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Protein Crystallography Research Group
Tetsuya ISHIKAWA
Group Director
Tetsuya ISHIKAWA (D.Eng.)
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Research Areas

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 Subject

  1. Application of Protein 3000 results for the benefit of society
  2. Development of advanced technology for structural biology
  3. Structural study of proteins for industrial applications

Related links

  1. RIKEN SPring-8 Center Website_Laboratories PageNew Window

Press release

February 24, 2012
Crystal structure of archael chromatin clarified in new study
July 23, 2009
World's largest database of analysis experiments on protein crystal structure unveiled
September 29, 2008
Progress in crystallographic protein analysis through the improved crystallization technique which is associated with the transformation of protein molecules
March 27, 2008
Teasing out the structure of a crucial protein
Researchers at RIKEN's SPring-8 Center clarify a process in cells important in drug discovery research New Window

RIKEN RESEARCH

January 30, 2009
An 'opening' role
Non-coding RNAs play a role in regulating the expression of genes in yeast New Window
August 15, 2008
Complexes full of energy
A crystal structure of a complex that generates energy shows scientists the way towards treatments for metabolic disorders New Window
March 21,2008
The key to controlling DNA copying
Researchers use beamlines at RIKEN's SPring-8 Center to glean new insights into how replication is regulated New Window

List of Selected Publications

  1. 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 ℃"
    FEBS J. 279, 78-90 (2012).
  2. 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).
  3. Matsuura Y., Ota M., Tanaka T., Takehira M., Ogasahara K., Bagautdinov B., Kunishima N., and Yutani K.:
    "Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design"
    J. Biochem. 148, 449-458 (2010).
  4. 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"
    Appl. Cryst. 43, 940-944 (2010).
  5. Sugahara, M., Asada, Y., Shimada, H., Taka, H., and Kunishima, N.:
    "HATODASII: heavy-atom database system with potentiality scorning"
    J. Appl. Cryst., 42, 540-544 (2009).
  6. 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).
  7. 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).
  8. 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).
  9. Tanaka, T., Sawano, M., Ogasahara, K., Sakaguchi, Y., Bagautdinov, B., Katoh, E., Kuroishi, C., Shinkai, A., Yokoyama, S., and Yutani, K.:
    "Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 ℃"
    FEBS Letters 580, 4224-4230 (2006).
  10. Kunishima, N., Asada, Y., Sugahara, Ma., Ishijima, J., Nodake, Y., Sugahara, Mitsu., Miyano, M., Kuramitsu, S., Yokoyama, S., and Sugahara M.:
    "A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PaaI"
    J. Mol. Biol., 352, 212-228 (2005).

Members

Principal Investigator

Tetsuya ISHIKAWA
Group Director

Staff Scientist

Naoki KUNISHIMA
Deputy Group Director
Katsuhide YUTANI
Senior Scientist
Hisashi NAITO
Senior Research Scientist
Michihiro SUGAHARA
Research Scientist
Saori MAKI-YONEKURA
Research Scientist
Sivaraman PADAVATTAN
Research Scientist

Postdoctoral Fellow

Tomoyuki TANAKA
Research Associate
Yoshinori MATSUURA
Research Associate
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