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Research Output 1991 2019

2019
1 Citation (Scopus)

Evidence for detection of rat P2X4 receptor expressed on cells by generating monoclonal antibodies recognizing the native structure

Igawa, T., Kishikawa, S., Abe, Y., Yamashita, T., Nagai, S., Shiroishi, M., Shinozaki, C., Tanaka, H., Saitoh, H., Makoto, T., Inoue, K. & Ueda, T., Jan 1 2019, (Accepted/In press) In : Purinergic Signalling.

Research output: Contribution to journalArticle

Purinergic P2X4 Receptors
Monoclonal Antibodies
Antibodies
Purinergic P2X Receptors
Head

Evidence for detection of rat P2X4 receptor expressed on cells by generating monoclonal antibodies recognizing the native structure

Igawa, T., Kishikawa, S., Abe, Y., Yamashita, T., Nagai, S., Shiroishi, M., Shinozaki, C., Tanaka, H., Tozaki-Saitoh, H., Tsuda, M., Inoue, K. & Ueda, T., Jan 25 2019, In : Purinergic Signalling.

Research output: Contribution to journalArticle

Purinergic P2X4 Receptors
Monoclonal Antibodies
Antibodies
Purinergic P2X Receptors
Head
1 Citation (Scopus)
Bacterial DNA
Single-Stranded DNA
DNA Replication
Dimers
Escherichia coli
9 Citations (Scopus)

Selective and reversible modification of kinase cysteines with chlorofluoroacetamides

Shindo, N., Fuchida, H., Sato, M., Watari, K., Shibata, T., Kuwata, K., Miura, C., Okamoto, K., Hatsuyama, Y., Tokunaga, K., Sakamoto, S., Morimoto, S., Abe, Y., Shiroishi, M., Caaveiro, J. M. M., Ueda, T., Tamura, T., Matsunaga, N., Nakao, T., Koyanagi, S. & 5 others, Ohdo, S., Yamaguchi, Y., Hamachi, I., Ono, M. & Ojida, A., Jan 14 2019, In : Nature Chemical Biology.

Research output: Contribution to journalArticle

Quinazolines
Epidermal Growth Factor Receptor
Cysteine
Phosphotransferases
Hydrolysis
2018

Crystallization of Human Erythrocyte Band 3, the anion exchanger, at the International Space Station “KIBO”

Hatae, H., Inaka, K., Okamura, R., Furubayashi, N., Kamo, M., Kobayashi, T., Abe, Y., Iwata, S. & Hamasaki, N., Oct 15 2018, In : Analytical Biochemistry. 559, p. 91-93 3 p.

Research output: Contribution to journalArticle

Chloride-Bicarbonate Antiporters
Space stations
Crystallization
Blood
Erythrocytes
Amyloid
Light
Amyloidosis
epigallocatechin gallate
Oxidation
2 Citations (Scopus)

Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody

Miyanabe, K., Yamashita, T., Abe, Y., Akiba, H., Takamatsu, Y., Nakakido, M., Hamakubo, T., Ueda, T., Martinez Caaveiro, J. M. & Tsumoto, K., Jul 17 2018, In : Biochemistry. 57, 28, p. 4177-4185 9 p.

Research output: Contribution to journalArticle

Antibody Affinity
Tyrosine
Peptides
Antibodies
Proteins
2017
2 Citations (Scopus)

The structure of an archaeal β-glucosaminidase provides insight into glycoside hydrolase evolution

Mine, S., Watanabe, M., Kamachi, S., Abe, Y. & Ueda, T., Mar 24 2017, In : Journal of Biological Chemistry. 292, 12, p. 4996-5006 11 p.

Research output: Contribution to journalArticle

Hexosaminidases
Glycoside Hydrolases
Galactosidases
Glucosamine
Catalytic Domain

X-ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation

Abe, Y., Shioi, S., Kita, S., Nakata, H., Maenaka, K., Kohda, D., Katayama, T. & Ueda, T., Nov 2017, In : FEBS Letters. 591, 22, p. 3805-3816 12 p.

Research output: Contribution to journalLetter

Crystal structure
X-Rays
X rays
Heat-Shock Proteins
Proteins

リゾチームの触媒機構:無脊椎動物型とニワトリ型の比較から

Translated title of the contribution: Catalytic Mechanism of Lysozyme Based on the Structures of Invertebrate-type Lysozyme and Chicken-type Lysozyme阿部義人, 2017, In : 生物物理. 57, 3, p. 140-143 4 p.

Research output: Contribution to journalArticle

Muramidase
Acetylglucosamine
Oligomers
Invertebrates
Hydrolysis
2016
3 Citations (Scopus)

Effect on catalysis by replacement of catalytic residue from hen egg white lysozyme to Venerupis philippinarum lysozyme*

Abe, Y., Kubota, M., Takazaki, S., Ito, Y., Yamamoto, H., Kang, D., Ueda, T. & Imoto, T., Sep 1 2016, In : Protein Science. p. 1637-1647 11 p.

Research output: Contribution to journalArticle

Egg White
Muramidase
Catalysis
Acetylglucosamine
Decomposition
2015
7 Citations (Scopus)

Basic and aromatic residues in the C-terminal domain of PriC are involved in ssDNA and SSB binding

Aramaki, T., Abe, Y., Furutani, K., Katayama, T. & Ueda, T., Jan 1 2015, In : Journal of Biochemistry. 157, 6, p. 529-537 9 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
DNA-Binding Proteins
Protein Binding
Basic Amino Acids
Aromatic Amino Acids
82 Citations (Scopus)

Crystal structure of the anion exchanger domain of human erythrocyte band 3

Arakawa, T., Kobayashi-Yurugi, T., Alguel, Y., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Ikeda-Suno, C., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A. D., Kobayashi, T., Hamasaki, N. & Iwata, S., Nov 6 2015, In : Science. 350, 6261, p. 680-684 5 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Anions
Erythrocytes
Congenital Hemolytic Anemia
Chloride-Bicarbonate Antiporters
3 Citations (Scopus)

Functional analysis of CedA based on its structure: Residues important in binding of DNA and RNA polymerase and in the cell division regulation

Abe, Y., Fujisaki, N., Miyoshi, T., Watanabe, N., Katayama, T. & Ueda, T., May 13 2015, In : Journal of biochemistry. 159, 2, p. 217-223 7 p.

Research output: Contribution to journalArticle

Functional analysis
DNA-Directed DNA Polymerase
DNA-Directed RNA Polymerases
Cell Division
Cells

Helicase and its interacting factors: Regulation mechanism, characterization, structure, and application for drug design

Huang, C. Y., Abe, Y., Ding, H. & Chung, I. F., Jan 1 2015, In : BioMed Research International. 2015, 909047.

Research output: Contribution to journalEditorial

3 Citations (Scopus)

Role of the osmolyte taurine on the folding of a model protein, hen egg white lysozyme, under a crowding condition

Abe, Y., Ohkuri, T., Yoshitomi, S., Murakami, S. & Ueda, T., May 1 2015, In : Amino Acids. 47, 5, p. 909-915 7 p.

Research output: Contribution to journalArticle

Taurine
Muramidase
Proteins
Protein Folding
Alanine
8 Citations (Scopus)

Solution structure of the rat P2X4 receptor head domain involved in inhibitory metal binding

Igawa, T., Abe, Y., Makoto, T., Inoue, K. & Ueda, T., Mar 12 2015, In : FEBS Letters. 589, 6, p. 680-686 7 p.

Research output: Contribution to journalArticle

Purinergic P2X4 Receptors
Rats
Metals
Head
Cations
2014
5 Citations (Scopus)

Denatured mammalian protein mixtures exhibit unusually high solubility in nucleic acid-free pure water

Futami, J., Fujiyama, H., Kinoshita, R., Nonomura, H., Honjo, T., Tada, H., Matsushita, H., Abe, Y. & Kakimi, K., Nov 18 2014, In : PloS one. 9, 11, e113295.

Research output: Contribution to journalArticle

Solubility
Nucleic Acids
nucleic acids
solubility
Water
13 Citations (Scopus)

Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase

Mine, S., Niiyama, M., Hashimoto, W., Ikegami, T., Koma, D., Ohmoto, T., Fukuda, Y., Inoue, T., Abe, Y., Ueda, T., Morita, J., Uegaki, K. & Nakamura, T., Jan 1 2014, In : FEBS Journal. 281, 11, p. 2584-2596 13 p.

Research output: Contribution to journalArticle

Chromosomes
Pyrococcus
Escherichia coli
Phosphates
Peptides
6 Citations (Scopus)

Involvement of histidine in complex formation of PriB and single-stranded DNA

Fujiyama, S., Abe, Y., Takenawa, T., Aramaki, T., Shioi, S., Katayama, T. & Ueda, T., Feb 1 2014, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1844, 2, p. 299-307 9 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
Histidine
Chemical shift
Biomolecular Nuclear Magnetic Resonance
Dimers
7 Citations (Scopus)

Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex

Fujiyama, S., Abe, Y., Tani, J., Urabe, M., Sato, K., Aramaki, T., Katayama, T. & Ueda, T., Jan 1 2014, In : FEBS Journal. 281, 23, p. 5356-5370 15 p.

Research output: Contribution to journalArticle

Escherichia coli
Proteolysis
Klebsiella pneumoniae
Histidine
Nuclear magnetic resonance spectroscopy
1 Citation (Scopus)

The structure of hyperthermophilic β-N-acetylglucosaminidase reveals a novel dimer architecture associated with the active site

Mine, S., Kado, Y., Watanabe, M., Fukuda, Y., Abe, Y., Ueda, T., Kawarabayasi, Y., Inoue, T. & Ishikawa, K., Nov 1 2014, In : FEBS Journal. 281, 22, p. 5092-5103 12 p.

Research output: Contribution to journalArticle

Acetylglucosaminidase
Dimers
Glycoside Hydrolases
Catalytic Domain
Catalysis
2013
6 Citations (Scopus)

Domain separation and characterization of PriC, a replication restart primosome factor in Escherichia coli

Aramaki, T., Abe, Y., Ohkuri, T., Mishima, T., Yamashita, S., Katayama, T. & Ueda, T., Sep 1 2013, In : Genes to Cells. 18, 9, p. 723-732 10 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
Binding Sites
Escherichia coli
Basic Amino Acids
DNA
20 Citations (Scopus)

Mechanism for retardation of amyloid fibril formation by sugars in Vλ6 protein

Abe, M., Abe, Y., Ohkuri, T., Mishima, T., Monji, A., Kanba, S. & Ueda, T., Apr 1 2013, In : Protein Science. 22, 4, p. 467-474 8 p.

Research output: Contribution to journalArticle

Amyloid
Sugars
Amyloidosis
Peptides
Proteins
5 Citations (Scopus)

Preparation and characterization of a monoclonal antibody against the refolded and functional extracellular domain of rat P2X4 receptor

Igawa, T., Higashi, S., Abe, Y., Ohkuri, T., Tanaka, H., Morimoto, S., Yamashita, T., Makoto, T., Inoue, K. & Ueda, T., Mar 1 2013, In : Journal of Biochemistry. 153, 3, p. 275-282 8 p.

Research output: Contribution to journalArticle

Purinergic P2X4 Receptors
Rats
Monoclonal Antibodies
Molecules
Neuralgia
4 Citations (Scopus)

Solution structure of the N-terminal domain of a replication restart primosome factor, PriC, in Escherichia coli

Aramaki, T., Abe, Y., Katayama, T. & Ueda, T., Sep 1 2013, In : Protein Science. 22, 9, p. 1279-1286 8 p.

Research output: Contribution to journalArticle

Escherichia coli
Biomolecular Nuclear Magnetic Resonance
Oligomerization
DNA
Chemical shift
12 Citations (Scopus)

The DnaA N-terminal domain interacts with Hda to facilitate replicase clamp-mediated inactivation of DnaA

Su'etsugu, M., Harada, Y., Keyamura, K., Matsunaga, C., Kasho, K., Abe, Y., Ueda, T. & Katayama, T., Dec 1 2013, In : Environmental Microbiology. 15, 12, p. 3183-3195 13 p.

Research output: Contribution to journalArticle

inactivation
Adenosine Triphosphate
hydrolysis
DNA
Hydrolysis
2012
1 Citation (Scopus)

Arg 901 in the AE1 C-terminal tail is involved in conformational change but not in substrate binding

Takazaki, S., Abe, Y., Yamaguchi, T., Yagi, M., Ueda, T., Kang, D. & Hamasaki, N., Mar 1 2012, In : Biochimica et Biophysica Acta - Biomembranes. 1818, 3, p. 658-665 8 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Hydrophobicity
Hydrophobic and Hydrophilic Interactions
Tail
Substrates
2010
1 Citation (Scopus)

Effect of protein concentration and pH on the chitinase activity of Tapes japonica lysozyme

Goto, T., Abe, Y., Imoto, T. & Ueda, T., 2010, In : Protein and Peptide Letters. 17, 2, p. 172-175 4 p.

Research output: Contribution to journalArticle

Chitinases
Muramidase
Tapes
Proteins
Dimers
5 Citations (Scopus)

Effects of His mutations on the fibrillation of amyloidogenic Vλ6 protein Wil under acidic and physiological conditions

Mishima, T., Ohkuri, T., Monji, A., Kanemaru, T., Abe, Y. & Ueda, T., Jan 1 2010, In : Biochemical and Biophysical Research Communications. 391, 1, p. 615-620 6 p.

Research output: Contribution to journalArticle

Amyloidogenic Proteins
Histidine
Mutation
Proteins
Experiments
9 Citations (Scopus)

Evaluation of the conformational equilibrium of reduced hen egg lysozyme by antibodies to the native form

Oda, M., Kitai, A., Murakami, A., Nishimura, M., Ohkuri, T., Abe, Y., Ueda, T., Nakamura, H. & Azuma, T., Feb 1 2010, In : Archives of Biochemistry and Biophysics. 494, 2, p. 145-150 6 p.

Research output: Contribution to journalArticle

Antibodies
Conformations
Rate constants
Epitopes
Monoclonal Antibodies

Evidence for the binding of phosphate ion to the C-terminus region in Aβ 1-40 using heteronuclear NMR analyses

Nagata-Uchiyama, M., Abe, Y., Monji, A., Kanba, S. & Ueda, T., Mar 31 2010, In : Protein and Peptide Letters. 17, 2, p. 176-180 5 p.

Research output: Contribution to journalArticle

Biomolecular Nuclear Magnetic Resonance
Phosphates
Nuclear magnetic resonance
Ions
Amyloid
14 Citations (Scopus)

Helical image reconstruction of the outward-open human erythrocyte band 3 membrane domain in tubular crystals

Yamaguchi, T., Fujii, T., Abe, Y., Hirai, T., Kang, D., Namba, K., Hamasaki, N. & Mitsuoka, K., Mar 1 2010, In : Journal of structural biology. 169, 3, p. 406-412 7 p.

Research output: Contribution to journalArticle

Computer-Assisted Image Processing
Erythrocytes
Membranes
Cryoelectron Microscopy
Immunoelectron Microscopy
4 Citations (Scopus)

Mutation of His 834 in human anion exchanger 1 affects substrate binding

Takazaki, S., Abe, Y., Yamaguchi, T., Yagi, M., Ueda, T., Kang, D. & Hamasaki, N., May 1 2010, In : Biochimica et Biophysica Acta - Biomembranes. 1798, 5, p. 903-908 6 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Alanine
Sulfates
Anions
Facings
34 Citations (Scopus)

Structure of the Membrane Domain of Human Erythrocyte Anion Exchanger 1 Revealed by Electron Crystallography

Yamaguchi, T., Ikeda, Y., Abe, Y., Kuma, H., Kang, D., Hamasaki, N. & Hirai, T., Mar 19 2010, In : Journal of Molecular Biology. 397, 1, p. 179-189 11 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Crystallography
Electrons
Membranes
Antiporters
2009
54 Citations (Scopus)

DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading

Keyamura, K., Abe, Y., Higashi, M., Ueda, T. & Katayama, T., Sep 11 2009, In : Journal of Biological Chemistry. 284, 37, p. 25038-25050 13 p.

Research output: Contribution to journalArticle

DnaB Helicases
Adenosine Triphosphate
Structural Models
Carrier Proteins
Binding Sites
8 Citations (Scopus)

Factor G utilizes a carbohydrate-binding cleft that is conserved between horseshoe crab and bacteria for the recognition of β-1,3-D-glucans

Ueda, Y., Ohwada, S., Abe, Y., Shibata, T., Iijima, M., Yoshimitsu, Y., Koshiba, T., Nakata, M., Ueda, T. & Kawabata, S. I., Sep 15 2009, In : Journal of Immunology. 183, 6, p. 3810-3818 9 p.

Research output: Contribution to journalArticle

Horseshoe Crabs
Carbohydrates
Bacteria
Endo-1,4-beta Xylanases
Cellvibrio
10 Citations (Scopus)

Residual Structures in the Acid-Unfolded States of Vλ6 Proteins Affect Amyloid Fibrillation

Mishima, T., Ohkuri, T., Monji, A., Kanemaru, T., Abe, Y. & Ueda, T., Oct 2 2009, In : Journal of Molecular Biology. 392, 4, p. 1033-1043 11 p.

Research output: Contribution to journalArticle

Amyloidogenic Proteins
Amyloid
Acids
Proteins
Disulfides
1 Citation (Scopus)

Structure and function of tapes japonica lysozyme

Abe, Y. & Ueda, T., 2009, In : Seikagaku. The Journal of Japanese Biochemical Society. 81, 4, p. 314-319 6 p.

Research output: Contribution to journalReview article

X ray crystallography
Muramidase
Seawater
Sodium Chloride
Tapes

アサリ貝リゾチームの構造と機能

Translated title of the contribution: Structure and function of Tapes japonica lysozyme阿部義人 & 植田正, Apr 25 2009, In : Seikagaku. The Journal of Japanese Biochemical Society. 81, 4, p. 314-319 6 p.

Research output: Contribution to journalArticle

2008
3 Citations (Scopus)

Crystal structures of K33 mutant hen lysozymes with enhanced activities

Goto, T., Ohkuri, T., Shioi, S., Abe, Y., Imoto, T. & Ueda, T., Nov 1 2008, In : Journal of biochemistry. 144, 5, p. 619-623 5 p.

Research output: Contribution to journalArticle

Muramidase
Crystal structure
Micrococcus luteus
Enzyme activity
Mutagenesis

Structural Analysis of Excitatory Nerupeptides TEP-1 and TEP-2 Isolated from the Prosobranch Gastopod Thais clavigera

Nose, T., Horiuchi, Y., Abe, Y., Shimohigashi, Y. & Morishita, F., Mar 2008, Peptide Science 2007. p. 273-276 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

2007
3 Citations (Scopus)

Assignment of 1H, 13C and 15N resonances of N-terminal domain of DnaA protein

Abe, Y., Watanabe, N., Yoshida, Y., Ebata, F., Katayama, T. & Ueda, T., Jul 1 2007, In : Biomolecular NMR Assignments. 1, 1, p. 57-59 3 p.

Research output: Contribution to journalArticle

DnaB Helicases
Oligomerization
Escherichia coli
Proteins
Protein Domains
59 Citations (Scopus)
Chitinases
Muramidase
Tapes
Crystal structure
Substrates
74 Citations (Scopus)

Structure and function of DnaA N-terminal domains: Specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC

Abe, Y., Jo, T., Matsuda, Y., Matsunaga, C., Katayama, T. & Ueda, T., Jun 15 2007, In : Journal of Biological Chemistry. 282, 24, p. 17816-17827 12 p.

Research output: Contribution to journalArticle

DnaB Helicases
Dimerization
Single-Stranded DNA
Nuclear magnetic resonance
DNA
2006
3 Citations (Scopus)

A simple search of TM segments in polytopic membrane protein using matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Abe, Y., Hamasaki, T., Turusaki, S., Takazaki, S., Jin, X., Kang, D. & Hamasaki, N., Aug 7 2006, In : Protein and Peptide Letters. 13, 8, p. 761-767 7 p.

Research output: Contribution to journalArticle

Ionization
Mass spectrometry
Desorption
Mass Spectrometry
Membrane Proteins
19 Citations (Scopus)

Identification of oxidized methionine sites in erythrocyte membrane protein by liquid chromatography/electrospray ionization mass spectrometry peptide mapping

Li, C., Takazaki, S., Jin, X., Kang, D., Abe, Y. & Hamasaki, N., Oct 3 2006, In : Biochemistry. 45, 39, p. 12117-12124 8 p.

Research output: Contribution to journalArticle

Electrospray ionization
Peptide Mapping
Electrospray Ionization Mass Spectrometry
Liquid chromatography
Erythrocyte Membrane
13 Citations (Scopus)

The functional role of arginine 901 at the C-terminus of the human anion transporter band 3 protein

Takazaki, S., Abe, Y., Kang, D., Li, C., Jin, X., Ueda, T. & Hamasaki, N., May 1 2006, In : Journal of biochemistry. 139, 5, p. 903-912 10 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Anions
Arginine
Membranes
Acids

複数回膜貫通型膜タンパク質の立体構造形成機構: バンド3タンパク質研究の成果より

Translated title of the contribution: Biosynthetic Mechanism of Polytopic Membrane Protein as Deduced by Study of Band 3 Protein阿部義人 & 濱崎直孝, Jan 25 2006, In : Biophysics (Japan). 46, 1, p. 4-9 6 p.

Research output: Contribution to journalArticle

Erythrocyte Anion Exchange Protein 1
Protein Sorting Signals
Membrane Proteins
Membranes
Lipids