178 results on '"Ogata, Hideaki"'
Search Results
152. Crystallization and preliminary X-ray analysis of the small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes.
- Author
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Ogata, Hideaki, Stolle, Patrick, Stehr, Matthias, Auling, Georg, and Lubitz, Wolfgang
- Subjects
- *
RIBONUCLEOSIDE diphosphate reductase , *CORYNEBACTERIUM , *CRYSTALLIZATION , *X-ray imaging , *BIOSYNTHESIS - Abstract
Ribonucleotide reduction, the unique step in DNA-precursor biosynthesis, involves radical-dependent redox chemistry and diverse metallo-cofactors. The metallo-cofactor (R2F) encoded by the nrdF ( nucleotide re duction) gene in Corynebacterium ammoniagenes ATCC 6872 was isolated after homologous expression and a new crystal form of ribonucleotide reductase R2F was obtained. R2F was crystallized at 277 K using the vapour-diffusion method with PEG as the precipitating agent. A data set was collected to 1.36 Å resolution from a single crystal at 100 K using synchrotron radiation. The crystal belonged to space group C2, with unit-cell parameters a = 96.21, b = 87.68, c = 83.25 Å, β = 99.29°. The crystal contained two molecules per asymmetric unit, with a Matthews coefficient ( VM) of 2.69 Å3 Da−1; the solvent content was estimated to be 54.3%. X-ray fluorescence spectroscopy and MAD diffraction data indicated the presence of manganese in the molecule and the absence of iron. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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153. Crystallization and preliminary X-ray analysis of the LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42.
- Author
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Ogata, Hideaki, Cao, Zhen, Losi, Aba, and Gärtner, Wolfgang
- Subjects
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PROTEIN research , *BACILLUS amyloliquefaciens , *CRYSTALLIZATION , *ETHOXYETHANOL , *SYNCHROTRON radiation , *SOLVENTS - Abstract
Light-oxygen-voltage (LOV) proteins play an important role in blue-light-dependent physiological processes in many organisms. The LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42 has been purified and crystallized at 277 K using the sitting-drop vapour-diffusion method with 2-ethoxyethanol as a precipitant. A data set was collected to 1.60 Å resolution from a single crystal at 100 K using synchrotron radiation. The LOV domain of YtvA crystallized in space group C2221, with unit-cell parameters a = 64.95, b = 83.76, c = 55.81 Å. The crystal structure of the LOV domain of YtvA was determined by the molecular-replacement method. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient ( VM) of 3.04 Å3 Da−1; the solvent content was estimated to be 59.5%. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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154. Purification, crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F.
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Ogata, Hideaki, Goenka Agrawal, Aruna, Kaur, Amrit Pal, Goddard, Richard, Gärtner, Wolfgang, and Lubitz, Wolfgang
- Subjects
- *
DESULFOVIBRIO vulgaris , *SULFUR , *OXIDATION , *ENERGY conservation , *CRYSTALS - Abstract
Sulfur in its various oxidation states is used for energy conservation in many microorganisms. Adenylylsulfate reductase is a key enzyme in the sulfur-reduction pathway of sulfate-reducing bacteria. The adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F has been purified and crystallized at 277 K using the vapour-diffusion method with ammonium sulfate as the precipitating agent. A data set was collected to 1.7 Å resolution from a single crystal at 100 K using synchrotron radiation. The crystal belonged to space group P31, with unit-cell parameters a = b = 125.93, c = 164.24 Å. The crystal contained two molecules per asymmetric unit, with a Matthews coefficient ( VM) of 4.02 Å3 Da−1; the solvent content was estimated to be 69.4%. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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155. P53: Nitrite dismutase – A “nitrite-only” source for NO.
- Author
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He, Chunmao and Ogata, Hideaki
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- *
PHYSIOLOGICAL effects of nitrites , *BLOODSUCKING insects , *RHODNIUS prolixus , *HEMOPROTEINS , *ENZYME kinetics , *RESONANCE Raman spectroscopy - Abstract
Background: Nitrophorins (NPs) are NO transporting proteins from the saliva of the blood-sucking insect Rhodnius prolixus. The delivery of NO is accomplished by storage on the protein’s ferriheme cofactor and the gas molecule is released when the protein is injected into a victim’s tissue. However, we demonstrated that nitrophorins can also produce NO from nitrite as the only substrate, i.e., in this reaction nitrite serves as both electron donor and electron acceptor. The enzymatic activity was termed nitrite dismutase activity and is now classified with the EC number 1.7.6.1. This study provides insight into the structural features required for the catalytic activity. Methods: Proteins were recombinantly expressed in Escherichia coli cells. They were characterized by X-ray crystallography, EPR spectroscopy, UV/vis spectroscopy, resonance Raman spectroscopy, and NMR spectroscopy. The enzymatic reaction was studied by absorbance detected stopped-flow kinetics. Results: The binding mode of nitrite to the NP Fe (III) is clearly different compared to that of the globins, i.e., N-bound. Contrary to the globins, the insertion of an H-donating residue (NP4(L130R)) into the protein pocket does not affect the nitrite binding mode; however, it cancels the enzymatic activity. On the other hand, mutation of the proximal Asp70 residue, which is H-bonded via a water to the iron coordinating His59, also affects the enzymatic activity, indicating that the charge distribution on the heme cofactor has a major influence on the iron reactivity. Conclusion: The nitrophorins are good model systems for the characterization of the nitrite dismutase catalysis. The absence of H-donating residues and the charge density on the proximal His were identified as important structural features that are required for the nitrite dismutase reaction. Among the many heme proteins expressed in the human organism some might bear a similar catalytic activity. We suggest the group of heme peroxidases as potential candidates for enzymatic “nitrite-only” NO production. Disclosure: Supported by the Deutsche Forschungsgemeinschaft (DFG), Grants KN 951-1/1 and 2. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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156. Cover Picture: Observation of the FeCN and FeCO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy (Angew. Chem. Int. Ed. 2/2013).
- Author
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Kamali, Saeed, Wang, Hongxin, Mitra, Devrani, Ogata, Hideaki, Lubitz, Wolfgang, Manor, Brian C., Rauchfuss, Thomas B., Byrne, Deborah, Bonnefoy, Violaine, Jenney, Francis E., Adams, Michael W. W., Yoda, Yoshitaka, Alp, Ercan, Zhao, Jiyong, and Cramer, Stephen P.
- Abstract
The active site of [NiFe] hydrogenase is an excellent catalyst for hydrogen conversion with an intriguing ability to recover from exposure to dioxygen. In their Communication on page 724 ff., W. Lubitz, S. P. Cramer, and co‐workers use the synchrotron technique of nuclear resonance vibrational spectroscopy to identify normal modes associated with active‐site FeCN and FeCO motion. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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157. Titelbild: Detektion von Fe-CN- und Fe-CO-Schwingungen im aktiven Zentrum der [NiFe]-Hydrogenase durch inelastische kernresonante Streuung (Angew. Chem. 2/2013).
- Author
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Kamali, Saeed, Wang, Hongxin, Mitra, Devrani, Ogata, Hideaki, Lubitz, Wolfgang, Manor, Brian C., Rauchfuss, Thomas B., Byrne, Deborah, Bonnefoy, Violaine, Jenney, Francis E., Adams, Michael W. W., Yoda, Yoshitaka, Alp, Ercan, Zhao, Jiyong, and Cramer, Stephen P.
- Abstract
Das aktive Zentrum der [NiFe] ‐ Hydrogenase ist ein exzellenter Katalysator der Wasserstoffumsetzung mit der faszinierenden Fähigkeit, sich nach Sauerstoffexposition zurückzubilden. W. Lubitz, S. P. Cramer et al. nutzen in ihrer Zuschrift auf S. 752 ff. die Synchrotrontechnik der kernresonanten inelastischen Streuung, um Normalmoden der Fe ‐ CN ‐ und Fe ‐ CO ‐ Bewegung im aktiven Zentrum zu identifizieren. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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158. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.
- Author
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Hiromoto T, Nishikawa K, Inoue S, Ogata H, Hori Y, Kusaka K, Hirano Y, Kurihara K, Shigeta Y, Tamada T, and Higuchi Y
- Abstract
[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O
2 -sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2 , as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)- Published
- 2023
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159. Comparison between a new assay system, Elecsys ® Anti-p53, and conventional MESACUP™ for the detection of serum anti-p53 antibodies: A multi-institutional study.
- Author
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Suzuki T, Oshima Y, Shiratori F, Nanami T, Yajima S, Sumazaki M, Ushigome M, Sugita H, Eberl M, Ogata H, Hayashida T, Nakamura S, Nakagawa T, and Shimada H
- Abstract
The sensitivity and specificity of a new automated electrochemiluminescence immunoassay system, Elecsys
® Anti-p53 (Elecsys), were compared with that of the conventional serum anti-p53 antibody (s-p53-Ab) enzyme-linked immunosorbent assay kit [MESACUP anti-p53 test (MESACUP)]. Elecsys and MESACUP were used to analyze the levels of s-p53-Abs in patients with esophageal, colorectal and breast cancer. A total of 532 controls and 288, 235 and 329 patients with esophageal, colorectal and breast cancer, respectively, were enrolled. Additionally, the sera of patients with benign diseases of the esophagus, colorectal system and breast, patients with autoimmune diseases and healthy volunteers were analyzed as controls. Sensitivity and specificity were compared between the two assay systems. Positive agreement rates were 58.7% in all samples, 71.2% in esophageal samples, 73.6% in colorectal samples and 35.1% in breast samples. Negative agreement rates for the different cancer types were ≥97.1% and the overall agreement rates were ≥92.3%. When the specificities of the two assays were aligned for all samples, Elecsys demonstrated higher sensitivities for all types of analyzed cancer together, as well as for esophageal, colorectal and breast cancer, respectively. Although positive concordance between the two assay systems was low in terms of specificity, Elecsys had a higher sensitivity than the MESACUP., Competing Interests: HSh received research funding from Ono Pharmaceutical, Taiho Pharmaceutical and Roche Diagnostics K.K. HSu was an employee of Roche Diagnostics K.K. ME is an employee of Roche Diagnostics GmbH. The Elecsys assay system is manufactured by Roche Diagnostics K. K., (Copyright: © Suzuki et al.)- Published
- 2022
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160. Structural Studies of Matrix Metalloproteinase by X-Ray Diffraction.
- Author
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Decaneto E, Lubitz W, and Ogata H
- Subjects
- Catalytic Domain, Crystallography, X-Ray, Escherichia coli genetics, Escherichia coli growth & development, Models, Molecular, Protein Conformation, Protein Engineering, Protein Refolding, Recombinant Fusion Proteins chemistry, Recombinant Fusion Proteins genetics, Matrix Metalloproteinase 14 chemistry, Matrix Metalloproteinase 14 genetics
- Abstract
Matrix Metalloproteinases (MMPs) are a family of proteolytic enzymes whose endopeptidase activity is dependent on the presence of specific metal ions. MT1-MMP (or MMP-14), which has been implicated in tumor progression and cellular invasion, contains a membrane-spanning region located C-terminal to a hemopexin-like domain and an N-terminal catalytic domain. We recombinantly expressed the catalytic domain of human MT1-MMP in E. coli and purified it from inclusion bodies using a refolding protocol that yielded significant quantities of active protein. Crystals of MT1-MMP were obtained using the vapour diffusion method. Here, we describe the protocols used for crystallization and the data analysis together with the resulting diffraction pattern.
- Published
- 2017
- Full Text
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161. Protein crystallography using free-electron lasers: water oxidation in photosynthesis.
- Author
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Ogata H and Lubitz W
- Subjects
- Electrons, Oxidation-Reduction, Photosynthesis, Water, Crystallography methods, Lasers
- Published
- 2014
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162. Phase II clinical trial of high-dose toremifene as primary hormone therapy in aromatase inhibitor-resistant breast cancer.
- Author
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Ogata H, Okamoto Y, Arima Y, Fukushima H, Takeyama H, Yamashita A, Kinoshita M, Suzuki N, Sawada T, Koshida Y, Matsui A, Tachibana A, Nakayama H, Oishi Y, Nogi H, and Uchida K
- Subjects
- Aged, Aged, 80 and over, Antineoplastic Agents, Hormonal administration & dosage, Antineoplastic Agents, Hormonal adverse effects, Aromatase Inhibitors administration & dosage, Aromatase Inhibitors adverse effects, Female, Humans, Middle Aged, Toremifene administration & dosage, Toremifene adverse effects, Antineoplastic Agents, Hormonal therapeutic use, Aromatase Inhibitors therapeutic use, Breast Neoplasms drug therapy, Drug Resistance, Neoplasm, Toremifene therapeutic use
- Abstract
Background: Third-generation aromatase inhibitors(AIs)are now common in adjuvant hormone therapy for breast cancer in postmenopausal women. However, a suitable treatment has yet to be established for patients who develop cancer recurrence during or after adjuvant AI therapy., Patients and Methods: This prospective study evaluated the efficacy and safety of 120mg/day toremifene citrate(TOR-120)administered orally to 23 patients with recurrent breast cancer who were receiving or had received adjuvant AI therapy. Primary therapy for recurrence was TOR-120 monotherapy., Results: The response rate was 13. 0%(partial response: three patients), the clinical benefit rate was 78. 3%(partial response: three patients; long-term stable disease: 15 patients), and median time to progression was 8. 1 months. Grade 1 adverse events such as loss of appetite, sweating, flushing and edema face were observed., Conclusion: TOR-120 monotherapy was effective and safe as a primary hormone therapy for recurrent breast cancer unresponsive to AIs.
- Published
- 2013
163. Complexes of ferriheme nitrophorin 4 with low-molecular weight thiol(ate)s occurring in blood plasma.
- Author
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He C, Nishikawa K, Erdem ÖF, Reijerse E, Ogata H, Lubitz W, and Knipp M
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- Animals, Hemeproteins chemistry, Molecular Structure, Molecular Weight, Rhodnius chemistry, Salivary Proteins and Peptides chemistry, X-Ray Absorption Spectroscopy, Hemin chemistry, Salivary Proteins and Peptides blood, Sulfhydryl Compounds chemistry
- Abstract
Nitrophorins are proteins occurring in the saliva of the blood-sucking insect Rhodnius prolixus to carry NO as a vasodilator and blood-coagulation inhibitor into the victim's tissue. It was suggested that the rate of NO release can be enhanced by the blood-plasma component L-cysteine [J.M.C.Ribeiro, Insect Biochem. Mol. Biol. 26 (1996) 899-905]. However, the mechanism of the reaction is not clear. In the attempt to exploit the reaction in detail, complexes of nitrophorin 4 (NP4) with the thiols 2-mercaptoethanol, L-cysteine, and L-homocysteine and with HS(-) were formed and characterized under anaerobic conditions using absorption spectroscopy, X-ray crystallography, and EPR spectroscopy. In contrast to met-myoglobin, which is reduced by L-cysteine, all four compounds form low-spin Fe(III) complexes with NP4. The weak equilibration constants (167-5200 M(-1)) neither support significant complexation nor the simple displacement of NO in vivo. Both amino acid based thiols form additional H-bonds with side chains of the heme pocket entry. Glutathione and L-methionine did not form a complex, indicating the specificity of the complexes with L-cysteine and L-homocysteine. Continuous wave EPR spectroscopy reveals the simultaneous existence of three low-spin systems in each case that are attributed to various protonation and/or conformational stages in the heme pocket. Electron nuclear double resonance (ENDOR) spectroscopy demonstrates that the thiol sulfurs are, at least in part, protonated. Overall, the results not only demonstrate the good accessibility of the NP4 heme center by biologically relevant thiols, but also represent the first structural characterization of a ferriheme protein in complex with L-cysteine L-homocysteine., (Copyright © 2013 Elsevier Inc. All rights reserved.)
- Published
- 2013
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164. Observation of the Fe-CN and Fe-CO vibrations in the active site of [NiFe] hydrogenase by nuclear resonance vibrational spectroscopy.
- Author
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Kamali S, Wang H, Mitra D, Ogata H, Lubitz W, Manor BC, Rauchfuss TB, Byrne D, Bonnefoy V, Jenney FE Jr, Adams MW, Yoda Y, Alp E, Zhao J, and Cramer SP
- Subjects
- Catalytic Domain, Electron Spin Resonance Spectroscopy, Hydrogenase metabolism, Iron Compounds chemistry, Models, Molecular, Oxidation-Reduction, Spectroscopy, Fourier Transform Infrared, Vibration, Hydrogenase chemistry
- Abstract
Nuclear inelastic scattering of (57)Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe-CO and Fe-CN bending and stretching vibrations of the active site outside the spectral range of the Fe-S cluster normal modes., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2013
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165. Insertion of an H-bonding residue into the distal pocket of the ferriheme protein nitrophorin 4: effect on nitrite-iron coordination and nitrite disproportionation.
- Author
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He C, Ogata H, and Knipp M
- Subjects
- Binding Sites, Crystallography, X-Ray, Hemeproteins genetics, Hemeproteins metabolism, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Models, Molecular, Mutation, Salivary Proteins and Peptides genetics, Salivary Proteins and Peptides metabolism, Hemeproteins chemistry, Hemin chemistry, Iron chemistry, Nitrites chemistry, Salivary Proteins and Peptides chemistry
- Abstract
Heme proteins are important entities for the metabolism of nitrite. Inspection of the structural features of the reported hemoprotein-nitrite crystal structures reveals that, except for nitrophorin 4 (NP4), H-bonding to the nitrite ligand is accomplished via histidine or arginine residues. These H-bonds probably play an important role for the nitrite coordination and/or reactivities. In nitrophorins, which catalyze the nitrite disproportionation reaction, such a residue is missing. Here, we report on the L130R mutant of the NP isoprotein NP4 that provides the Arg130 residue as part of the flexible G-H loop as a potential H-bonding residue in the distal heme pocket. Similar to the wild-type protein, nitrite remains N-bonded in the crystal structure of NP4(L130R). However, spectroscopic investigations show that, in solution, a second ligand-rotational orientation exists, which is in fast-exchange equilibrium with the normal, parallel ligand orientation. Moreover, the nitrite disproportionation is inhibited in NP4(L130R). Comparison with another, also less active mutant NP4(D30N) suggests that the displacement of H(2)O molecules from the heme cavity prevents the proton donation pathway through Asp30., (Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.)
- Published
- 2012
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166. Guanidine-ferroheme coordination in the mutant protein nitrophorin 4(L130R).
- Author
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He C, Fuchs MR, Ogata H, and Knipp M
- Subjects
- Organometallic Compounds chemistry, Water chemistry, Guanidine chemistry, Heme chemistry, Hemeproteins chemistry, Mutant Proteins chemistry, Salivary Proteins and Peptides chemistry
- Published
- 2012
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167. [Remarkable improvement in a patient with metastatic and locally advanced HER2-positive breast cancer treated with trastuzumab plus vinorelbine].
- Author
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Kanazawa S, Ogata H, Magoshi S, Saito F, Ito T, Kubota Y, and Kaneko H
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- Adult, Antibodies, Monoclonal, Humanized administration & dosage, Breast Neoplasms metabolism, Breast Neoplasms pathology, Fatal Outcome, Female, Humans, Neoplasm Metastasis, Receptor, ErbB-2 metabolism, Tomography, X-Ray Computed, Trastuzumab, Vinblastine administration & dosage, Vinblastine analogs & derivatives, Vinorelbine, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Breast Neoplasms drug therapy
- Abstract
A 39-year-old premenopausal nulliparous woman presented with severe pain in her right breast, bleeding and pus-like discharge, and a deep ulcer approximately 18 cm in diameter.Contralateral breast metastasis, bilateral axillary lymph node metastases, and multiple lung and bone metastases were detected on computed tomography.Five years previously she had undergone surgery for ovarian cancer and had prematurely discontinued adjuvant chemotherapy because of side effects. Following the administration of pain control, the patient received trastuzumab(Tr)plus vinorelbine(VNR)for her breast cancer as first-line therapy to avoid hair loss.The ulcer on her right chest wall underwent complete epithelialization and the patient's performance status improved from 3 to 0.The pus-like discharge, pain, bleeding, and odor from the breast resolved completely, and 5 months later, her quality of life had improved.The lung metastases also resolved completely.No adverse affects, including hematotoxicity and hair loss, were seen until treatment failure 12.5 months later. Second-line and third-line treatments were performed, but brain metastases developed, and the patient's overall condition deteriorated because of the development of ileus of unknown etiology.She died 21 months later.The patient received all therapies on an outpatient basis. Combination therapy using Tr and VNR is superior in safety and tolerability, and has been considered an option for first-line treatment of metastatic, locally advanced HER2-positive breast cancer.
- Published
- 2012
168. Crystallization and preliminary X-ray crystallographic analysis of the membrane-binding haemprotein nitrophorin 7 from Rhodnius prolixus.
- Author
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Ogata H and Knipp M
- Subjects
- Animals, Crystallization, Crystallography, X-Ray, Models, Molecular, Protein Structure, Tertiary, Hemeproteins chemistry, Rhodnius chemistry, Salivary Proteins and Peptides chemistry
- Abstract
Nitrophorins (nitric oxide transport proteins) are haemproteins originating from the blood-feeding insect Rhodnius prolixus. They consist of an eight-stranded β-barrel, which classifies them into the lipocalin family. Nitrophorin 7 (NP7) and the E27V mutant protein NP7(E27V) were crystallized at 277 K using the vapour-diffusion method with PEG as the precipitating agent. Data sets for wild-type NP7 and NP7(E27V) were collected to 1.80 Å resolution from single crystals at 100 K using synchrotron radiation. The crystals belonged to space group P2(1), with unit-cell parameters a = 38, b = 67, c = 39 Å, β = 117°. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (V(M)) of 2.11 Å(3) Da(-1); the solvent content was estimated to be 41.8%., (© 2012 International Union of Crystallography. All rights reserved.)
- Published
- 2012
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169. A tyrosyl-dimanganese coupled spin system is the native metalloradical cofactor of the R2F subunit of the ribonucleotide reductase of Corynebacterium ammoniagenes.
- Author
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Cox N, Ogata H, Stolle P, Reijerse E, Auling G, and Lubitz W
- Subjects
- Crystallography, X-Ray, Dimerization, Electron Spin Resonance Spectroscopy, Freezing, Models, Molecular, Protein Structure, Secondary, Temperature, Coenzymes chemistry, Corynebacterium enzymology, Manganese chemistry, Protein Subunits chemistry, Ribonucleotide Reductases chemistry, Tyrosine chemistry
- Abstract
The X-ray crystallographic structure of the native R2F subunit of the ribonucleotide reductase (RNR) of Corynebacterium ammoniagenes ATCC 6872 is reported, with a resolution of 1.36 A. The metal site contains an oxo/hydroxo-bridged manganese dimer, located near a tyrosine residue (Y115). The coordination of the manganese dimer and its distance to a nearby tyrosine residue resemble the di-iron metalloradical cofactor of class I RNR from Escherichia coli . Multifrequency EPR measurements of the highly active C. ammoniagenes R2F subunit show that the metal site contains a ferromagnetically exchange-coupled Mn(III)Mn(III) dimer weakly coupled to a tyrosyl radical. A mechanism for the metalloradical cofactor (Mn(III)Mn(III)Y(*)) generation is proposed. H(2)O(2) (HO(2)(-)) instead of O(2) is hypothesized as physiological oxidant for the Mn dimer which in turn oxidizes the tyrosine Y115. Changes in the ligand sphere of both manganese ions during metalloradical generation direct the complex formation of this cofactor, disfavoring alternate reaction pathways such as H(2)O(2) dismutation, as observed for manganese catalase, a structural analogue of the R2F metal site. The presented results demonstrate the importance of manganese for radical formation in this RNR and confirm the assignment of this enzyme to class Ib.
- Published
- 2010
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170. Formation of the complex of nitrite with the ferriheme b beta-barrel proteins nitrophorin 4 and nitrophorin 7.
- Author
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He C, Ogata H, and Knipp M
- Subjects
- Animals, Crystallography, X-Ray, Electron Spin Resonance Spectroscopy, Heme chemistry, Heme metabolism, Hemeproteins, Hemin metabolism, Kinetics, Ligands, Methemoglobin metabolism, Metmyoglobin metabolism, Rhodnius chemistry, Rhodnius metabolism, Salivary Proteins and Peptides, Hemin chemistry, Nitrites metabolism
- Abstract
The interaction of ferriheme proteins with nitrite has recently attracted interest as a source for NO or other nitrogen oxides in mammalian physiology. However, met-hemoglobin (metHb), which was suggested as a key player in this process, does not convert nitrite unless small amounts of NO are added in parallel. We have recently reported that, in contrast, nitrophorins (NPs) convert nitrite as the sole substrate to form NO even at pH 7.5, which is an unprecedented case among ferrihemes [He, C., and Knipp, M. (2009) J. Am. Chem. Soc. 131, 12042-12043]. NPs, which comprise a class of unique heme b proteins from the saliva of the blood-sucking insect Rhodnius prolixus, appear in a number of concomitant isoproteins. Herein, the first spectroscopic characterization of the initial complexes of the two isoproteins NP4 and NP7 with nitrite is presented and compared to the data reported for metHb and met-myoglobin (metMb). Because upon nitrite binding, NPs, in contrast to metHb and metMb, continue to react with nitrite, resonance Raman spectroscopy and continuous wave electron paramagnetic resonance spectroscopy were applied to frozen samples. As a result, the existence of two six-coordinate ferriheme low-spin complexes was established. Furthermore, X-ray crystallography of NP4 crystals soaked with nitrite revealed the formation of an eta(1)-N nitro complex, which is in contrast to the eta(1)-O-bound nitrite in metMb and metHb. Stopped-flow kinetic experiments show that although the ligand dissociation constants of NP4 and NP7 (15-190 M(-1)) are comparable to those of metHb and metMb, the rates of ligand binding and release are significantly slower. Moreover, not only the reaction kinetics but also electron paramagnetic resonance spectroscopy reveals notable differences between the two isoproteins.
- Published
- 2010
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171. Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity.
- Author
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Pandelia ME, Ogata H, Currell LJ, Flores M, and Lubitz W
- Subjects
- Bacterial Proteins chemistry, Carbon Monoxide metabolism, Enzyme Activation, Hydrogen Bonding, Hydrogenase chemistry, Isotopes metabolism, Models, Molecular, Oxidation-Reduction, Protein Conformation, Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared, Bacterial Proteins metabolism, Desulfovibrio vulgaris enzymology, Hydrogenase metabolism, Light, Nickel metabolism
- Abstract
The [NiFe] hydrogenase from the sulphate-reducing bacterium Desulfovibrio vulgaris Miyazaki F is reversibly inhibited in the presence of molecular oxygen. A key intermediate in the reactivation process, Ni-SI(r), provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SI(a), Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SI(r) was found to be light-sensitive (T
- Published
- 2009
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172. Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum.
- Author
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Kellers P, Ogata H, and Lubitz W
- Subjects
- Chromatography, Gel, Crystallization, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Hydrogenase isolation & purification, Protein Conformation, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Hydrogenase chemistry, Proteobacteria enzymology
- Abstract
The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 A. X-ray diffraction data have been collected to 2.5 A resolution.
- Published
- 2008
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173. Periostin and bone marrow fibrosis.
- Author
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Oku E, Kanaji T, Takata Y, Oshima K, Seki R, Morishige S, Imamura R, Ohtsubo K, Hashiguchi M, Osaki K, Yakushiji K, Yoshimoto K, Ogata H, Hamada H, Izuhara K, Sata M, and Okamura T
- Subjects
- Aged, Bone Marrow pathology, Cell Proliferation, Female, Humans, Male, Megakaryocytes metabolism, Megakaryocytes pathology, Middle Aged, Monocytes metabolism, Monocytes pathology, Primary Myelofibrosis pathology, Stromal Cells metabolism, Stromal Cells pathology, Transforming Growth Factor beta biosynthesis, Bone Marrow metabolism, Cell Adhesion Molecules biosynthesis, Primary Myelofibrosis metabolism
- Abstract
Periostin is a secreted protein that shares structural homology with the insect axon guidance protein fasciclin 1. Periostin is expressed predominantly in collagen-rich fibrous connective tissues that are subjected to constant mechanical stresses. We have shown previously that periostin is a novel component of subepithelial fibrosis in bronchial asthma. Here, we investigated the relationship between periostin and bone marrow (BM) fibrosis. Periostin was expressed in the stroma and stromal cells of BM fibrosis specimens and to a great extent its expression levels correlated closely to the grade of fibrosis, as estimated by silver staining. However, in the present study, we found no relationship between plasma periostin levels and the extent of BM fibrosis. We also demonstrated that periostin is secreted by human BM hTERT stromal cells and that its secretion is enhanced by TGF-beta, a cytokine produced by clonal proliferation of megakaryocytes and/or monocytes. These results indicate that periostin is a component of BM fibrosis and that it may play a role in the disease progression.
- Published
- 2008
- Full Text
- View/download PDF
174. Roles of charged residues in pH-dependent redox properties of cytochrome c 3 from Desulfovibrio vulgaris Miyazaki F.
- Author
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Yahata N, Ozawa K, Tomimoto Y, Morita K, Komori H, Ogata H, Higuchi Y, and Akutsu H
- Abstract
Complicated pH-properties of the tetraheme cytochrome c
3 (cyt c3 ) from Desulfovibrio vulgaris Miyazaki F ( Dv MF) were examined by the pH titrations of1 H-15 N HSQC spectra in the ferric and ferrous states. The redox-linked p Ka shift for the propionate group at C13 of heme 1 was observed as the changes of the NH signals around it. This p Ka shift is consistent with the redox-linked conformational alteration responsible for the cooperative reduction between hemes 1 and 2. On the other hand, large chemical shift changes caused by the protonation/deprotonation of Glu41 and/or Asp42, and His67 were redox-independent. Nevertheless, these charged residues affect the redox properties of the four hemes. Furthermore, one of interesting charged residues, Glu41, was studied by site-directed mutagenesis. E41K mutation increased the microscopic redox potentials of heme 1 by 46 and 34 mV, and heme 2 by 35 and 30 mV at the first and last reduction steps, respectively. Although global folding in the crystal structure of E41K cyt c3 is similar to that of wild type, local change was observed in1 H NMR spectrum. Glu41 is important to keep the stable conformation in the region between hemes 1 and 2, controlling the redox properties of Dv MF cyt c3 . In contrast, the kinetic parameters for electron transfer from Dv MF [NiFe] hydrogenase were not influenced by E41K mutation. This suggests that the region between hemes 1 and 2 is not involved in the interaction with [NiFe] hydrogenase, and it supports the idea that heme 4 is the exclusive entrance gate to accept the electron in the initial reduction stage.- Published
- 2006
- Full Text
- View/download PDF
175. A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
- Author
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van Gastel M, Stein M, Brecht M, Schröder O, Lendzian F, Bittl R, Ogata H, Higuchi Y, and Lubitz W
- Subjects
- Binding Sites, Crystallization, Cysteine chemistry, Electron Spin Resonance Spectroscopy methods, Hydrogenase metabolism, Ligands, Oxidation-Reduction, Protein Conformation, Protons, Sulfur chemistry, Desulfovibrio vulgaris enzymology, Hydrogenase chemistry
- Abstract
The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme.
- Published
- 2006
- Full Text
- View/download PDF
176. Blastoid variant of mantle cell lymphoma with lactic acidosis: a case report.
- Author
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Ohtsubo K, Imamura R, Seki R, Ohshima K, Hashiguchi M, Yakushiji K, Yoshimoto K, Ogata H, Okamura T, and Sata M
- Subjects
- Acidosis, Lactic etiology, Aged, Antibodies, Monoclonal therapeutic use, Antibodies, Monoclonal, Murine-Derived, Antigens, CD blood, Antineoplastic Agents therapeutic use, Bone Marrow pathology, Drug Therapy, Combination, Humans, Lymphatic Diseases etiology, Lymphatic Diseases pathology, Lymphoma, Mantle-Cell blood, Lymphoma, Mantle-Cell complications, Lymphoma, Mantle-Cell diagnostic imaging, Lymphoma, Mantle-Cell drug therapy, Male, Radiography, Rituximab, Splenomegaly diagnostic imaging, Splenomegaly etiology, Splenomegaly pathology, Acidosis, Lactic pathology, Lymphoma, Mantle-Cell pathology
- Abstract
Approximately 20% of mantle cell lymphomas (MCL) present with the blastoid variant associated with poor prognosis. Lactic acidosis complicated with hematologic malignancies is seen infrequently and is associated with a poor outcome. Here we report the case of a patient with the blastoid variant of MCL complicated by lactic acidosis and who achieved complete remission through chemotherapy combined with rituximab therapy. A 77-year-old man presented with peripheral blood lymphoma cells, huge splenomegaly, abdominal and mediastinal lymphadenopathy, and pleural effusion. A bone marrow smear showed an increase in large, abnormal lymphoid cells with oval or round nuclei, distinct nucleoli, and abundant basophilic cytoplasm with vacuolization. Splenic sections also showed massive and diffuse infiltration by these cells. Flow cytometry analysis showed these cells to be positive for CD5, CD19, CD20, and kappa chain and negative for CD10 and CD23. A blastoid variant of MCL was diagnosed from the results of histologic, immunohistochemical (cyclin D1), and cytogenetic (chimeric bcl-1/IgH fusion gene) analyses. The patient recovered from the 2 episodes of severe lactic acidosis for which he had been given chemotherapy, and he achieved complete remission after subsequent chemotherapy combined with rituximab treatment.
- Published
- 2004
- Full Text
- View/download PDF
177. Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
- Author
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Foerster S, Stein M, Brecht M, Ogata H, Higuchi Y, and Lubitz W
- Subjects
- Bacterial Proteins chemistry, Bacterial Proteins metabolism, Binding Sites, Electron Spin Resonance Spectroscopy, Hydrogenase metabolism, Models, Chemical, Models, Molecular, Oxidation-Reduction, Protein Conformation, Desulfovibrio vulgaris enzymology, Hydrogenase chemistry
- Abstract
In the catalytic cycle of [NiFe] hydrogenase the paramagnetic Ni-C intermediate is of key importance, since it is believed to carry the substrate hydrogen, albeit in a yet unknown geometry. Upon illumination at low temperatures, Ni-C is converted to the so-called Ni-L state with markedly different spectroscopic parameters. It is suspected that Ni-L has lost the "substrate hydrogen". In this work, both paramagnetic states have been generated in single crystals obtained from the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. Evaluation of the orientation dependent spectra yielded the magnitudes of the g tensors and their orientations in the crystal axes system for both Ni-C and Ni-L. The g tensors could further be related to the atomic structure by comparison with the X-ray crystallographic structure of the reduced enzyme. Although the g tensor magnitudes of Ni-C and Ni-L are quite different, the orientations of the resulting g tensors are very similar but differ from those obtained earlier for Ni-A and Ni-B (Trofanchuk et al. J. Biol. Inorg. Chem. 2000, 5, 36-44). The g tensors were also calculated by density functional theory (DFT) methods using various structural models of the active site. The calculated g tensor of Ni-C is, concerning magnitudes and orientation, in good agreement with the experimental one for a formal Ni(III) oxidation state with a hydride (H(-)) bridge between the Ni and the Fe atom. Satisfying agreement is obtained for the Ni-L state when a formal Ni(I) oxidation state is assumed for this species with a proton (H(+)) removed from the bridge between the nickel and the iron atom.
- Published
- 2003
- Full Text
- View/download PDF
178. [A 5'-DFUR + CPA + THP therapy that was effective for paclitaxel-refractory pulmonary metastasis of breast cancer--a case report].
- Author
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Kitahara S, Ogata H, Katagiri T, Nonaka K, and Shiba T
- Subjects
- Adult, Antineoplastic Agents, Phytogenic pharmacology, Cyclophosphamide administration & dosage, Doxorubicin administration & dosage, Doxorubicin analogs & derivatives, Drug Administration Schedule, Drug Resistance, Neoplasm, Female, Floxuridine administration & dosage, Humans, Paclitaxel pharmacology, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Breast Neoplasms drug therapy, Breast Neoplasms pathology, Lung Neoplasms drug therapy, Lung Neoplasms secondary
- Abstract
What should be the standard treatment for taxane-refractory metastatic breast cancer remains controversial. In this paper, a case in which the 5'-DFUR + CPA + THP therapy was effective for paclitaxel-refractory metastatic breast cancer is reported. A 41-year-old female received pectoral muscle preserved mastectomy under diagnosis of the left breast cancer in May 1996. In June, 1999, a coin lesion of 2.2 cm diameter was found in the left middle lung field with chest X-ray. Paclitaxel 210 mg/m2 (once for three weeks, 8 cycles in total) resulted in marked improvement. The regimen of paclitaxel 70 mg/m2 (medication consecutive once-weekly for three weeks, and withdrawal for next week; 1 cycle) was carried out continuously with the patient ambulatory. Because resistance to the treatment appeared at the time the total dose reached 2,700 mg, 5'-DFUR + CPA + THP therapy (THP 30 mg/m2 (i.v.) x day 1, CPA 77 mg/m2 (p.o.) x 14 days, 5'-DFUR 460 mg/m2 (p.o.) x 14 days; 3 weeks with 1 cycle) was carried out, and definite improvement in the lung findings were observed. 5'-DFUR + CPA + THP therapy may be of use as a second-line therapy in paclitaxel-refractory recurrent breast cancer.
- Published
- 2002
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