SHIRO, Yoshitsugu X 1. 1 CYP119 1
3 C 2, 3
solfataricus CO NO n-butyl-isocyanide
FG 4 1 1 STAP 2 1
S 5 So-S4
x NO FG n- n- P450Bsβ
4 6 His81 E1/2 = +20mV
I helix
P450BS β II = - 2 3 X 6 7 6 6 FixL/Fix.J FixL FTIR So S1 S1 S2 S2 S3 S3 So ATP FixL nifA    fixK S2 S3 So So S1 S3 Fix.J S1 S² S3 S3 So S'2 O 2
CO 6 C c 20 x 2 x 1 FixL / ATP 500 1 X 3 7   Pseudomonas aeruginosa 3 nor NO N 2 O bc nor nor pcr FixL 5 5 aeruginosa nor Pseudomonas FixL / 2. 1 FixL/FixJ Thermotoga maritima FixL 30% FixL FixL II 2 3 2 3 3 1 ETR1 2 4 4 II ETR1 ETR1 3  NO X P450nor 2 NO Cu K-edge x XANES 2 3 FAD FAD 3. 7 FAD DNA 3 λCro Tie2 1 5 2 60 native PAGE XAFS XAFS 4 NMR 4. 1
μL XAFS 1 μ L XAFS ETR1 -
R XANES 10.2% 1.0 Å 3
6 4 7 5 1 FAD 1 X 1 FAD Research Subjects and Members of Biophysical Chemistry Laboratory 1. Molecular Structures and Functions of Metalloen- zymes 2. Structural and Functional Analyses of Signal Trans- ducing Metalloproteins 3. De Novo Protein Design 4. Development and Application of New Techniques of Protein Crystallography
Head
Dr. Yoshitsugu SHIRO
Members
Dr. Yasuhiro ISOGAI Dr. Hiro NAKAMURA Dr. Takumi NOGUCHI Dr. Shin-ichi ADACHI Dr. Hiroshi AOYAMA Dr. Hiroshi SUGIMOTO Dr. Akihiro KIKUCHI  ¹ Dr. Hideyuki KUMITA  ¹ Dr. Eiji OBAYASHI  ¹ Dr. Dong-Sun Lee  ² Dr. Seiji YAMADA  ² ¹ Special Postdoctoral Researcher ² Contract Researcher in collaboration with Dr. Kunio MIKI (Theoretical Structural Biology Lab.) Mr. Hirofumi KOMORI (Theoretical Structural Biology Lab.)
Visiting Members
Mr. Satoru AKIMOTO (Fac. Sci., Yokohama City Univ.) Mr. Manabu ISHIDA (Fac. Sci., Himeji Inst. Technol.) Prof. Tsutomu KOYAMA (Grad. Sch. Sci., Nagoya Univ.) Dr. Genzi KURISU (Protein Res. Inst., Osaka Univ.) Dr. Yukio MORIMOTO (Fac. Sci., Himeji Inst. Tech- nol.) Dr. Takamasa NONAKA (Dept. Biol. Eng., Nagaoka Univ. Technol.) Dr. Hiroshi YAMAGUCHI (Sch. Sci., Kwansei Gakuin Univ.) Prof. Shin-ya YOSHIKAWA (Fac. Sci., Himeji Inst. Technol.)
Trainees
Ms. Kei FUJISHIMA (Fac. Sci., Himeji Inst. Technol.) Mr. Kaito HOSONO (Fac. Eng., Hosei Univ.) Mr. Syun-ichiro ODA (Fac. Sci., Himeji Inst. Technol.) Mr. Ken SAITO (Fac. Sci., Saitama Univ.) Ms. Hitomi SAWAI (Fac. Sci., Himeji Inst. Technol.) Mr. Atsunari TANAKA (Fac. Sci., Yokohama City Univ.) Ms. Akari YAMADA (Fac. Sci., Himeji Inst. Technol.) Mr. Kazuhide YAMANE (Fac. Sci., Himeji Inst. Tech- nol.)
Publications
Nakamura  H.,  Saito  K.,  and Shiro  Y.:    “Quantitative measurement of radioactive phosphorylated proteins in wet polyacrylamide gels", Anal. Biochem. 294 , 187–188 (2001). Nakasako M., Fujisawa T., Adachi S., Kudo T., and Higuchi S.: "Large-scale domain movements and hydra- tion structure changes in the active-site cleft of unligated glutamate dehydrogenase from thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering", Biochemistry 40, 3069– 3079 (2001). Lee D., Kim N., and Lee S.:  "2,2-diphenyl-1-picrylhydrazyl hydrate, a stable free radical, is an α-glucosidase in- hibitor", Biol. Pharm. Bull. 24, 727–728 (2001). Lee D. and Lee S.:  "Genistein, a soy isoflavone, is a potent α-glucosidase inhibitor", FEBS Lett. 501, 84–86 (2001). Odoko M., Yao M., Yamashita E., Nakashima R., Hirata K., Aoyama H., Muramoto K., Shinzawa-Itoh K., Yoshikawa S., and Tsukihara T.: "Optimization of the energy constant of the methionine S δ -C c bond for X- PLOR refinement of protein structure", J. Appl. Crys- tallogr. 34, 80–81 (2001). Adachi S., Oguchi T., Tanida H., Park S., Shimizu H., Miyatake H., Kamiya N., Shiro Y., Inoue Y., Ueki T., and Iizuka T.:  "The RIKEN structural biology beamline II (BL44B2) at the SPring-8", Nucl. Instrum. Methods Phys. Res. A 467/468 , 711–714 (2001). Sasaki Y. C., Okumura Y., Adachi S., Suda H., Taniguchi Y., and Yagi N.: "Picometer-scale dynamical X-ray imaging of single DNA molecules", Phys. Rev. Lett. 87, 248102-1–248102-4 (2001). Ota M., Isogai Y., and Nishikawa K.: "Knowledge-based potential defined for a rotamer library to design protein sequences", Protein Eng. 14 , 557–564 (2001). Shimizu H., Park S., Shiro Y., and Adachi S.:  "X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution", Acta Cryst. D: Biol. 58, 81-89 (2002). Matsunaga I., Yamada A., Lee D., Obayashi E., Fujiwara N., Kobayashi K., Ogura H., and Shiro Y.:  "Enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome P450s:  Kinetic deuterium isotope effects and analyses by resonance Raman spectroscopy", Bio- chemistry 41 , 1886–1892 (2002). Noguchi T. and Sugiura M.: "Flash-induced FTIR differ- ence spectra of the water oxidizing complex in moder- ately hydrated photosystem II core films: Effect of hy- dration extent on S-state transitions", Biochemistry 41 , 2322–2330 (2002). Komatsuzaki Y., Kusunoki M., Hasegawa K., Ono T., and Noguchi T.: "Highly structure-sensitive EXAFS spec- tra from multinuclear Mn model compounds. Ab ini- tio refinement of a diamond-structure of the S 1 -state Mn 4 CaCl cluster in photosystem II", Proc. of 12th Int. Congr. on Photosynthesis (PS2001), Brisbane, Aus- tralia, 2001–8, CSIRO, Collingwood, pp. S13-012-1–S13- 012-4 (2001).
Oral Presentations
Noguchi T. and Sugiura M.:  "Flash-induced reactions of the oxygen-evolving complex of photosystem II as stud- ied by Fourier transform infrared spectroscopy", 4th Int. Conf. on Biological Physics (ICBP 2001), Kyoto, July– Aug. (2001). Komatsuzaki Y., Kusunoki M., Hasegawa K., Ono T., and Noguchi T.: "Highly structural-sensitive EXAFS spec- tra from multinuclear Mn model compounds:  Ab ini- tio refinement of a diamond-structure of the S1-state Mn 4 -Ca-Cl cluster in photosystem II", 12th Int. Congr. on Photosynthesis (PS 2001), Brisbane, Australia, Aug. (2001). Higuchi M., Noguchi T., and Sonoike K.: "Reduction of the Mn cluster in oxygen evolving complex under dark- chilling condition", 12th Int. Congr. on Photosynthesis (PS 2001), Brisbane, Australia, Aug. (2001). Noguchi T. and Sugiura M.:  "FTIR detection of the molec- ular reactions during the oxygen-evolving S-state cycle", 12th Int. Congr. on Photosysthesis (PS 2001), Brisbane, Australia, Aug. (2001). Shiro Y.: "Insight from high resolution structures of cy- tochrome P450: Multi-conformation and ligand coordi- nation geometry", 12th Int. Conf. on Cytochrome P450, La Grande Motte, France, Sept. (2001). Noguchi T.:  "FTIR studies on the reactions of cofactors in photosystem II", Int. Symp. on Protein-Cofactor In- teractions, Berlin, Germany, Nov. (2001). Shiro Y.: "Structural and functional divergency of cy- tochrome P450: NO reductase and fatty acid peroxy- genase", 4th National Symp. in Chemistry, (National Chemical Laboratory and University of Pune), Pune, In- dia, Feb. (2002). Shiro Y.: "Functional genomics of metalloenzymes", Canada-UK-Japan Joint Symp. on Toward Post DNA- Sequencing Era, Yokohama, Feb. (2002). 39 ,       , 12      (2001). , 10     (2001). ":"""""""""""""""""" ", ,       , 3      (2002).