Refine your search:     
Report No.
 - 
Search Results: Records 1-18 displayed on this page of 18
  • 1

Presentation/Publication Type

Initialising ...

Refine

Journal/Book Title

Initialising ...

Meeting title

Initialising ...

First Author

Initialising ...

Keyword

Initialising ...

Language

Initialising ...

Publication Year

Initialising ...

Held year of conference

Initialising ...

Save select records

Journal Articles

TRAIL-R2 superoligomerization induced by human monoclonal agonistic antibody KMTR2

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 ${AA}$ 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.

Journal Articles

Nucleoside diphosphate kinase from psychrophilic ${it Pseudoalteromonas}$ sp. AS-131 isolated from Antarctic Ocean

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 ${it Pseudoalteromonas}$ sp. AS-131 (ASNDK) was expressed in ${it Escherichia coli}$ and purified to homogeneity. Comparing to mesophilic NDK isolated from ${it Pseudomonas aeruginosa}$, ASNDK exhibited highly elevated thermolability: (1) ${it E. coli}$ expression at 37$$^{circ}$$C as a denatured insoluble form, and (2) 30$$^{circ}$$C lower optimum temperature of enzymatic activity. The subunit structure of ASNDK was suggested to be dimer, as in NDKs isolated from moderate halophiles.

Journal Articles

Structure of a highly acidic $$beta$$-lactamase from the moderate halophile ${it Chromohalobacter}$ sp.560 and the discovery of a Cs$$^{+}$$-selective binding site

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 $$beta$$-lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr$$^{2+}$$ 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-$$pi$$ 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.

Journal Articles

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium ${it Halomonas}$ sp.593

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 ${it Halomonas}$ sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1${AA}$ 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.

Journal Articles

A Structural mechanism for dimeric to tetrameric oligomer conversion in ${it Halomonas}$ sp. nucleoside diphosphate kinase

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 ${it Halomonas}$ 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.

Journal Articles

Dimer-tetramer assembly of nucleoside diphosphate kinase from moderately halophilic bacterium ${it Chromohalobacter salexigens}$ DSM3043; Both residues 134 and 136 are critical for the tetramer assembly

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 ${it Chromohalobacter salexigens}$ (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.

Journal Articles

Effects of salt concentration on association of the amyloid protofilaments of hen egg white lysozyme studied by time-resolved neutron scattering

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.

Journal Articles

An Insight into the pathway of the amyloid fibril formation of hen egg white lysozyme obtained from a small-angle X-ray and neutron scattering study

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.

Journal Articles

Neutron crystallography of hen egg-white lysozyme at pH4.9

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

Oral presentation

Ologomeric structure of nucleoside diphosphate kinase from Halomonas sp. 593 (HaNDK)

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.

Oral presentation

Oligomeric structure of nucleoside diphosphate kinase from Halomonas sp.593 (HaNDK)

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 ${it Halomonas}$ sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the ${it Myxococcus}$ NDK tetramer and Type II seen in the ${it E.coli}$ 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.

Oral presentation

Oligomeric structure of nucleoside diphosphate kinase from ${it Halomonas}$ sp.593 (HaNDK)

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.

Oral presentation

Structural analysis of troponin mutants causing cardiomyopathy by small-angle X-ray scattering

Fujiwara, Satoru; Yonezawa, Yasushige*; Matsumoto, Fumiko; Oda, Toshiro*; Takeda, Soichi*

no journal, , 

no abstracts in English

Oral presentation

X-ray crystallographic analysis of $$beta$$-Lactamase derived from ${it Chromohalobacter}$ sp.560

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 $$beta$$-Lactamase obtained from ${it Chromohalobacter}$ 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$$^{2+}$$ and Cs$$^{+}$$ binding sites of halophilic $$beta$$-Lactamase from determined crystal structure.

Oral presentation

X-ray crystallographic analysis of $$beta$$-Lactamase derived from ${it Chromohalobacter}$ sp.560

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 $$beta$$-Lactamase (HaBLA) derived from ${it Chromohalobacter}$ sp.560 at 3.0 ${AA}$ 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.

Oral presentation

Cs$$^{+}$$ and Sr$$^{2+}$$ recognition mechanism of halophilic $$beta$$-lactamase

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 $$beta$$-Lactamase (HaBLA) derived from ${it Chromohalobacter}$ sp.560 under the existence of Cs+ and Sr2+. Diffraction data at 2.0 ${AA}$ resolution (space group P31, Unit cell a = b =115.9 ${AA}$, c =67.9 ${AA}$, Rmerge 9.6%) was collected. Three Cs$$^{+}$$ and six Sr$$^{2+}$$ 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$$^{2+}$$ binding site on the protein molecules.

Oral presentation

X-ray crystallographic analysis of Alkaline Phosphatase derived from a moderate halophilic Halomonas sp.593

Arai, Shigeki; Yonezawa, Yasushi*; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

Structural characteristics of Halophilic proteins investigated by X-ray crystallography

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 ${it Halomonas}$ sp.593 (HaAP) and $$beta$$-Lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) determined to 2.1${AA}$ and 2.0${AA}$ resolution, respectively, and the other is nucleoside diphosphate kinase from ${it Halomonas}$ sp.593 (HaNDK) determined to 2.3${AA}$ resolution.

18 (Records 1-18 displayed on this page)
  • 1