Centers & Labs

RIKEN SPring-8 Center

Bio-specimen platform Group

Group Director: Naoki Kunishima

To understand rationally the function of protein that supports life activities, it is necessary to determine its 3D-structure at atomic level. The X-ray crystallography analysis had previously been the most efficient and popular way to determine protein 3D-structures at atomic level. However, it was revealed that proteins which can crystallize were only 40% of all genomes, even in the proteins originated in thermo-stable microorganism, as a result of structural genomics. It is too hard to crystallize the rest 60% proteins by conventional technology. To construct a high-throughput framework for the structure determination of challenging targets such as membrane proteins, we develop a new methodology using XFEL as well as extend the technical basis of protein crystallography established in the Protein 3000 Project.

Research Subjects

  • Application of Protein 3000 results for the benefit of society
  • Development of advanced technology for structural biology
  • Structural study of proteins for industrial applications

Publications

  1. Asada Y., Sugahara M., Mizutani H., Naitow H., Tanaka T., Matsuura Y., Agari Y., Ebihara A., Shinkai A., Kuramitsu S., Yokoyama S., Kaminuma E., Kobayashi N., Nishikata K., Shimoyama S., Toyoda T., Ishikawa T., and Kunishima N.:
    "Integrated database of information from structural genomics experiments"
    Acta Crystallogr. D, in press.
  2. Sugahara M.:
    "A fiber-based crystal mounting technique for protein cryocrystallography"
    J. Appl. Cryst. 45, 362-366 (2012)
  3. Tanaka T, Padavattan S, and Kumarevel T.:
    "Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1"
    J. Biol. Chem. 287, 10394-10402 (2012)
  4. Matsuura Y, Takehira M, Sawano M, Ogasahara K, Tanaka T, Yamamoto H, Kunishima N, Kato E, and Yutani K.:
    "Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C"
    FEBS J. 279, 78-90 (2012)
  5. Sugahara M., Kageyama-Morikawa Y., and Kunishima N.:
    "Packing space expansion of protein crystallization screening with synthetic zeolite as a heteroepitaxic nucleant"
    Crystal Growth & Design 11, 110-120 (2011)
  6. Sugahara M., Shimizu K., Asada Y., Fukunishi H., Kodera H., Fujii T., Osada E., Kasazaki T., Sawada T., Chikusa H., Kondo K., Yorihiro A., and Kunishima N.:
    "Autolabo: an automated system for ligand-soaking experiments with protein crystals"
    J. Appl. Cryst. 43, 940-944 (2010)
  7. Sugahara, M., Asada, Y., Shimada, H., Taka, H., and Kunishima, N.:
    "HATODAS II: heavy-atom database system with potentiality scorning"
    J. Appl. Cryst., 42, 540-544 (2009)
  8. Mizutani, H., Saraboji, K., Malathy-Sony, S. M., Ponnuswamy, M. N., Kumarevel, T., Krishna-Swamy, B. S., Simanshu, D. K., Murthy, M. R. N., and Kunishima, N.:
    "Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality"
    Acta Crystallogr. D 64, 1020-1033 (2008)
  9. Sugahara, M., Asada, Y., Shimizu, K., Yamamoto, H., Lokanath, N. K., Mizutani, H., Bagautdinov, B., Matsuura, Y., Taketa, M., Kageyama, Y., Ono, N., Morikawa, Y., Tanaka, Y., Shimada, H., Nakamoto, T., Sugahara, Mitsu., Yamamoto, M., and Kunishima, N.:
    "High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center"
    J. Struct. Funct. Genomics 9, 21-28 (2008)
  10. Bagautdinov, B., Matsuura, Y., Bagautdinova, S., and Kunishima, N.:
    "Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate"
    J. Biol. Chem. 283, 14739-14750 (2008)