.; Ueda, H.; Yoshikawa, S.; Aoyama, H.; Yamashita, E.; Tsukihara, T. Effects of Ethyleneglycol Chain Length of Dodecyl Polyethylene glycol Monoether on Crystallization of Bovine Heart Cytochrome c Oxidase. J. Mol. Biol. 1995, 246, 572-575.
16. Tsukihara, T.; Aoyama, H.; Yamashita, E.; Tomizaki, T.; Yamaguchi, H.; Shinzawa-Itoh, K.; Nakashima, R.; Yaono, R.; Yoshikawa, S. Structure of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 A Resolution. Science 1995, 269, 1069-1074.
17. Odahara, T.; Ataka, M.; Katsura, T. Phase Diagram Determination to Elucidate the Crystal Growth of the Photoreaction Center from Rhodobacter sphaeroides. Acta Crystallogr. D 1994, 50, 639-542.
18. Palczewski, K.; Kumasaka, T.; Hori, T.; Behnke, C. A.; Motoshima, H.; Fox, B. A.; Le Trong, I.; Teller, D. C.; Okada, T.; Stenkamp, R. E.; Yamamoto, M.; Miyano, M. Crystal Structure of Rhodopsin: a G Protein-coupled Receptor. Science 2000, 289, 739-745.
19. Okada, T.; Ernst, O.; Palczewski, K.; Hofmann, K. P. Activation of Rhodopsin: New Insights from Structural and Biochemical Studies. Trends Biochem. Sci. 2001, 26, 318-324.
20. Okada, T.; Fujiyoshi, Y.; Silow, M.; Navarro, J.; Landau, E. M.; Shichida, Y. Functional Role of Internal Water Molecules in Rhodopsin Revealed by X-ray Crystallography. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5982-5987.
21. Okada, T.; Le Trong, I.; Fox, B. A.; Behnke, C. A.; Stenkamp, R. E.; Palczewski, K. X-ray Diffraction Analysis of Three-dimensional Crystals of Bovine Rhodopsin Obtained from Mixed Micelles. J. Struct. Biol. 2000, 130, 73-80.
22. Arora, A.; Abildgaard, F.; Bushweller, J. H.; Tamm, L. K.; Structure of Outer Membrane Protein A Transmembrane Domain by NMR Spectroscopy. Nat. Struct. Biol. 2001, 8, 334-338.
23. Takahashi, H.; Nakanishi, T.; Kami, K.; Arata Y.; Shimada, I. A Novel NMR Method for the Determination of the Interface of Large Protein-protein Complexes. Nat. Struct. Biol. 2000, 7, 220-223.
24. Nakanishi, T.; Miyazawa, M.; Sakakura, M.; Terasawa, H.; Takahashi, H.; Shimada, I. Determination of the Interface of a Large Protein Complex by Transferred Cross-saturation Measurements. J. Mol. Biol. 2002, 318, 245-249.
25. Raleigh, D. P.; Levitt, M. H.; Griffin, R. G. Rotational Resonance in Solid State NMR. Chem. Phys. Lett. 1988, 146, 71-76.
26. Gullion, T.; Schaefer, J. Rotational-echo Double-resonance NMR. J. Magn. Reson. 1989, 81, 196-200.
27. Balazs, Y. S.; Thompson, L. K. Practical Methods for Solid-state NMR Distance Measurements on Large Biomolecules: Constant Time Rotational Resonance. J. Magn. Reson. 1999, 139, 371-376.
28. 15N Signals: An Application to Adenosine. J. Am. Chem. Soc. 1995, 117, 11351-11352.
29. 13C Dipolar Interactions under Magic-angle Spinning Conditions. J. Chem. Phys. 1998, 109, 2380-2393.
30. Shirai, H.; Nakajima, N.; Higo, J.; Kidera, A.; Nakamura, H. Conformational Sampling of CDR-H3 in Antibodies by Multicanonical Molecular Dynamics Simulation. J. Mol. Biol. 1998, 278, 481-496.
31. Nakajima, N.; Higo, J.; Kidera, A.; Nakamura, H. Free Energy Landscapes of Peptides by Enhanced Conformational Sampling. J. Mol. Biol. 2000, 296, 197-216.
32. Kamiya, N.; Higo, J.; Nakamura, H. Conformational Transition States of a β-hairpin Peptide between the Ordered and Disordered Conformations in Explicit Water. Protein Sci. 2002, 11, 12297-2307.
33. Nakajima, N.; Higo, J.; Kidera, A.; Nakamura, H. Flexible Docking of a Ligand Peptide to a Receptor Protein by Multicanonical Molecular Dynamics Simulation. Chem. Phys. Lett. 1997, 278, 297-301.
34. Fukuda, I.; Nakamura, H. Tsallis Dynamics Using the Nose-Hoover Approach. Phys. Rev. E 2002, 65, 26105.
35. Nomura, N.; Miyajima, N.; Suzaka, T.; Tanaka A.; Kawarabayasi Y.; Sato S.; Nagase T.; Seki N.; Ishikawa K.; Tabata S. Prediction of the Coding Sequences of Unidentified Human Genes. I. The Coding Sequences of 40 New Genes (KIAA0001-KIAA0040) Deduced by Analysis of Randomly Sampled cDNA Clones from Human Immature Myeloid Cell Line KG-1. DNA Res. 1994, 1, 27-35.
36. Wiemann, S.; Weil, B.; Wellenreuther, R.; Gassenhuber, J.; Glassl, S.; Ansorge, W.; et al. Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs. Genome Res. 2001, 11, 422-435.
37. Strausberg, R. L.; Feingold, E. A.; Klausner, R. D.; Collins, F. S. The Mammalian Gene Collection. Science 1999, 286, 455-457.
38. Suzuki, Y.; Yoshitomo, K.; Maruyama, K.; Suyama, A.; Sugano, S. Construction and Characterization of a Full Length-enriched and a 5′-end-enriched cDNA Library. Gene 1997, 200, 149-156.
39. Nishikawa, T.; Ota, T.; Kawai, Y.; Ishii, S.; Saito, K.; Yamamoto, J.-i.; Wakamatsu, A.; Ozawa, M.; Suzuki, Y.; Sugano, S.; Isogai, T. Comparison of Sequences of cDNA Clones Obtained from Oligo-capping cDNA Libraries with Those from Unigene. DNA Res. 2001, 8, 255-262.