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Higuchi, Mariko; Pinak, M.
no journal, ,
Ionizing radiation leads to clustered DNA damage sites, which are defined as two or more single lesions induced within 10-20 base pairs (bp). In general, these sites are repaired with less efficiency than single lesions. So far the detail mechanism of repair of multiple lesions is not known. A cluster damage containing a single strand break (SSB) within a few base pairs opposite to a 8-oxo-7,8-dihydroguanine (8oxoG) is one example of damage that is difficult to repair. In this study, we present results of molecular dynamics (MD) simulation of the models of complex of hOGG1 and cluster damaged DNA. Each model DNA contains two damages, SSB and 8oxoG. The separation of the location of the SSB from the 8oxoG on the opposite strand were +1bp, -1bp and -3bp, respectively. According to the observed results, the fluctuation of each damaged DNA was dependence on the separation between the two damages because the extent of contact with hOGG1 was different.
Yamasaki, Satoshi*; Kono, Hidetoshi; Shimizu, Kentaro*; Sarai, Akinori*; Terada, Toru*
no journal, ,
Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. We determined the crystal structure of E134A mutant NDK from 
sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the 
NDK tetramer and Type II seen in the 
NDK tetramer, appeared in the asymmetric unit. Change in the assembly form may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.
sp. A-471Tamada, Taro; Okazaki, Nobuo; Ueda, Mitsuhiro*; Nakazawa, Masami*; Miyatake, Kazutaka*; Kuroki, Ryota
no journal, ,
Crystal structure of a novel chitinase (Ra-ChiC), a member of GH family 23, from the moderately thermophilic bacterium sp. A-471 has been solved in the active site to 1.9 
resolution. Crystal structure of Ra-ChiC was resemble to that of g-type lysozyme. It is well known that the residues involved in catalysis of the g-type lysozymes are Glu73, Asp90, and Asp101. The Glu73 (proton donor) in g-type lysozymes was conserved as Glu141 in the catalytic domain of Ra-ChiC.
Ohara, Takashi; Adachi, Motoyasu; Shimizu, Rumi; Tamada, Taro; Kuroki, Ryota; Nishimiya, Yoshiyuki*; Kondo, Hidemasa*; Tsuda, Sakae*
no journal, ,
no abstracts in English
Kurihara, Kazuo; Tamada, Taro; Ohara, Takashi; Kuroki, Ryota
no journal, ,
no abstracts in English
Meguro, Mizue; Adachi, Motoyasu; Okazaki, Nobuo; Tamada, Taro; Kuroki, Ryota; Kato, Takashi
no journal, ,
Erythropoietin (EPO) is a glycoprotein regulating the level of erythrocytes. We have first identified EPO from Xenopus laevis. The proliferation assay of xlEPO prepared using E. coli expression system showed that xlEPO stimulates proliferation of cells expressing xlEPO receptors and the cells expressing huEPO receptors. Cross activity between xlEPO and huEPO against corresponding receptors suggests that receptor recognition scheme of xlEPO is conserved with that of huEPO. Further, we have succeeded in crystallization of recombinant EPO from Xenopus laevis by sitting drop vapor diffusion method. The X-ray diffraction data at 2.9 was obtained. The phase was determined molecular replacement method.
Adachi, Motoyasu; Arai, Shigeki; Tamada, Taro; Kuroki, Ryota; Hidaka, Koshi*; Kimura, Toru*; Kiso, Yoshiaki*
no journal, ,
To obtain information for design of inhibitor against drug resistant mutant HIV protease, we determined X-ray crystal structures of A17 type HIV-1 protease complexed with inhibitors of lopinavir and KNI-1657. The gene of A17 type HIV-1 protease was synthesized chemically, and prepared using E. coli expression system. The results showed that affinity of lopinavir to the protease was 700 times lower than that of wild-type, and KNI-1657 has 20 times higher affinity to the protease than lopinavir. The crystals of complex were obtained using PEG4000 as precipitant. The diffraction data were collected at PF and SPring-8, and the structures were refined at R-factor of 19%.
Nakaniwa, Tetsuko*; Fukata, Harumi*; Inoue, Tatsuya*; Kinoshita, Takayoshi*; Adachi, Motoyasu; Tamada, Taro; Kuroki, Ryota; Tada, Toshiji*
no journal, ,
JNK1 is a MAP kinase responsible for response of stress. JNK1 has 4 and 3 cysteine residues in embedded region and at molecular surface, respectively. Those cysteine residues would cause inactivation and aggregation of the molecule. Based of the analysis of packing in crystal of isozyme of JNK1, we found more salt bridge and hydrogen bonding interactions on the interface. In this study, we focus on the two cysteine residues and introduced modification into M3 mutant previously reported.
Fernandez, M.*; Fujii, Satoshi*; Kono, Hidetoshi; Sarai, Akinori*
no journal, ,