Laboratories & Administration Office

Laboratory of Protein Informatics

member

Director Haruki NAKAMURA
Associate Professor Akira KINJO
Instructor Yu TAKANO
Technical Assistant Takashi KOSADA

Correspondence

Tel 81-6-6879-4310
Fax 81-6-6879-4310
E-mail
URL http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_en.html

Research

Our laboratory constructs and manages the international protein structural database (PDB), and develops the advanced database, as PDB Japan (PDBj). The aim of our laboratory is to elucidate the relationship between structures and functions of biological macromolecules, and mutual interactions (proteomics) by X-ray crystallography, NMR spectroscopy, molecular simulation and structural bioinformatics.


<Fig.1>
The home page of PDBj (Protein Data Bank Japan: http://www.pdbj.org/),
displaying the Electron Density Map for the deposited structure factor. For
maintaining the database of the protein structures, PDBj manages the
international database, wwPDB, collaborating with the Research Collaboratory
for Structural Bioinformatics (RCSB) and the European Bioinformatics
Institute (EBI) in EU. In addition, PDBj continues its own research and
development of protein structure databases. In particular, a canonical XML
description of PDB data, PDBML, has been based developed by PDBj
and RCSB. Several other applications have been developed: molecular
graphics viewer, jV, molecular surface database for functional sites, eF-site,
with a new service, eF-seek, for the search of similar molecular surface,
and the navigation of the sequence and structure neighbours.


<Fig.2>
Docking simulation for the putative interfaces of RID domain of RalGDS at the
top left and that of Ras at the bottom left. A putative complex structure indicated
with sky lines at the right was built, where yellow and blue lines are complex
crystal structures of RID domain of RalGDS and RAS, respectively.

Current Research Programs

1) Construction of Protein Data Bank (PDB) as PDBj
2) Bioinformatics studies focused on protein structures and protein-protein interactions
3) Development of new algorithms for simulations to examine free energy landscapes of biomolecular systems and their electronic states by a hybrid-QM/MM method
4) Protein X-ray crystallography for structural biology

References

1. ASH structure alignment package: Sensitivity and selectivity in domain classification. Standley, D. M. Toh, H., Nakamura, H. (2007) BMC Bioinformatics 8: 116 .
2. Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase. Takano, Y., Nakamura, H. (2006) Chem. Phys. Lett. 430, 149-155.
3. Molecular dynamics simulation study on water associated with π-electrons of benzene by using QM/MM potential. Yonezawa, Y., Nakata, K., Takada, T., Nakamura, H. (2006) Chem. Phys. Lett. 428, 73-77.

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