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Tamada, Taro; Shinmi, Daisuke*; Ikeda, Masahiro*; Yonezawa, Yasushi*; Kataoka, Shiro*; Kuroki, Ryota; Mori, Eiji*; Motoki, Kazuhiro*
Scientific Reports (Internet), 5, p.17936_1 - 17936_12, 2015/12
Times Cited Count:22 Percentile:63.8(Multidisciplinary Sciences)The fully human monoclonal antibody KMTR2 acts as a strong direct agonist for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor 2 (TRAIL-R2), which is capable of inducing apoptotic cell death without cross-linking. To investigate the mechanism of direct agonistic activity induced by KMTR2, the crystal structure of the extracellular region of TRAIL-R2 and a Fab fragment derived from KMTR2 (KMTR2-Fab) was determined to 2.1 resolution. Two KMTR2-Fabs assembled with the complementarity-determining region 2 of the light chain via two-fold crystallographic symmetry, suggesting that the KMTR2-Fab assembly tended to enhance TRAIL-R2 oligomerization. A single mutation at Asn53 to Arg located at the two-fold interface in the KMTR2 resulted in a loss of its apoptotic activity, although it retained its antigen-binding activity. These results indicate that the strong agonistic activity, such as apoptotic signaling and tumor regression, induced by KMTR2 is attributed to TRAIL-R2 superoligomerization induced by the interdimerization of KMTR2.
Yonezawa, Yasushi*; Nagayama, Aiko*; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arai, Shigeki; Kuroki, Ryota; Watanabe, Keiichi*; Arakawa, Tsutomu*; Tokunaga, Masao*
Protein Journal, 34(4), p.275 - 283, 2015/08
Times Cited Count:4 Percentile:11.22(Biochemistry & Molecular Biology)Nucleoside diphosphate kinase isolated from psychrophilic sp. AS-131 (ASNDK) was expressed in and purified to homogeneity. Comparing to mesophilic NDK isolated from , ASNDK exhibited highly elevated thermolability: (1) expression at 37C as a denatured insoluble form, and (2) 30C lower optimum temperature of enzymatic activity. The subunit structure of ASNDK was suggested to be dimer, as in NDKs isolated from moderate halophiles.
Arai, Shigeki; Yonezawa, Yasushi*; Okazaki, Nobuo*; Matsumoto, Fumiko*; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu*; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide*; et al.
Acta Crystallographica Section D, 71(3), p.541 - 554, 2015/03
Times Cited Count:7 Percentile:50.91(Biochemical Research Methods)The crystal structure of halophilic -lactamase from sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr and Cs ions were identified by anomalous X-ray diffraction. The location of one Cs specific binding site was identified on HaBLA even in the presence of 9-fold molar excess of Na (90 mM Na /10 mM Cs). This Cs binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs by the cation- interaction. The observation of a selective and high-affinity Cs binding site provides important information that is useful for designing artificial Cs binding sites useful in bioremediation of radioactive isotopes.
Arai, Shigeki; Yonezawa, Yasushi*; Ishibashi, Matsujiro*; Matsumoto, Fumiko*; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota
Acta Crystallographica Section D, 70(3), p.811 - 820, 2014/03
Times Cited Count:11 Percentile:63.22(Biochemical Research Methods)In order to clarify the structural basis of halophilic characteristics of an alkaline phosphatase derived from the moderate halophile sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1 resolution by X-ray crystallography. Structural properties of surface negative charge and core hydrophobicity are shown to be intermediate between halophile and non-halophile characteristics, and may explain the unique functional adaptation to a wide-range of salt concentration.
Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota
Protein Science, 21(4), p.498 - 510, 2012/04
Times Cited Count:14 Percentile:34.65(Biochemistry & Molecular Biology)In order to clarify the oligomer state of nucleoside diphosphate kinase (NDK) from moderately halophilic sp. 593 (HaNDK), the crystal structure of HaNDK was determined by X-ray crystallography. The crystal structures of the wild-type HaNDK and the mutant HaNDK (E134A) showed a dimer and a tetramer, respectively. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.
Tokunaga, Hiroko*; Izutsu, Kenichi*; Arai, Shigeki; Yonezawa, Yasushi; Kuroki, Ryota; Arakawa, Tsutomu*; Tokunaga, Masao*
Enzyme and Microbial Technology, 46(2), p.129 - 135, 2010/02
Times Cited Count:6 Percentile:20.79(Biotechnology & Applied Microbiology)Both wild-type nucleoside diphosphate kinase from moderately halophilc (CsNDK (GNE), GNE represents Gly134-Asn135-Glu136) and mutant CsNDK (ANE), both of which have a neutral amino acid at residue 134, were found to form a dimer. These constructs contain Glu136, which may also cause steric barrier and charge repulsion. A double mutant, CsNDK (ANT), having Thr at 136 resulted in stable tetrameric assembly, supporting the above notion. A mutant CsNDK (GNT) reverted, however, to a dimer again, indicating that the introduced Ala residue at 134th in the double mutant generated a hydrophobic cluster consisting of the Ala residues and thereby stabilized dimer-dimer association of CsNDK assembly, while Gly destabilized it due to the loss of this cluster. Based on these observations, it is evident that both residues 134 and 136 contribute to the subunit assembly of CsNDK.
Fujiwara, Satoru; Matsumoto, Fumiko*; Yonezawa, Yasushige*
Journal of Molecular Biology, 331(1), p.21 - 28, 2003/08
Times Cited Count:43 Percentile:59.16(Biochemistry & Molecular Biology)The kinetic process of the fibril formation of hen egg white lysozyme (HEWL) in 90% ethanol in various salt concentrations has been investigated with time-resolved neutron scattering. It was shown that by addition of NaCl in a range between 0.3 mM and 1.0 mM, gelation occurred, and this gelation proceed through a two-step process; the lateral association of the protofilaments formed by HEWL, followed by the cross-linking of these fibrils formed. Both the structures of the fibrils and the rate of the gelation depended on NaCl concentration. Above 2 mM NaCl, precipitation occurred because of the formation of amorphous aggregates. Sensitivity of the aggregated structures to salt concentration suggests that electrostatic interaction plays an essential role in the formation of these structures. The structural diversity both in the fibrils and the aggregated structures of the fibrils can be interpreted in terms of the difference in the degree of the electrostatic shielding at different salt concentrations.
Yonezawa, Yasushige*; Tanaka, Shimpei*; Kubota, Tomomi*; Wakabayashi, Katsuzo*; Yutani, Katsuhide*; Fujiwara, Satoru
Journal of Molecular Biology, 323(2), p.237 - 251, 2002/10
Times Cited Count:74 Percentile:74.85(Biochemistry & Molecular Biology)It is known that hen egg white lysozyme (HEWL) forms amyloid fibrils in highly concentrated ethanol solutions. In order to gain an insight into the mechanism of the amyloid fibril formation, the structures of HEWL in solutions of various protein and ethanol concentrations were investigated with small-angle X-ray and neutron scattering. It was shown that the structural states of HEWL were distinguished as the monomer state, the state of the dimer formation, the state of the protofilament formation, the protofilament state, and the state towards the formation of the amyloid fibrils. Circular dichroism measurements showed that the large changes in the secondary structures of HEWL occurred during the dimer formation. Structural characterization showed that the dimers had an elongated shape, the protofilaments were formed by stacking of the dimers with their long axis (nearly) perpendicular to the protofilament axis, and the changes of the structural states towards the amyloid fibril formation occurred via lateral association of the protofilaments.
Maeda, Mitsuru; Fujiwara, Satoru; Yonezawa, Yasushige*; Niimura, Nobuo
Journal of the Physical Society of Japan, Vol.70, Supplement A, p.403 - 405, 2001/05
no abstracts in English
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 Halomonas sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the Myxococcus NDK tetramer and Type II seen in the E.coli 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.
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.
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. In order to understand the oligomeric structure of NDK, the wild-type NDK from Halomonas sp. 593 (HaNDK) was determined by X-ray crystallography. The wild-type HaNDK only exhibited a dimeric form that is the same as a common dimer unit seen in other NDKs. This is the first evidence of a dimeric structure for HaNDK. To explore the effect of mutation on the assembly form of HaNDK, E134, which is a key interface residue for other tetrameric NDKs, was replaced with Ala, and the structure was determined by X-ray crystallography. Two kinds of tetrameric assemblies, Type I and Type II, appeared in the asymmetric unit of the E134A mutant HaNDK. The change from dimeric to tetrameric assembly is attributed to the removal of negative charge repulsion caused by the E134 in the wild-type HaNDK.
Fujiwara, Satoru; Yonezawa, Yasushige*; Matsumoto, Fumiko; Oda, Toshiro*; Takeda, Soichi*
no journal, ,
no abstracts in English
Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
We determined the crystal structure of halophilic -Lactamase obtained from sp.560 by X-ray crystallography. Since halophilic enzymes can bind many metal ions on its molecular surface, we are tring to find the Na, Mg and Cs binding sites of halophilic -Lactamase from determined crystal structure.
Arai, Shigeki; Tokunaga, Hiroko*; Tamada, Taro; Yonezawa, Yasushi; Adachi, Motoyasu; Yamada, Mitsugu; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
Halophilic proteins can bind various inorganic ions with its negative charges located over the molecular surface. We are investigating the molecular structure of the halophilic proteins because halophilic proteins might be used as a material capturing for the rare metals and/or the radioactive metal ions. Recently, we succeeded in X-ray crystallographic analysis of the halophilic -Lactamase (HaBLA) derived from sp.560 at 3.0 resolution. From this structural analysis, we found that the back bone structure and the positively charged active site feature of HaBLA was similar to those of non-halophilic BLA. The molecular surface of HaBLA were, however, occupied by large number of negative charges. This structural information is very useful to improve the specificity of metals such as Cs or Sr.
Arai, Shigeki; Yonezawa, Yasushi; Adachi, Motoyasu; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
Proteins can distinguish various metal ions. Recently, we succeeded in X-ray crystallographic analysis of the halophilic -Lactamase (HaBLA) derived from sp.560 under the existence of Cs+ and Sr2+. Diffraction data at 2.0 resolution (space group P31, Unit cell a = b =115.9 , c =67.9 , Rmerge 9.6%) was collected. Three Cs and six Sr metal ion binding sites of HaBLA molecules in the asymmetric unit were identified. This structural information is very useful to create the artificial Cs or Sr binding site on the protein molecules.
Arai, Shigeki; Yonezawa, Yasushi*; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
no abstracts in English
Arai, Shigeki; Yonezawa, Yasushi*; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota
no journal, ,
Halophilic proteins have unique structural characteristics: high content of acidic residues creating negatively charged surface, high reversibility of tertiary structure and activity even in high salt concentration, which make it possible to create potent adhesives for metal ions. As part of our structure-function studies for halophilic proteins, we succeeded in crystallization of several halophilic proteins using divalent metal ions as additives. Here, we show successful examples of structural determination of three halophilic proteins: two are alkaline phosphatase from sp.593 (HaAP) and -Lactamase from sp.560 (HaBLA) determined to 2.1 and 2.0 resolution, respectively, and the other is nucleoside diphosphate kinase from sp.593 (HaNDK) determined to 2.3 resolution.