Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies.
Kasahara K, Kawade R, Nakakido M, Matsunaga R, Akiba H, Entzminger KC, Maruyama T, Okumura SCJ, Caaveiro JMM, Kuroda D, Tsumoto K
J Biol Chem. 2024 Nov 12

Structural basis for the ligand promiscuity of the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes.
Fernandez-Perez J, Senoo A, Caaveiro JMM, Nakakido M, de Vega S, Nakagawa I, Tsumoto K
Structure. 2024 Oct 3

Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning.
Yospanya W, Matsumura A, Imasato Y, Itou T, Aoki Y, Nakazawa H, Matsui T, Yokoyama T, Ui M, Umetsu M, Nagatoishi S, Tsumoto K, Tanaka Y, Kinbara K
Bull Chem Soc Jpn. 2024 Sep 2

Development of novel humanized VHH synthetic libraries based on physicochemical analyses.
Nakakido M, Kinoshita S, Tsumoto K
Sci Rep. 2024 Aug 22

Systematic Preparation of a 66-IgG Library with Symmetric and Asymmetric Homogeneous Glycans and Their Functional Evaluation.
Manabe S, Iwamoto S, Nagatoishi S, Hoshinoo A, Mitani A, Sumiyoshi W, Kinoshita T, Yamaguchi Y, Tsumoto K
J Am Chem Soc. 2024 Aug 6

Triphenylphosphonium-modified catiomers enhance in vivo mRNA delivery through stabilized polyion complexation.
Norimatsu J, Mizuno HL, Watanabe T, Obara T, Nakakido M, Tsumoto K, Cabral H, Kuroda D, Anraku Y
Mater Horiz. 2024 Jul 11

Impact of single-residue mutations on protein thermal stability: The case of threonine 83 of BC2L-CN lectin.
Hoya M, Matsunaga R, Nagatoishi S, Ide T, Kuroda D, Tsumoto K
Int J Biol Macromol. 2024 May 28

High-throughput system for the thermostability analysis of proteins.
Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K
Protein Sci. 2024 May 27

Cryo-EM structures elucidate the multiligand receptor nature of megalin.
Goto S, Tsutsumi A, Lee Y, Hosojima M, Kabasawa H, Komochi K, Nagatoishi S, Takemoto K, Tsumoto K, Nishizawa T, Kikkawa M, Saito A
Proc Natl Acad Sci U S A. 2024 May 21

Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Asano R, Takeuchi M, Nakakido M, Ito S, Aikawa C, Yokoyama T, Senoo A, Ueno G, Nagatoishi S, Tanaka Y, Nakagawa I, Tsumoto K
Protein Sci. 2024 May 15

A High-Resolution Structural Characterization and Physicochemical Study of How a Peptoid Binds to an Oncoprotein MDM2.
Yokomine M, Morimoto J, Fukuda Y, Ueda T, Takeuchi K, Umezawa K, Ago H, Matsuura H, Ueno G, Senoo A, Nagatoishi S, Tsumoto K, Sando S
Chem Sci. 2024 Apr 19

Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.
Asano R, Nakakido M, Pérez JF, Ise T, Caaveiro JMM, Nagata S, Tsumoto K
Biochem Biophys Res Commun. 2024 Apr 18

Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody.
Miyanabe K, Yamashita T, Tsumoto K
Sci Rep. 2024 Apr 15

Next-Generation Anti-TNFα Agents: The Example of Ozoralizumab.
Tsumoto K, Takeuchi T
BioDrugs. 2024 Apr 8

Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain VHH antibodies.
Yamamoto K, Nagatoishi S, Nakakido M, Kuroda D, Tsumoto K
Biochem Biophys Res Commun. 2024 Mar 27

THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring.
Akabane T, Suzuki N, Ikeda K, Yonezawa T, Nagatoishi S, Matsumura H, Yoshizawa T, Tsuchiya W, Kamino S, Tsumoto K, Ishimaru K, Katoh E, Hirotsu N
Sci Rep. 2024 Mar 21

Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes.
Senoo A, Hoshino M, Shiomi T, Nakakido M, Nagatoishi S, Kuroda D, Nakagawa I, Tame JRH, Caaveiro JMM, Tsumoto K
Sci Rep. 2024 Mar 5

Unveiling the affinity-stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction.
Paul R, Kasahara K, Sasaki J, Pérez JF, Matsunaga R, Hashiguchi T, Kuroda D, Tsumoto K
Front Mol Biosci. 2024 Mar 1

Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen.
Sumikawa T, Nakakido M, Matsunaga R, Kuroda D, Nagatoishi S, Tsumoto K
J Biol Chem. 2024 Jan 8

Experimental modification in thermal stability of oligomers by alanine substitution and site saturation mutagenesis of interfacial residues.
Hoya M, Matsunaga R, Nagatoishi S, Tsumoto K
Biochem Biophys Res Commun. 2023 Nov 25

High-throughput analysis system of interaction kinetics for data-driven antibody design.
Matsunaga R, Ujiie K, Inagaki M, Fernández Pérez J, Yasuda Y, Mimasu S, Soga S, Tsumoto K
Sci Rep. 2023 Nov 21

Enhancing Thermal Stability in the CH2 Domain to Suppress Aggregation through the Introduction of Simultaneous Disulfide Bonds in Pichia pastoris.
Oyama K, Nakakido M, Ohkuri T, Nakamura H, Tsumoto K, Ueda T
Protein Sci. 2023 Nov 4

Conformational features and interaction mechanisms of VH H antibodies with β-hairpin CDR3: A case of Nb8-HigB2 interaction.
Yamamoto K, Nagatoishi S, Matsunaga R, Nakakido M, Kuroda D, Tsumoto K
Protein Sci. 2023 Nov 2

Safe and efficient oral allergy immunotherapy using one-pot-prepared mannan-coated allergen nanoparticles.
Li S, Toriumi H, Takahashi D, Kamasaki T, Fujioka Y, Nagatoishi S, Li J, Liu Y, Hosokawa T, Tsumoto K, Ohba Y, Katayama Y, Murakami D, Hase K, Mori T
Biomaterials. 2023 Oct 31

Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex.
Mori C, Nagatoishi S, Matsunaga R, Kuroda D, Nakakido M, Tsumoto K
Biochem Biophys Res Commun. 2023 Oct 4

Specific peptide conjugation to a therapeutic antibody leads to enhanced therapeutic potency and thermal stability by reduced Fc dynamics.
Kiyoshi M, Nakakido M, Rafique A, Tada M, Aoyama M, Terao Y, Nagatoishi S, Shibata H, Ide T, Tsumoto K, Ito Y, Ishii-Watabe A
Sci Rep. 2023 Oct 2

Discovery of a cystathionine γ-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5′-phosphate (PLP) via Schiff base formation.
Echizen H, Hanaoka K, Shimamoto K, Hibi R, Toma-Fukai S, Ohno H, Sasaki E, Komatsu T, Ueno T, Tsuchiya Y, Watanabe Y, Otsuka T, Saito H, Nagatoishi S, Tsumoto K, Kojima H, Okabe T, Shimizu T, Urano Y
Sci Rep. 2023 Sep 30

Quantitative analysis of antibody aggregates by combination of pinched-flow fractionation and coulter method.
Nagatoishi S, Toyoshima T, Furukawa K, Tsumoto K
Anal Biochem. 2023 Sep 27

Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.
Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K
Commun Biol. 2023 Sep 27

Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.
Yamazaki T, Nagatoishi S, Yamawaki T, Nozawa T, Matsunaga R, Nakakido M, Caaveiro JMM, Nakagawa I, Tsumoto K
J Biol Chem. 2023 Sep 14

Megalin is involved in angiotensinogen-induced, angiotensin II-mediated ERK1/2 signaling to activate Na+-H+ exchanger 3 in proximal tubules.
Goto S, Yoshida Y, Hosojima M, Kuwahara S, Kabasawa H, Aoki H, Iida T, Sawada R, Ugamura D, Yoshizawa Y, Takemoto K, Komochi K, Kobayashi R, Kaseda R, Yaoita E, Nagatoishi S, Narita I, Tsumoto K, Saito A
J Hypertens. 2023 Sep 8

Ferguson plot analysis of multiple intermediate species of thermally unfolded bovine serum albumin.
Tomioka Y, Nagatoishi S, Nakagawa M, Tsumoto K, Arakawa T, Akuta T
Biophys Chem. 2023 Aug 15

Arginine cluster introduction on framework region in anti-Lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops.
Maeta S, Nakakido M, Matsuura H, Sakai N, Hirata K, Kuroda D, Fukunaga A, Tsumoto K
Protein Sci. 2023 Aug 7

Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion.
Senoo A, Nagatoishi S, Kuroda D, Ito S, Ueno G, Caaveiro JMM, Tsumoto K
Protein Sci. 2023 Aug 2

Group A Streptococcus cation diffusion facilitator proteins contribute to immune evasion by regulating intracellular metal concentrations.
Aikawa C, Shimizu A, Nakakido M, Murase K, Nozawa T, Tsumoto K, Nakagawa I
Biochem Biophys Res Commun. 2023 July 24

Investigating the Antiviral Properties of Copper-and Silver-containing Polyoxometalates using a High-throughput Screening Method.
Yonesato K, Nakakido M, Tsumoto K, Egami Y, Miyamae N, Wakihara T, Suzuki K, Yamaguchi K
Chem Lett. 2023 July 22

PRELP secreted from mural cells protects the function of blood brain barrier through regulation of endothelial cell-cell integrity
Davaapil H, Asada K, Hopkins J, Bonnin N, Papadaki V, Leung A, Kosuge H, Tashima T, Nakakido M, Sekido R, Tsumoto K, Hamamoto R, Sagoo MS, Ohnuma S
Front Cell Dev Biol. 2023 July 13

One-pot preparation of mannan-coated antigen nanoparticles using human serum albumin as a matrix for tolerance induction.
Li S, Murakami D, Nagatoishi S, Liu Y, Tsumoto K, Katayama Y, Mori T
J Colloid Interface Sci. 2023 June 26

Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
Valenciano-Bellido S, Caaveiro JMM, Nakakido M, Kuroda D, Aikawa C, Nakagawa I, Tsumoto K
J Biol Chem. 2023 June 15

Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames.
Kozuka-Hata H, Hiroki T, Miyamura N, Kitamura A, Tsumoto K, Inoue J, Oyama M
Biomolecules. 2023 June 12

Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.
Liu N, Konuma T, Sharma R, Wang D, Zhao N, Cao L, Ju Y, Liu D, Wang S, Bosch A, Sun Y, Zhang S, Ji D, Nagatoishi S, Suzuki N, Kikuchi M, Wakamori M, Zhao C, Ren C, Zhou TJ, Xu Y, Meslamani J, Fu S, Umehara T, Tsumoto K, Akashi S, Zeng L, Roeder RG, Walsh MJ, Zhang Q, Zhou MM
Mol Cell. 2023 June 6

A Proximity-Induced Fluorogenic Reaction Triggered by Antibody-Antigen Interactions with Adjacent Epitopes.
Nishiyama K, Akiba H, Nagata S, Tsumoto K, Kamada H, Ohno H
Angew Chem Int Ed Engl. 2023 May 31

Dispersion function of a protein, DP-1, identified in Collimonas sp. D-25, for the synthesis of gold nanoparticles.
Tang D, Kato Y, Zhang D, Negishi L, Kurumizaka H, Hirata T, Nakakido M, Tsumoto K, Fujisawa S, Saito T, Okumura T, Nagata K, Suzuki M
Chembiochem. 2023 May 26

Raman Spectroscopic Analysis of Highly-Concentrated Antibodies under the Acid-Treated Conditions.
Sato Y, Nagatoishi S, Noguchi S, Tsumoto K
Pharm Res. 2023 May 9

An Engineered Synthetic Receptor-Aptamer Pair for an Artificial Signal Transduction System.
Liu H, Baeumler TA, Nakamura K, Okada Y, Cho S, Eguchi A, Kuroda D, Tsumoto K, Ueki R, Sando S
ACS Nano. 2023 May 8

Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene.
Yui A, Kuroda D, Maruno T, Nakakido M, Nagatoishi S, Uchiyama S, Tsumoto K
Sci Rep. 2023 Apr 20

Design of single-domain VHH antibodies to increase the binding activity in SPR amine coupling.
Hirao A, Nagatoishi S, Ikeuchi E, Yamawaki T, Mori C, Nakakido M, Tsumoto K
Biochem Biophys Res Commun. 2023 Apr 19

Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters Using Protein Cages.
Hishikawa Y, Noya H, Nagatoishi S, Yoshidome T, Maity B, Tsumoto K, Abe S, Ueno T
Chemistry. 2023 Apr 18

Ligand Installation to Polymeric Micelles for Pediatric Brain Tumor Targeting.
Watanabe T, Mizuno HL, Norimatsu J, Obara T, Cabral H, Tsumoto K, Nakakido M, Kawauchi D, Anraku Y
Polymers. 2023 Apr 6

Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex.
Yamaguchi K, Nakagawa S, Saku A, Isobe Y, Yamaguchi R, Sheridan P, Takane K, Ikenoue T, Zhu C, Miura M, Okawara Y, Nagatoishi S, Kozuka-Hata H, Oyama M, Aikou S, Ahiko Y, Shida D, Tsumoto K, Miyano S, Imoto S, Furukawa Y
iScience. 2023 Apr 1

Inactivation and spike protein denaturation of novel coronavirus variants by CuxO/TiO2 nano-photocatalysts.
Tatsuma T, Nakakido M, Ichinohe T, Kuroiwa Y, Tomioka K, Liu C, Miyamae N, Onuki T, Tsumoto K, Hashimoto K, Wakihara T
Sci Rep. 2023 Mar 10

Agarose native gel electrophoresis analysis of thermal aggregation controlled by Hofmeister series.
Tomioka Y, Sato R, Takahashi R, Nagatoishi S, Shiba K, Tsumoto K, Arakawa T, Akuta T
Biophys Chem. 2023 Feb 20

Non-Affinity Purification of Antibodies.
Arakawa T, Tomioka Y, Nakagawa M, Sakuma C, Kurosawa Y, Ejima D, Tsumoto K, Akuta T.
Antibodies (Basel). 2023 Feb 13

Peripheral administration of nanomicelle-encapsulated anti-Aβ oligomer fragment antibody reduces various toxic Aβ species in the brain.
Amano A, Sanjo N, Araki W, Anraku Y, Nakakido M, Matsubara E, Tomiyama T, Nagata T, Tsumoto K, Kataoka K, Yokota T
J Nanobiotechnology. 2023 Jan 31

In vitro validation of chromogenic substrate assay for evaluation of surrogate FVIII-activity of emicizumab.
Yamaguchi T, Shinozawa K, Nagatoishi S, Mitsuhashi A, Bingo M, Inaba H, Amano K, Tsumoto K, Kinai E
Thromb Res. 2023 Jan 13

Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450.
Gilep A, Varaksa T, Bukhdruker S, Kavaleuski A, Ryzhykau Y, Smolskaya S, Sushko T, Tsumoto K, Grabovec I, Kapranov I, Okhrimenko I, Marin E, Shevtsov M, Mishin A, Kovalev K, Kuklin A, Gordeliy V, Kaluzhskiy L, Gnedenko O, Yablokov E, Ivanov A, Borshchevskiy V, Strushkevich N.
Front Mol Biosci. 2023 Jan 9

Effects of network connectivity on viscoelastic relaxation in transient networks using experimental approach.
Katashima T, Kudo R, Onishi R, Naito M, Nagatoishi S, Miyata K, Tsumoto K, Chung U, Sakai T
Front Soft Matter. 2022 Nov 23

Human antibody recognition and neutralization mode on the NTD and RBD domains of SARS-CoV-2 spike protein.
Otsubo R, Minamitani T, Kobiyama K, Fujita J, Ito T, Ueno S, Anzai I, Tanino H, Aoyama H, Matsuura Y, Namba K, Imadome KI, Ishii KJ, Tsumoto K, Kamitani W, Yasui T
Sci Rep. 2022 Nov 22

Repression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer.
Shozu K, Kaneko S, Shinkai N, Dozen A, Kosuge H, Nakakido M, Machino H, Takasawa K, Asada K, Komatsu M, Tsumoto K, Ohnuma SI, Hamamoto R
Clin Epigenetics. 2022 Nov 12

Structural Classification of CDR-H3 in Single-Domain VHH Antibodies.
Kuroda D, Tsumoto K
Methods Mol Biol. 2022 Nov 9

Analytical Method for Experimental Validation of Computer-Designed Antibody.
Tanabe A, Tsumoto K
Methods Mol Biol. 2022 Nov 9

Extracellular matrix-inspired hydrogel of hyaluronan and gelatin crosslinked via a Link module with a transglutaminase reactive sequence.
Okawa M, Tanabe A, Ohta S, Nagatoishi S, Tsumoto K, Ito T
Commun. Mater. 2022 Oct 30

PRELP Regulates Cell-Cell Adhesion and EMT and Inhibits Retinoblastoma Progression.
Hopkins J, Asada K, Leung A, Papadaki V, Davaapil H, Morrison M, Orita T, Sekido R, Kosuge H, Reddy MA, Kimura K, Mitani A, Tsumoto K
Cancers (Basel) 2022 Oct 8

Performance Comparison of Spectral Distance Calculation Methods.
Oyama T, Suzuki S, Horiguchi Y, Yamane A, Akao K, Nagamori K, Tsumoto K
Appl Spectrosc 2022 Oct 5

Molecular basis for thermal stability and affinity in a VHH: contribution of the framework region and its influence in the conformation of the CDR3.
Kinoshita S, Nakakido M, Mori C, Kuroda D, Caaveiro JMM, Tsumoto K
Protein Sci 2022 Sep 25

Nucleic Acid-triggered Tumoral Immunity Propagates pH-selective Therapeutic Antibodies through Tumor-driven Epitope Spreading.
Furuya G, Katoh H, Atsumi S, Hashimoto I, Komura D, Hatanaka R, Senga S, Hayashi S, Akita S, Matsumura H, Miura A, Mita H, Nakakido M, Nagatoishi S, Sugiyama A, Suzuki R, Konishi H, Yamamoto A, Abe H, Hiraoka N, Aoki K, Kato Y, Seto Y, Yoshimura C, Miyadera K, Tsumoto K, Ushiku T, Ishikawa S
Cancer Sci 2022 Sep 22

Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint.
Kim J, Kobayashi H, Yokomine M, Shiratori Y, Ueda T, Takeuchi K, Umezawa K, Kuroda D, Tsumoto K, Morimoto J, Sando S
Org Biomol Chem 2022 Aug 22

Analysis of bovine serum albumin unfolding in the absence and presence of ATP by SYPRO Orange staining of agarose native gel electrophoresis.
Tomioka Y, Nakagawa M, Sakuma C, Kurosawa Y, Nagatoishi S, Tsumoto K, Arakawa T, Akuta T
Anal Biochem 2022 Jul 18

Ladder observation of bovine serum albumin by high resolution agarose native gel electrophoresis.
Tomioka Y, Nakagawa M, Sakuma C, Nagatoishi S, Tsumoto K, Arakawa T, Akuta T
Int J Biol Macromol 2022 Jun 22

Mirror-image streptavidin with specific binding to L-biotin, the unnatural enantiomer.
Suganuma M, Kubo T, Ishiki K, Tanaka K, Suto K, Ejima D, Toyota M, Tsumoto K, Sato T, Nishikawa Y
Sci Rep 2022 Jun 10

Biophysical Characterization of the Contribution of the Fab Region to the IgG-FcγRIIIa Interaction.
Kosuge H, Nagatoishi S, Kiyoshi M, Ishii-Watabe A, Terao Y, Ide T, Tsumoto K
Biochemistry 2022 May 23

Experimental Comparison of Bond Lifetime and Viscoelastic Relaxation in Transient Networks with Well-Controlled Structures.
Katashima T, Kudo R, Naito M, Nagatoishi S, Miyata K, Chung UI, Tsumoto K, Sakai T
ACS Macro Lett 2022 May 20

Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus.
Valenciano-Bellido S, Caaveiro JMM, Morante K, Sushko T, Nakakido M, Nagatoishi S, Tsumoto K
J Biol Chem 2022 Apr 29

Development of a high-throughput method to screen novel antiviral materials.
Nakakido M, Tanaka N, Shimojo A, Miyamae N, Tsumoto K
PLoS One 2022 Apr 27

Antibody recognition of complement Factor H reveals a flexible loop involved in Atypical Hemolytic Uremic Syndrome pathogenesis.
Yokoo T, Tanabe A, Yoshida Y, Caaveiro JMM, Nakakido M, Ikeda Y, Fujimura Y, Matsumoto M, Entzminger K, Maruyama T, Okumura CJ, Nangaku M, Tsumoto K
J Biol Chem 2022 Apr 19

Effects of salicylate derivatives on localization of p.H723R allele product of SLC26A4.
Murakoshi M, Koike Y, Koyama S, Usami S, Kamiya K, Ikeda K, Haga Y, Tsumoto K, Nakamura H, Hirasawa N, Ishihara K, Wada H
Auris Nasus Larynx 2022 Mar 16

Addition of arginine hydrochloride and proline to the culture medium enhances recombinant protein expression in Brevibacillus choshinensis: The case of RBD of SARS-CoV-2 spike protein and its antibody.
Matsunaga R, Tsumoto K
Protein Expr Purif 2022 Feb 26

Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics.
Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR
MAbs 2022 Feb 1

Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites.
Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S
Angew Chem Int Ed Engl 2022 Jan 28

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations.
Yasuda S, Akiyama T, Kojima K, Ueta T, Hayashi T, Ogasawara S, Nagatoishi S, Tsumoto K, Kunishima N, Sudo Y, Kinoshita M, Murata T
J Phys Chem B 2022 Jan 28

Improvement of the affinity of an anti-rat P2X4 receptor antibody by introducing electrostatic interactions.
Shinozaki C, Kohno K, Shiroishi M, Takahashi D, Yoshikawa Y, Abe Y, Hamase K, Nakakido M, Tsumoto K, Inoue K, Tsuda M, Ueda T
Sci Rep 2022 Jan 7

B cell-intrinsic TBK1 is essential for germinal center formation during infection and vaccination in mice.
Lee MSJ, Inoue T, Ise W, Matsuo-Dapaah J, Wing JB, Temizoz B, Kobiyama K, Hayashi T, Patil A, Sakaguchi S, Simon AK, Bezbradica JS, Nagatoishi S, Tsumoto K, Inoue JI, Akira S, Kurosaki T, Ishii KJ, Coban C
J Exp Med 2021 Dec 15

Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.
Kori S, Shibahashi Y, Ekimoto T, Nishiyama A, Yoshimi S, Yamaguchi K, Nagatoishi S, Ohta M, Tsumoto K, Nakanishi M, Defossez PA, Ikeguchi M, Arita K
Bioorg Med Chem 2021 Nov 10

The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis.
Sekiya M, Kainoh K, Sugasawa T, Yoshino R, Hirokawa T, Tokiwa H, Nakano S, Nagatoishi S, Tsumoto K, Takeuchi Y, Miyamoto T, Matsuzaka T, Shimano H
Nat Commun 2021 Nov 2

Unfolding is the driving force for mitochondrial import and degradation of Parkinson’s disease-related protein DJ-1.
Queliconi BB, Kojima W, Kimura M, Imai K, Udagawa C, Motono C, Hirokawa T, Tashiro S, Caaveiro JMM, Tsumoto K, Yamano K, Tanaka K, Matsuda N
J Cell Sci 2021 Oct 22

Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies.
Ikeuchi E, Kuroda D, Nakakido M, Murakami A, Tsumoto K
Sci Rep 2021 Oct 18

Structural and thermodynamical insights into the binding and inhibition of FIH-1 by the N-terminal disordered region of Mint3.
Ten T, Nagatoishi S, Maeda R, Hoshino M, Nakayama Y, Seiki M, Sakamoto T, Tsumoto K
J Biol Chem 2021 Oct 13

Production of IgG1-based bispecific antibody without extra cysteine residue via intein-mediated protein trans-splicing.
Akiba H, Ise T, Nagata S, Kamada H, Ohno H, Tsumoto K
Sci Rep 2021 Sep 30

A glutamine sensor that directly activates TORC1.
Tanigawa M, Yamamoto K, Nagatoishi S, Nagata K, Noshiro D, Noda NN, Tsumoto K, Maeda T
Commun Biol 2021 Sep 17

Epitope-dependent thermodynamic signature of single-domain antibodies against hen egg lysozyme.
Akiba H, Tamura H, Caaveiro JMM, Tsumoto K
J Biochem 2021 Sep 14

Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion.
Senoo A, Ito S, Nagatoishi S, Saito Y, Ueno G, Kuroda D, Yoshida K, Tashima T, Kudo S, Sando S, Tsumoto K
Commun Biol 2021 Sep 7

Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease.
Kuroda D, Tsumoto K
Biophys Physicobiol 2021 Aug 21

An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes.
Padhi AK, Kumar A, Haruna KI, Sato H, Tamura H, Nagatoishi S, Tsumoto K, Yamaguchi A, Iraha F, Takahashi M, Sakamoto K, Zhang KYJ
Brief Bioinform 2021 Aug 20

Electrostatic-triggered exothermic antibody adsorption to the cellulose nanoparticles.
Murakami K, Nagatoishi S, Kasahara K, Nagai H, Sasajima Y, Sasaki R, Tsumoto K
Anal Biochem 2021 Aug 12

Mechanism of dimerization and structural features of human LI-cadherin.
Yui A, Caaveiro JMM, Kuroda D, Nakakido M, Nagatoishi S, Goda S, Maruno T, Uchiyama S, Tsumoto K
J Biol Chem 2021 Aug 5

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions.
Fukuda Y, Yokomine M, Kuroda D, Tsumoto K, Morimoto J, Sando S.
Chem Sci 2021 Aug 3

Single-chain variable fragment (scFv) targeting streptolysin O controls group A Streptococcus infection.
Aikawa C, Kawashima K, Fukuzaki C, Nakakido M, Murase K, Nozawa T, Tsumoto K, Nakagawa I
Biochem Biophys Res Commun 2021 June 12

Novel neutralizing human monoclonal antibodies against tetanus neurotoxin.
Minamitani T, Kiyose K, Otsubo R, Ito T, Akiba H, Furuta RA, Inoue T, Tsumoto K, Satake M, Yasui T
Sci Rep 2021 June 9

Characterization of a putative maltodextrin-binding protein of Streptococcus pyogenes, SPs0871 and the development of a VHH inhibitor.
Yamawaki T, Nakakido M, Ujiie K, Aikawa C, Nakagawa I, Tsumoto K
Biochem Biophys Res Commun 2021 May 30

Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range.
Kasahara K, Kuroda D, Tanabe A, Kawade R, Nagatoishi S, Tsumoto K
Biochem Biophys Res Commun 2021 May 28

Elaboration of non-naturally occurring helical tripeptides as p53-MDM2/MDMX interaction inhibitors.
Su A, Tabata Y, Aoki K, Sada A, Ohki R, Nagatoishi S, Tsumoto K, Wang S, Otani Y, Ohwada T
Chem Pharm Bull (Tokyo) 2021 Apr 29

A Novel Cell-Based Intracellular Protein-Protein Interaction Detection Platform (SOLIS) for Multimodality Screening.
Kashima D, Kageoka M, Kimura Y, Horikawa M, Miura M, Nakakido M, Tsumoto K, Nagamune T, Kawahara M
ACS Synth Biol 2021 Apr 28

Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Nishinaga M, Sugimoto H, Nishitani Y, Nagai S, Nagatoishi S, Muraki N, Tosha T, Tsumoto K, Aono S, Shiro Y, Sawai H
Commun Biol 2021 Apr 13

Development of biparatopic bispecific antibody possessing tetravalent scFv-Fc capable of binding to ROBO1 expressed in hepatocellular carcinoma cells.
Watanabe Y, Tanabe A, Hamakubo T, Nagatoishi S, Tsumoto K
J Biochem 2021 Apr 12

A DNA Aptamer That Inhibits the Aberrant Signaling of Fibroblast Growth Factor Receptor in Cancer Cells.
Eguchi A, Ueki A, Hoshiyama J, Kuwata K, Chikaoka Y, Kawamura T, Nagatoishi S, Tsumoto K, Ueki R, Sando S
JACS Au 2021 Apr 8

Molecular basis for the activation of actinoporins by lipids.
Caaveiro JMM, Tsumoto K
Methods Enzymol 2021

Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope.
Makabe K, Yokoyama T, Uehara S, Uchikubo-Kamo T, Shirouzu M, Kimura K, Tsumoto K, Asano R, Tanaka Y, Kumagai I
Sci Rep 2021 Mar 11

Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors.
Yoshimura C, Nagatoishi S, Kuroda D, Kodama Y, Uno T, Kitade M, Chong-Takata K, Oshiumi H, Muraoka H, Yamashita S, Kawai Y, Ohkubo S, Tsumoto K
J Med Chem 2021 Feb 23

A new twist of rubredoxin function in M. tuberculosis.
Sushko T, Kavaleuski A, Grabovec I, Kavaleuskaya A, Vakhrameev D, Bukhdruker S, Marin E, Kuzikov A, Masamrekh R, Shumyantseva V, Tsumoto K, Borshchevskiy V, Gilep A, Strushkevich N
Bioorg Chem 2021 Feb 11

Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Ota T, Senoo A, Shirakawa M, Nonaka H, Saito Y, Ito S, Ueno G, Nagatoishi S, Tsumoto K, Sando S
iScience 2021 Feb 19

Proteomic Identification and Validation of Novel Interactions of the Putative Tumor Suppressor PRELP with Membrane Proteins Including IGFI-R and p75NTR.
Kosuge H, Nakakido M, Nagatoishi S, Fukuda T, Bando Y, Ohnuma SI, Tsumoto K
J Biol Chem 2021 Jan 8

Structural Basis for Antigen Recognition by Methylated Lysine Specific Antibodies.
Ishii M, Nakakido M, Caaveiro JMM, Kuroda D, Okumura CJ, Maruyama T, Entzminger K, Tsumoto K
J Biol Chem 2020 Dec 10

Two Secreted Proteoglycans, Activators of Urothelial Cell-Cell Adhesion, Negatively Contribute to Bladder Cancer Initiation and Progression.
Papadaki V, Asada K, Watson JK, Tamura T, Leung A, Hopkins J, Dellett M, Sasai N, Davaapil H, Nik-Zainal S, Longbottom R, Nakakido M, Torii R, Veerakumarasivam A, Kaneko S, Sagoo MS, Murphy G, Mitani A, Tsumoto K, Kelly JD, Hamamoto R, Ohnuma SI
Cancers (Basel) 2020 Nov 13

Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
Ito S, Senoo A, Nagatoishi S, Ohue M, Yamamoto M, Tsumoto K, Wakui N
J Med Chem 2020 Nov 13

Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis.
Chiba S, Tanabe A, Nakakido M, Okuno Y, Tsumoto K, Ohta M
Sci Rep 2020 Oct 16

Unique Electronic Structures of the Highly Ruffled Hemes in Heme-Degrading Enzymes ofStaphylococcus aureus, IsdG and IsdI, by Resonance Raman and Electron Paramagnetic Resonance Spectroscopies.
Takahashi S, Nambu S, Matsui T, Fujii H, Ishikawa H, Mizutani Y, Tsumoto K, Ikeda-Saito M
Biochemistry 2020 Sep 29

The Kg-antigen, RhAG with a Lys164Gln mutation, gives rise to haemolytic disease of the newborn.
Tanaka M, Abe T, Minamitani T, Akiba H, Horikawa T, Tobita R, Isa K, Ogasawara K, Takahashi H, Tateyama H, Tone S, Tsumoto K, Yasui T, Kimura T, Fujimura Y, Hirayama F, Tani Y, Takihara Y
Br J Haematol 2020 Jul 23

Polymeric Nanocarriers with Controlled Chain Flexibility Boost mRNA Delivery In Vivo through Enhanced Structural Fastening.
Miyazaki T, Uchida S, Nagatoishi S, Koji K, Hong T, Fukushima S, Tsumoto K, Ishihara K, Kataoka K, Cabral H
Adv Healthc Mater 2020 Jun 25

Dual-Sensitive Nanomicelles Enhancing Systemic Delivery of Therapeutically Active Antibodies Specifically into the Brain.
Xie J, Gonzalez-Carter D, Tockary TA, Nakamura N, Xue Y, Nakakido M, Akiba H, Dirisala A, Liu X, Toh K, Yang T, Wang Z, Fukushima S, Li J, Quader S, Tsumoto K, Yokota T, Anraku Y, Kataoka K
ACS Nano 2020 May 20

Highly sensitive HPLC analysis and biophysical characterization of N-glycans of IgG-Fc domain in comparison between CHO and 293 cells using FcγRIIIa ligand.
Kosuge H, Nagatoishi S, Kiyoshi M, Ishii-Watabe A, Tanaka T, Terao Y, Oe S, Ide T, Tsumoto K
Biotechnol Prog 2020 May 11

64Cu-labeled minibody D2101 visualizes CDH17-positive gastric cancer xenografts with short waiting time.
Fujiwara K, Akiba H, Tsuji AB, Sudo H, Sugyo A, Nagatsu K, Zhang MR, Iwanari H, Kusano-Arai O, Kudo S, Kikuchi C, Tsumoto K, Momose T, Hamakubo T, Higashi T
Nucl Med Commun 2020 May 1

GPC1 specific CAR-T cells eradicate established solid tumor without adverse effects and synergize with anti-PD-1 Ab.
Kato D, Yaguchi T, Iwata T, Katoh Y, Morii K, Tsubota K, Takise Y, Tamiya M, Kamada H, Akiba H, Tsumoto K, Serada S, Naka T, Nishimura R, Nakagawa T, Kawakami Y
Elife 2020 Mar 31

Computer-guided library generation applied to the optimization of single-domain antibodies.
Akiba H, Tamura H, Caaveiro JMM, Tsumoto K
Protein Eng Des Sel 2020 Mar 13

System-Wide Analysis of Protein Acetylation and Ubiquitination Reveals a Diversified Regulation in Human Cancer Cells.
Kozuka-Hata H, Kitamura A, Hiroki T, Aizawa A, Tsumoto K, Inoue JI, Oyama M
Biomolecules 2020 Mar 6

Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained.
Yasuda S, Akiyama T, Nemoto S, Hayashi T, Ueta T, Kojima K, Tsukamoto T, Nagatoishi S, Tsumoto K, Sudo Y, Kinoshita M, Murata T
J Chem Inf Model 2020 Mar 10

Generation of biparatopic antibody through two-step targeting of fragment antibodies on antigen using SpyTag and SpyCatcher.
Akiba H, Takayanagi K, Kusano-Arai O, Iwanari H, Hamakubo T, Tsumoto K
Biotechnol Rep (Amst) 2020 Mar

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design.
Kuroda D, Tsumoto K
J Pharm Sci 2020 Jan 17

Per-residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions.
Morimoto J, Kim J, Kuroda D, Nagatoishi S, Tsumoto K, Sando S
J Am Chem Soc 2020 Jan 9

Discovery of chemical probes that suppress Wnt/β-catenin signaling through high-throughput screening.
Yamaguchi K, Nagatoishi S, Tsumoto K, Furukawa Y
Cancer Sci 2020 Jan 7

Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16.
Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y
Sci Rep 2019 Dec 27

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations.
Kawade R, Kuroda D, Tsumoto K
FEBS Lett 2019 Nov 12

Technical capabilities and limitations of optical spectroscopy and calorimetry using water-miscible solvents: The case of dimethyl sulfoxide, acetonitrile and 1,4-dioxane.
Hirano A, Nagatoishi S, Wada M, Tsumoto K, Maluf KN, Arakawa T
J Pharm Sci 2019 Nov 1

Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.
Akiba H, Tamura H, Kiyoshi M, Yanaka S, Sugase K, Caaveiro JMM, Tsumoto K
Sci Rep 2019 Oct 29

¹¹¹In-labeled anti-cadherin17 antibody D2101 has potential as a noninvasive imaging probe for diagnosing gastric cancer and lymph-node metastasis.
Fujiwara K, Tsuji AB, Sudo H, Sugyo A, Akiba H, Iwanari H, Kusano-Arai O, Tsumoto K, Momose T, Hamakubo T, Higashi T
Ann Nucl Med 2019 Oct 12

Biophysical characterization of the breast cancer-related BIG3-PHB2 interaction: Effect of non-conserved loop region of BIG3 on the structure and the interaction.
Chigira T, Nagatoishi S, Takeda H, Yoshimaru T, Katagiri T, Tsumoto K
Biochem Biophys Res Commun 2019 Aug 14

A Peptoid with Extended Shape in Water.
Morimoto J, Fukuda Y, Kuroda D, Watanabe T, Yoshida F, Asada M, Nakamura T, Senoo A, Nagatoishi S, Tsumoto K, Sando S
J Am Chem Soc 2019 Aug 12

Highly sensitive biomolecular interaction detection method using optical bound/free separation with grating-coupled surface plasmon field-enhanced fluorescence spectroscopy (GC-SPFS).
Kaya T, Nagatoishi S, Nagae K, Nakamura Y, Tsumoto K
PLoS One 2019

The Isolation of New Pore-Forming Toxins from the Sea AnemoneActinia fragaceaProvides Insights into the Mechanisms of Actinoporin Evolution.
Morante K, Bellomio A, Viguera AR, González-Mañas JM, Tsumoto K, Caaveiro JMM
Toxins (Basel) 2019 Jul 10

Structural features of methionine aminopeptidase2-active core peptide essential for binding with S100A4.
Katagiri N, Nagatoishi S, Tsumoto K, Endo H
Biochem Biophys Res Commun2019 Jul 5

Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes.
Nakamura H, Fujii K, Gupta V, Hata H, Koizumu H, Hoshikawa M, Naruki S, Miyata Y, Takahashi I, Miyazawa T, Sakai H, Tsumoto K, Takagi M, Saji H, Nishimura T
PLoS One 2019

An epitope-directed antibody affinity maturation system utilizing mammalian cell survival as readout.
Eguchi A, Nakakido M, Nagatoishi S, Kuroda D, Tsumoto K, Nagamune T, Kawahara M
Biotechnol Bioeng 2019 Mar 18

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations.
Yoshida K, Kuroda D, Kiyoshi M, Nakakido M, Nagatoishi S, Soga S, Shirai H, Tsumoto K
Sci Rep 2019 Mar 14

Design strategy for serine hydroxymethyltransferase probes based on retro-aldol-type reaction.
Nonaka H, Nakanishi Y, Kuno S, Ota T, Mochidome K, Saito Y, Sugihara F, Takakusagi Y, Aoki I, Nagatoishi S, Tsumoto K, Sando S
Nat Commun 2019 Feb 20

Control of protein adsorption to cyclo olefin polymer by the Hofmeister effect.
Fujita R, Nagatoishi S, Adachi S, Nishioka H, Ninomiya H, Kaya T, Takai M, Arakawa T, Tsumoto K
J Pharm Sci 2019 Jan 8

Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium.
Yoshida K, Nagatoishi S, Kuroda D, Suzuki N, Murata T, Tsumoto K
Biochemistry 2019 Feb 12

Generation and characterization of antagonistic anti-human interleukin (IL)-18 monoclonal antibodies with high affinity: Two types of monoclonal antibodies against full-length IL-18 and the neoepitope of inflammatory caspase-cleaved active IL-18.
Nariai Y, Kamino H, Obayashi E, Kato H, Sakashita G, Sugiura T, Migita K, Koga T, Kawakami A, Sakamoto K, Kadomatsu K, Nakakido M, Tsumoto K, Urano T
Arch Biochem Biophys 2019 Mar 15

Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.
Yamashita T, Mizohata E, Nagatoishi S, Watanabe T, Nakakido M, Iwanari H, Mochizuki Y, Nakayama T, Kado Y, Yokota Y, Matsumura H, Kawamura T, Kodama T, Hamakubo T, Inoue T, Fujitani H, Tsumoto K
Structure 2018 Nov 20

Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition.
Takahashi T, Nagatoishi S, Kuroda D, Tsumoto K
PLoS One 2018

Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.
Tashima T, Nagatoishi S, Caaveiro JMM, Nakakido M, Sagara H, Kusano-Arai O, Iwanari H, Mimuro H, Hamakubo T, Ohnuma SI, Tsumoto K
Commun Biol 2018

Antibody Affinity Maturation by Computational Design.
Kuroda D, Tsumoto K
Methods Mol Biol 2018

Structural behavior of keratin-associated protein 8.1 in human hair as revealed by a monoclonal antibody.
Akiba H, Ikeuchi E, Ganbat J, Fujikawa H, Arai-Kusano O, Iwanari H, Nakakido M, Hamakubo T, Shimomura Y, Tsumoto K
J Struct Biol 2018 Nov

Improvement of antibody affinity by introduction of basic amino acid residues into the framework region.
Fukunaga A, Maeta S, Reema B, Nakakido M, Tsumoto K
Biochem Biophys Rep 2018 Sep

[Biophysical Analysis of the Protein-Small Molecule Interactions to Develop Small Molecule Drug Discovery].
Nagatoishi S, Caaveiro JMM, Tsumoto K
Yakugaku Zasshi 2018

Discovery and Optimization of Inhibitors of the Parkinson’s Disease Associated Protein DJ-1.
Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K
ACS Chem Biol 2018 Sep 21

Long-Term Stability and Reversible Thermal Unfolding of Antibody Structure at Low pH: Case Study.
Fukada H, Tsumoto K, Arakawa T, Ejima D
J Pharm Sci 2018 Nov

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, Caaveiro JMM, Tsumoto K
Biochemistry 2018 Jul 17

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.
Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K
J Biochem 2018 Jul 1

Roles of the disulfide bond between the variable and the constant domains of rabbit immunoglobulin kappa chains in thermal stability and affinity.
Kawade R, Akiba H, Entzminger K, Maruyama T, Okumura CJ, Tsumoto K
Protein Eng Des Sel 2018 Jul 1

Inhibition of homophilic dimerization and disruption of cell adhesion by P-cadherin-specific small molecules from SPR-based assays.
Senoo A, Nagatoishi S, Moberg A, Babol LN, Mitani T, Tashima T, Kudo S, Tsumoto K
Chem Commun (Camb) 2018 May 22

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.
Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ
Front Immunol 2018

A combination of¹⁹F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.
Nagatoishi S, Yamaguchi S, Katoh E, Kajita K, Yokotagawa T, Kanai S, Furuya T, Tsumoto K
Bioorg Med Chem 2018 May 1

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column.
Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, Ishii-Watabe A
Sci Rep 2018 Mar 2

Synergistic Cytotoxic Effect on Gastric Cancer Cells of an Immunotoxin Cocktail in Which Antibodies Recognize Different Epitopes on CDH17.
Kusano-Arai O, Iwanari H, Kudo S, Kikuchi C, Yui A, Akiba H, Matsusaka K, Kaneda A, Fukayama M, Tsumoto K, Hamakubo T
Monoclon Antib Immunodiagn Immunother 2018 Feb

Structures of the prefusion form of measles virus fusion protein in complex with inhibitors.
Hashiguchi T, Fukuda Y, Matsuoka R, Kuroda D, Kubota M, Shirogane Y, Watanabe S, Tsumoto K, Kohda D, Plemper RK, Yanagi Y
Proc Natl Acad Sci U S A 2018 Mar 6

Development of drug discovery screening system by molecular interaction kinetics-mass spectrometry.
Obi N, Fukuda T, Nakayama N, Ervin J, Bando Y, Nishimura T, Nagatoishi S, Tsumoto K, Kawamura T
Rapid Commun Mass Spectrom 2018 Apr 30

A secondary RET mutation in the activation loop conferring resistance to vandetanib.
Nakaoku T, Kohno T, Araki M, Niho S, Chauhan R, Knowles PP, Tsuchihara K, Matsumoto S, Shimada Y, Mimaki S, Ishii G, Ichikawa H, Nagatoishi S, Tsumoto K, Okuno Y, Yoh K, McDonald NQ, Goto K
Nat Commun 2018 Feb 12

Characterization of glycoengineered anti-HER2 monoclonal antibodies produced by using a silkworm-baculovirus expression system.
Egashira Y, Nagatoishi S, Kiyoshi M, Ishii-Watabe A, Tsumoto K
J Biochem 2018 Jun 1

Enzymatically cleavable traceless biotin tags for protein PEGylation and purification.
Wawro AM, Aoki Y, Muraoka T, Tsumoto K, Kinbara K
Chem Commun (Camb) 2018 Feb 15

Production and characterization of a novel site-specific-modifiable anti-OX40-receptor single-chain variable fragment for targeted drug delivery.
Tanabe A, Nakano K, Nakakido M, Nagatoishi S, Tanaka Y, Tsumoto K, Uchimaru K, Watanabe T
Biochem Biophys Res Commun 2018 Feb 5

Introduction: Antibody-Mediated Therapy Special Issue Part 2.
Nakamura A, Tsumoto K, Takai T
Int Immunol 2017 Dec 30

PRDM14 directly interacts with heat shock proteins HSP90α and glucose-regulated protein 78.
Moriya C, Taniguchi H, Nagatoishi S, Igarashi H, Tsumoto K, Imai K
Cancer Sci 2018 Feb

Thermodynamic analyses of amino acid residues at the interface of an antibody B2212A and its antigen roundabout homolog 1.
Yui A, Akiba H, Kudo S, Nakakido M, Nagatoishi S, Tsumoto K
J Biochem 2017 Oct 1

Analysis of Pore Formation and Protein Translocation Using Large Biological Nanopores.
Watanabe H, Gubbiotti A, Chinappi M, Takai N, Tanaka K, Tsumoto K, Kawano R
Anal Chem 2017 Nov 7

Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity.
Lee Y, Nishizawa T, Takemoto M, Kumazaki K, Yamashita K, Hirata K, Minoda A, Nagatoishi S, Tsumoto K, Ishitani R, Nureki O
Nat Plants 2017 Oct

Polymeric SpyCatcher Scaffold Enables Bioconjugation in a Ratio-Controllable Manner.
Jia L, Minamihata K, Ichinose H, Tsumoto K, Kamiya N
Biotechnol J 2017 Dec

Biophysical characterization of the interaction between heme and proteins responsible for heme transfer in Streptococcus pyogenes.
Hoshino M, Nakakido M, Nagatoishi S, Aikawa C, Nakagawa I, Tsumoto K
Biochem Biophys Res Commun 2017 Nov 18

Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Naoe Y, Nakamura N, Rahman MM, Tosha T, Nagatoishi S, Tsumoto K, Shiro Y, Sugimoto H
Proteins 2017 Dec

Elucidation of potential sites for antibody engineering by fluctuation editing.
Yanaka S, Moriwaki Y, Tsumoto K, Sugase K
Sci Rep 2017 Aug 30

Insight in the Evolution of Therapeutic Monoclonal Antibodies-Fundamental Technologies for Creation and Evaluation of Next Generation mAbs.
Ishii-Watabe A, Tsumoto K
Yakugaku Zasshi 2017

Glycosylation of IgG-Fc: a molecular perspective.
Kiyoshi M, Tsumoto K, Ishii-Watabe A, Caaveiro JMM
Int Immunol 2017 Jul 1

Use of SpyTag/SpyCatcher to construct bispecific antibodies that target two epitopes of a single antigen.
Yumura K, Akiba H, Nagatoishi S, Kusano-Arai O, Iwanari H, Hamakubo T, Tsumoto K
J Biochem 2017 Sep 1

Haemolytic actinoporins interact with carbohydrates using their lipid-binding module.
Tanaka K, Caaveiro JMM, Morante K, Tsumoto K
Philos Trans R Soc Lond B Biol Sci 2017 Aug 5

Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane.
Rujas E, Insausti S, García-Porras M, Sánchez-Eugenia R, Tsumoto K, Nieva JL, Caaveiro JM
J Mol Biol 2017 Apr 21

Peripheral Membrane Interactions Boost the Engagement by an Anti-HIV-1 Broadly Neutralizing Antibody.
Rujas E, Caaveiro JM, Insausti S, García-Porras M, Tsumoto K, Nieva JL
J Biol Chem 2017 Mar 31

The carboxyl-terminal region of Dok-7 plays a key, but not essential, role in activation of muscle-specific receptor kinase MuSK and neuromuscular synapse formation.
Ueta R, Tezuka T, Izawa Y, Miyoshi S, Nagatoishi S, Tsumoto K, Yamanashi Y
J Biochem 2017 Mar 1

Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin.
Kudo S, Caaveiro JM, Nagatoishi S, Miyafusa T, Matsuura T, Sudou Y, Tsumoto K
Sci Rep 2017 Jan 3

Differential Effect of Membrane Composition on the Pore-Forming Ability of Four Different Sea Anemone Actinoporins.
García-Linares S, Rivera-de-Torre E, Morante K, Tsumoto K, Caaveiro JM, Gavilanes JG, Slotte JP, Martínez-Del-Pozo Á
Biochemistry 2016 Dec 6

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface.
Rujas E, Caaveiro JM, Partida-Hanon A, Gulzar N, Morante K, Apellániz B, García-Porras M, Bruix M, Tsumoto K, Scott JK, Jiménez MÁ, Nieva JL
Sci Rep 2016 Dec 1

Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers.
Pica A, Russo Krauss I, Parente V, Tateishi-Karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F
Nucleic Acids Res 2017 Jan 9

Production and characterization of genetically modified human IL-11 variants.
Sano E, Takei T, Ueda T, Tsumoto K
Biochim Biophys Acta Gen Subj 2017 Feb

Improved Brain Expression of Anti-Amyloid β scFv by Complexation of mRNA Including a Secretion Sequence with PEG-based Block Catiomer.
Perche F, Uchida S, Akiba H, Lin CY, Ikegami M, Dirisala A, Nakashima T, Itaka K, Tsumoto K, Kataoka K
Curr Alzheimer Res 2017

Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism.
Kudo S, Caaveiro JM, Tsumoto K
Structure 2016 Sep 6

In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis.
Sigala PA, Morante K, Tsumoto K, Caaveiro JM, Goldberg DE
Biochemistry 2016 Aug 30

Identification of a Membrane-bound Prepore Species Clarifies the Lytic Mechanism of Actinoporins.
Morante K, Bellomio A, Gil-Cartón D, Redondo-Morata L, Sot J, Scheuring S, Valle M, González-Mañas JM, Tsumoto K, Caaveiro JMM
J Biol Chem 2016 Sep 9

Structural basis for amino acid export by DMT superfamily transporter YddG.
Tsuchiya H, Doki S, Takemoto M, Ikuta T, Higuchi T, Fukui K, Usuda Y, Tabuchi E, Nagatoishi S, Tsumoto K, Nishizawa T, Ito K, Dohmae N, Ishitani R, Nureki O
Nature 2016 Jun 16

Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome analysis.
Narushima Y, Kozuka-Hata H, Tsumoto K, Inoue J, Oyama M
Bioinformatics 2016 Jul 15

Reply to “The Broadly Neutralizing, Anti-HIV Antibody 4E10: an Open and Shut Case?”.
Rujas E, Gulzar N, Morante K, Tsumoto K, Scott JK, Nieva JL, Caaveiro JM
J Virol 2016 Mar

Assessment of the Protein-Protein Interactions in a Highly Concentrated Antibody Solution by Using Raman Spectroscopy.
Ota C, Noguchi S, Nagatoishi S, Tsumoto K
Pharm Res 2016 Apr

Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties.
Narushima Y, Kozuka-Hata H, Koyama-Nasu R, Tsumoto K, Inoue J, Akiyama T, Oyama M
Mol Cell Proteomics 2016 Mar

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations.
Moriwaki Y, Terada T, Tsumoto K, Shimizu K
PLoS One 2015

Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.
Kado Y, Mizohata E, Nagatoishi S, Iijima M, Shinoda K, Miyafusa T, Nakayama T, Yoshizumi T, Sugiyama A, Kawamura T, Lee YH, Matsumura H, Doi H, Fujitani H, Kodama T, Shibasaki Y, Tsumoto K, Inoue T
J Biol Chem 2016 Jan 29

Mitochonic Acid 5 Binds Mitochondria and Ameliorates Renal Tubular and Cardiac Myocyte Damage.
Suzuki T, Yamaguchi H, Kikusato M, Hashizume O, Nagatoishi S, Matsuo A, Sato T, Kudo T, Matsuhashi T, Murayama K, Ohba Y, Watanabe S, Kanno S, Minaki D, Saigusa D, Shinbo H, Mori N, Yuri A, Yokoro M, Mishima E, Shima H, Akiyama Y, Takeuchi Y, Kikuchi K, Toyohara T, Suzuki C, Ichimura T, Anzai J, Kohzuki M, Mano N, Kure S, Yanagisawa T, Tomioka Y, Toyomizu M, Tsumoto K, Nakada K, Bonventre JV, Ito S, Osaka H, Hayashi K, Abe T
J Am Soc Nephrol 2016 Jul

Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States.
Tanaka K, Caaveiro JM, Tsumoto K
Biochemistry 2015 Nov 24

Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach.
Bai Y, Tashiro S, Nagatoishi S, Suzuki T, Yan D, Liu R, Tsumoto K, Bartlam M, Yamamoto T
Protein Cell 2015 Dec

Structural analysis of Fc/FcγR complexes: a blueprint for antibody design.
Caaveiro JM, Kiyoshi M, Tsumoto K
Immunol Rev 2015 Nov

Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus.
Nakano K, Chigira T, Miyafusa T, Nagatoishi S, Caaveiro JM, Tsumoto K
Sci Rep 2015 Oct 16

Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10.
Rujas E, Gulzar N, Morante K, Tsumoto K, Scott JK, Nieva JL, Caaveiro JM
J Virol 2015 Dec

Differential Effects of IFN-β on the Survival and Growth of Human Vascular Smooth Muscle and Endothelial Cells.
Sano E, Tashiro S, Tsumoto K, Ueda T
Biores Open Access 2015

Thermodynamic characterization of the interaction between the human Y-box binding protein YB-1 and nucleic acids.
Tanabe Y, Nagatoishi S, Tsumoto K
Mol Biosyst 2015 Sep

Functional characterization of Val60, a key residue involved in the membrane-oligomerization of fragaceatoxin C, an actinoporin from Actinia fragacea.
Morante K, Caaveiro JM, Viguera AR, Tsumoto K, González-Mañas JM
FEBS Lett 2015 Jul 8

Differential binding of prohibitin-2 to estrogen receptor α and to drug-resistant ERα mutants.
Chigira T, Nagatoishi S, Tsumoto K
Biochem Biophys Res Commun 2015 Aug 7

Osteomodulin regulates diameter and alters shape of collagen fibrils.
Tashima T, Nagatoishi S, Sagara H, Ohnuma S, Tsumoto K
Biochem Biophys Res Commun 2015 Jul 31

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.
Akiba H, Tsumoto K
J Biochem 2015 Jul

Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI.
Kiyoshi M, Caaveiro JM, Kawai T, Tashiro S, Ide T, Asaoka Y, Hatayama K, Tsumoto K
Nat Commun 2015 Apr 30

Protein stabilization by an amphiphilic short monodisperse oligo(ethylene glycol).
Sadhukhan N, Muraoka T, Ui M, Nagatoishi S, Tsumoto K, Kinbara K
Chem Commun (Camb) 2015 May 18

The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region.
Apellániz B, Rujas E, Serrano S, Morante K, Tsumoto K, Caaveiro JM, Jiménez MÁ, Nieva JL
J Biol Chem 2015 May 22

A pore-forming toxin requires a specific residue for its activity in membranes with particular physicochemical properties.
Morante K, Caaveiro JM, Tanaka K, González-Mañas JM, Tsumoto K
J Biol Chem 2015 Apr 24

Click conjugation of a binuclear terbium(III) complex for real-time detection of tyrosine phosphorylation.
Akiba H, Sumaoka J, Tsumoto K, Komiyama M
Anal Chem 2015 Apr 7

Structural basis for self-assembly of a cytolytic pore lined by protein and lipid.
Tanaka K, Caaveiro JM, Morante K, González-Mañas JM, Tsumoto K
Nat Commun 2015 Feb 26

pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides.
Takei T, Tsumoto K, Okonogi A, Kimura A, Kojima S, Yazaki K, Takei T, Ueda T, Miura K
Protein Sci 2015 May

Revealing the peptide presenting process of human leukocyte antigen through the analysis of fluctuation.
Yanaka S, Ueno T, Tsumoto K, Sugase K
Biophysics (Nagoya-shi) 2015

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.
Nakayama T, Mizohata E, Yamashita T, Nagatoishi S, Nakakido M, Iwanari H, Mochizuki Y, Kado Y, Yokota Y, Satoh R, Tsumoto K, Fujitani H, Kodama T, Hamakubo T, Inoue T
Protein Sci 2015 Mar

Quantitative laser diffraction method for the assessment of protein subvisible particles.
Totoki S, Yamamoto G, Tsumoto K, Uchiyama S, Fukui K
J Pharm Sci 2015 Feb

Crystal structure of streptavidin mutant with low immunogenicity.
Kawato T, Mizohata E, Meshizuka T, Doi H, Kawamura T, Matsumura H, Yumura K, Tsumoto K, Kodama T, Inoue T, Sugiyama A
J Biosci Bioeng 2015 Jun

The molecular interaction of a protein in highly concentrated solution investigated by Raman spectroscopy.
Ota C, Noguchi S, Tsumoto K
Biopolymers 2015 Apr

Efficacy of ribavirin against malignant glioma cell lines.
Ogino A, Sano E, Ochiai Y, Yamamuro S, Tashiro S, Yachi K, Ohta T, Fukushima T, Okamoto Y, Tsumoto K, Ueda T, Yoshino A, Katayama Y
Oncol Lett 2014 Dec

Preparation and characterization of anti-tissue factor single-chain variable fragment antibody for cancer diagnosis.
Sato R, Obonai T, Tsumura R, Tsumoto K, Koga Y, Yasunaga M, Matsumura Y
Cancer Sci 2014 Dec

Reversible ion transportation switch by a ligand-gated synthetic supramolecular ion channel.
Muraoka T, Endo T, Tabata KV, Noji H, Nagatoishi S, Tsumoto K, Li R, Kinbara K
J Am Chem Soc 2014 Nov 5

Recent advances in antibody engineering.
Tsumoto K, Hagihara Y, Saerens D
Biochim Biophys Acta 2014 Nov

Grafting synthetic transmembrane units to the engineered low-toxicity α-hemolysin to restore its hemolytic activity.
Ui M, Harima K, Takei T, Tsumoto K, Tabata KV, Noji H, Endo S, Akiyama K, Muraoka T, Kinbara K
Mol Biosyst 2014 Dec

Effects of syringe material and silicone oil lubrication on the stability of pharmaceutical proteins.
Krayukhina E, Tsumoto K, Uchiyama S, Fukui K
J Pharm Sci 2015 Feb

Protective effect of the long pentraxin PTX3 against histone-mediated endothelial cell cytotoxicity in sepsis.
Daigo K, Nakakido M, Ohashi R, Fukuda R, Matsubara K, Minami T, Yamaguchi N, Inoue K, Jiang S, Naito M, Tsumoto K, Hamakubo T
Sci Signal 2014 Sep 16

Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex.
Yanaka S, Ueno T, Shi Y, Qi J, Gao GF, Tsumoto K, Sugase K
J Biol Chem 2014 Aug 29

Next generation drying technologies for pharmaceutical applications.
Walters RH, Bhatnagar B, Tchessalov S, Izutsu KI, Tsumoto K, Ohtake S
J Pharm Sci 2014 Sep

Alternative downstream processes for production of antibodies and antibody fragments.
Arakawa T, Tsumoto K, Ejima D
Biochim Biophys Acta 2014 Nov

The staphylococcal elastin-binding protein regulates zinc-dependent growth/biofilm formation.
Nakakido M, Aikawa C, Nakagawa I, Tsumoto K
J Biochem 2014 Sep

Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
Tashiro S, Caaveiro JM, Wu CX, Hoang QQ, Tsumoto K
Biochemistry 2014 Apr 15

Role of positions e and g in the fibrous assembly formation of an amphipathic α-helix-forming polypeptide.
Takei T, Tsumoto K, Yoshino M, Kojima S, Yazaki K, Ueda T, Takei T, Arisaka F, Miura K
Biopolymers 2014 May

Identification and characterization of the X-dimer of human P-cadherin: implications for homophilic cell adhesion.
Kudo S, Caaveiro JM, Goda S, Nagatoishi S, Ishii K, Matsuura T, Sudou Y, Kodama T, Hamakubo T, Tsumoto K
Biochemistry 2014 Mar 25

Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex.
Kiyoshi M, Caaveiro JM, Miura E, Nagatoishi S, Nakakido M, Soga S, Shirai H, Kawabata S, Tsumoto K
PLoS One 2014

Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.
Moriwaki Y, Terada T, Caaveiro JM, Takaoka Y, Hamachi I, Tsumoto K, Shimizu K
Biochemistry 2013 Dec 10

Improving the affinity of an antibody for its antigen via long-range electrostatic interactions.
Fukunaga A, Tsumoto K
Protein Eng Des Sel 2013 Dec

Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.
Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K
FEBS Lett 2013 Nov 29

Discovery of an uncovered region in fibrin clots and its clinical significance.
Hisada Y, Yasunaga M, Hanaoka S, Saijou S, Sugino T, Tsuji A, Saga T, Tsumoto K, Manabe S, Kuroda J, Kuratsu J, Matsumura Y
Sci Rep 2013

Effects of subclass change on the structural stability of chimeric, humanized, and human antibodies under thermal stress.
Ito T, Tsumoto K
Protein Sci 2013 Nov

Hyperthin nanochains composed of self-polymerizing protein shackles.
Matsunaga R, Yanaka S, Nagatoishi S, Tsumoto K
Nat Commun 2013

Bidirectional binding property of high glycine-tyrosine keratin-associated protein contributes to the mechanical strength and shape of hair.
Matsunaga R, Abe R, Ishii D, Watanabe SI, Kiyoshi M, Nöcker B, Tsuchiya M, Tsumoto K
J Struct Biol 2013 Sep

Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus.
Vu NT, Moriwaki Y, Caaveiro JM, Terada T, Tsutsumi H, Hamachi I, Shimizu K, Tsumoto K
Protein Sci 2013 Jul

Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
Miyafusa T, Caaveiro JM, Tanaka Y, Tanner ME, Tsumoto K
Biosci Rep 2013 Jun 11

Heme degradation by Staphylococcus aureus IsdG and IsdI liberates formaldehyde rather than carbon monoxide.
Matsui T, Nambu S, Ono Y, Goulding CW, Tsumoto K, Ikeda-Saito M
Biochemistry 2013 May 7

Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation.
Takei T, Hasegawa K, Imada K, Namba K, Tsumoto K, Kuriki Y, Yoshino M, Yazaki K, Kojima S, Takei T, Ueda T, Miura K
Biochemistry 2013 Apr 23

Incorporation of rapid thermodynamic data in fragment-based drug discovery.
Kobe A, Caaveiro JM, Tashiro S, Kajihara D, Kikkawa M, Mitani T, Tsumoto K
J Med Chem 2013 Mar 14

Identification of small-molecule inhibitors of the human S100B-p53 interaction and evaluation of their activity in human melanoma cells.
Yoshimura C, Miyafusa T, Tsumoto K
Bioorg Med Chem 2013 Mar 1

Secretory production of single-chain antibody (scFv) in Brevibacillus choshinensis using novel fusion partner.
Tokunaga M, Mizukami M, Yamasaki K, Tokunaga H, Onishi H, Hanagata H, Ishibashi M, Miyauchi A, Tsumoto K, Arakawa T
Appl Microbiol Biotechnol 2013 Oct

Mutations for decreasing the immunogenicity and maintaining the function of core streptavidin.
Yumura K, Ui M, Doi H, Hamakubo T, Kodama T, Tsumoto K, Sugiyama A
Protein Sci 2013 Feb

Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion.
Harada K, Yamashita E, Nakagawa A, Miyafusa T, Tsumoto K, Ueno T, Toyama Y, Takeda S
Biochim Biophys Acta 2013 Jan

Phosphoproteome of human glioblastoma initiating cells reveals novel signaling regulators encoded by the transcriptome.
Kozuka-Hata H, Nasu-Nishimura Y, Koyama-Nasu R, Ao-Kondo H, Tsumoto K, Akiyama T, Oyama M
PLoS One 2012

Type 1 IFN inhibits the growth factor deprived apoptosis of cultured human aortic endothelial cells and protects the cells from chemically induced oxidative cytotoxicity.
Sano E, Tashiro S, Tadakuma H, Takei T, Ueda T, Tsumoto K
J Cell Biochem 2012 Dec

Thermodynamic analysis of a multifunctional RNA-binding protein, PhoRpp38, in the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Oshima K, Nakashima T, Kakuta Y, Tsumoto K, Kimura M
Biosci Biotechnol Biochem 2012

Structural and thermodynamic characterization of the self-adhesive properties of human P-cadherin.
Kudo S, Caaveiro JM, Miyafusa T, Goda S, Ishii K, Matsuura T, Sudou Y, Kodama T, Hamakubo T, Tsumoto K
Mol Biosyst 2012 Aug

Application of photoactive yellow protein as a photoresponsive module for controlling hemolytic activity of staphylococcal α-hemolysin.
Ui M, Tanaka Y, Araki Y, Wada T, Takei T, Tsumoto K, Endo S, Kinbara K
Chem Commun (Camb) 2012 May 16

Establishment of a microcarrier culture system with serial sub-cultivation for functionally active human endothelial cells.
Tashiro S, Tsumoto K, Sano E
J Biotechnol 2012 Aug 31

Mapping ultra-weak protein-protein interactions between heme transporters of Staphylococcus aureus.
Abe R, Caaveiro JM, Kozuka-Hata H, Oyama M, Tsumoto K
J Biol Chem 2012 May 11

Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains.
Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K
Biochem J 2012 May 1

Interleukin-11 links oxidative stress and compensatory proliferation.
Nishina T, Komazawa-Sakon S, Yanaka S, Piao X, Zheng DM, Piao JH, Kojima Y, Yamashina S, Sano E, Putoczki T, Doi T, Ueno T, Ezaki J, Ushio H, Ernst M, Tsumoto K, Okumura K, Nakano H
Sci Signal 2012 Jan 17

Catalytic activity of MsbA reconstituted in nanodisc particles is modulated by remote interactions with the bilayer.
Kawai T, Caaveiro JM, Abe R, Katagiri T, Tsumoto K
FEBS Lett 2011 Nov 16

Gene expression profiles predicting the response to IFN-β and a combination of temozolomide and IFN-β in malignant gliomas.
Yoshino A, Tashiro S, Ogino A, Yachi K, Ohta T, Fukushima T, Watanabe T, Katayama Y, Okamoto Y, Sano E, Tsumoto K
Int J Oncol 2011 Sep

Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus.
Moriwaki Y, Caaveiro JM, Tanaka Y, Tsutsumi H, Hamachi I, Tsumoto K
Biochemistry 2011 Aug 30

Hydration is required in DNA G-quadruplex-protein binding.
Nagatoishi S, Isono N, Tsumoto K, Sugimoto N
Chembiochem 2011 Aug 16

Monoubiquitination of Tob/BTG family proteins competes with degradation-targeting polyubiquitination.
Suzuki T, Kim M, Kozuka-Hata H, Watanabe M, Oyama M, Tsumoto K, Yamamoto T
Biochem Biophys Res Commun 2011 May 27

Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding.
Nagatoishi S, Isono N, Tsumoto K, Sugimoto N
Biochimie 2011 Aug

Stepwise characterization of the thermodynamics of trichocyte intermediate filament protein supramolecular assembly.
Ishii D, Abe R, Watanabe S, Tsuchiya M, Nöcker B, Tsumoto K
J Mol Biol 2011 May 20

Refolding single-chain antibody (scFv) using lauroyl-L-glutamate as a solubilization detergent and arginine as a refolding additive.
Kudou M, Ejima D, Sato H, Yumioka R, Arakawa T, Tsumoto K
Protein Expr Purif 2011 May

An approach to rational ligand-design based on a thermodynamic analysis.
Ui M, Tsumoto K
Recent Pat Biotechnol 2010 Nov

Structural and energetic hot-spots for the interaction between a ladder-like polycyclic ether and the anti-ciguatoxin antibody 10C9Fab.
Ui M, Tanaka Y, Tsumuraya T, Fujii I, Inoue M, Hirama M, Tsumoto K
Mol Biosyst 2011 Mar

Non-core region modulates interleukin-11 signaling activity: generation of agonist and antagonist variants.
Yanaka S, Sano E, Naruse N, Miura K, Futatsumori-Sugai M, Caaveiro JM, Tsumoto K
J Biol Chem 2011 Mar 11

Chemical and pharmacological chaperones: application for recombinant protein production and protein folding diseases.
Rajan RS, Tsumoto K, Tokunaga M, Tokunaga H, Kita Y, Arakawa T
Curr Med Chem 2011

Salicylate restores transport function and anion exchanger activity of missense pendrin mutations.
Ishihara K, Okuyama S, Kumano S, Iida K, Hamana H, Murakoshi M, Kobayashi T, Usami S, Ikeda K, Haga Y, Tsumoto K, Nakamura H, Hirasawa N, Wada H
Hear Res 2010 Dec 1

A novel protein refolding system using lauroyl-l-glutamate as a solubilizing detergent and arginine as a folding assisting agent.
Kudou M, Yumioka R, Ejima D, Arakawa T, Tsumoto K
Protein Expr Purif 2011 Jan

The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin.
Shinohara M, Guo JX, Mori M, Nakashima T, Takagi H, Nishimoto E, Yamashita S, Tsumoto K, Kakuta Y, Kimura M
Biochem Biophys Res Commun 2010 Sep 24

Expression of antibody variable region-human alkaline phosphatase fusion proteins in mammalian cells.
Sasajima Y, Iwasaki R, Tsumoto K, Kumagai I, Ihara M, Ueda H
J Immunol Methods 2010 Sep 30

Gene expression profiling predicts response to temozolomide in malignant gliomas.
Yoshino A, Ogino A, Yachi K, Ohta T, Fukushima T, Watanabe T, Katayama Y, Okamoto Y, Naruse N, Sano E, Tsumoto K
Int J Oncol 2010 Jun

Salicylate-induced translocation of prestin having mutation in the GTSRH sequence to the plasma membrane.
Kumano S, Iida K, Ishihara K, Murakoshi M, Tsumoto K, Ikeda K, Kumagai I, Kobayashi T, Wada H
FEBS Lett 2010 Jun 3

Solubilization of membrane proteins with novel N-acylamino acid detergents.
Abe R, Caaveiro JM, Kudou M, Tsumoto K
Mol Biosyst 2010 Apr

Step-wise refolding of recombinant proteins.
Tsumoto K, Arakawa T, Chen L
Curr Pharm Biotechnol 2010 Apr

Non-denaturing solubilization of inclusion bodies.
Tsumoto K, Abe R, Ejima D, Arakawa T
Curr Pharm Biotechnol 2010 Apr

Contribution of the flexible loop region to the function of staphylococcal enterotoxin B.
Yanaka S, Kudou M, Tanaka Y, Sasaki T, Takemoto S, Sakata A, Hattori Y, Koshi T, Futaki S, Tsumoto K, Nakashima T
Protein Eng Des Sel 2010 May

Reactive oxygen species induced by Streptococcus pyogenes invasion trigger apoptotic cell death in infected epithelial cells.
Aikawa C, Nozawa T, Maruyama F, Tsumoto K, Hamada S, Nakagawa I
Cell Microbiol 2010 Jun

Temperature and salt concentration alter base-sequence selectivity of a duplex DNA-binding protein.
Nagatoishi S, Tanaka Y, Kudou M, Tsumoto K
Mol Biosyst 2010 Jan

Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme.
Yokota A, Tsumoto K, Shiroishi M, Nakanishi T, Kondo H, Kumagai I
J Biol Chem 2010 Mar 5

Direct and selective immobilization of proteins by means of an inorganic material-binding peptide: discussion on functionalization in the elongation to material-binding peptide.
Yokoo N, Togashi T, Umetsu M, Tsumoto K, Hattori T, Nakanishi T, Ohara S, Takami S, Naka T, Abe H, Kumagai I, Adschiri T
J Phys Chem B 2010 Jan 14

Signal peptide design for improving recombinant protein secretion in the baculovirus expression vector system.
Futatsumori-Sugai M, Tsumoto K
Biochem Biophys Res Commun 2010 Jan 1

MEP HyperCel chromatography II: binding, washing and elution.
Arakawa T, Futatsumori-Sugai M, Tsumoto K, Kita Y, Sato H, Ejima D
Protein Expr Purif 2010 Jun

[Rational fragment-design method based on a thermodynamic analysis].
Tsumoto K, Ui M
Yakugaku Zasshi 2009 Nov

Screening of effective column rinse solvent for Protein-A chromatography.
Yumioka R, Tsumoto K, Arakawa T, Ejima D
Protein Expr Purif 2010 Apr

Observation of the membrane binding activity and domain structure of gpV, which comprises the tail spike of bacteriophage P2.
Kageyama Y, Murayama M, Onodera T, Yamada S, Fukada H, Kudou M, Tsumoto K, Toyama Y, Kado S, Kubota K, Takeda S
Biochemistry 2009 Oct 27

The interaction of hyperthermophilic TATA-box binding protein with single-stranded DNA is entropically favorable and exhibits a large negative heat capacity change at high salt concentration.
Nagatoishi S, Tanaka Y, Kudou M, Tsumoto K
Mol Biosyst 2009 Sep

[Recognition mechanism for poly-cyclic ether toxin by anti-ciguatoxin antibody].
Ui M, Tsumoto K
Tanpakushitsu Kakusan Koso 2009 Jul

To be excluded or to bind, that is the question: Arginine effects on proteins.
Nakakido M, Kudou M, Arakawa T, Tsumoto K
Curr Pharm Biotechnol 2009 Jun

Contributions of interfacial residues of human Interleukin15 to the specificity and affinity for its private alpha-receptor.
Sakamoto S, Caaveiro JM, Sano E, Tanaka Y, Kudou M, Tsumoto K
J Mol Biol 2009 Jun 26

Impact of intrinsic cooperative thermodynamics of peptide-MHC complexes on antiviral activity of HIV-specific CTL.
Motozono C, Yanaka S, Tsumoto K, Takiguchi M, Ueno T
J Immunol 2009 May 1

Utilization of Arg-elution method for FLAG-tag based chromatography.
Futatsumori-Sugai M, Abe R, Watanabe M, Kudou M, Yamamoto T, Ejima D, Arakawa T, Tsumoto K
Protein Expr Purif 2009 Oct

Immobilized metal affinity chromatography in the presence of arginine.
Abe R, Kudou M, Tanaka Y, Arakawa T, Tsumoto K
Biochem Biophys Res Commun 2009 Apr 10

Molecular glues carrying multiple guanidinium ion pendants via an oligoether spacer: stabilization of microtubules against depolymerization.
Okuro K, Kinbara K, Tsumoto K, Ishii N, Aida T
J Am Chem Soc 2009 Feb 11

Activation of leukemia-associated RhoGEF by Galpha13 with significant conformational rearrangements in the interface.
Suzuki N, Tsumoto K, Hajicek N, Daigo K, Tokita R, Minami S, Kodama T, Hamakubo T, Kozasa T
J Biol Chem 2009 Feb 20

Growth control of hybridoma cells with an artificially induced EpoR-gp130 heterodimer.
Kawahara M, Ogo Y, Tsumoto K, Kumagai I, Ueda H, Nagamune T
Cytotechnology 2006 Nov

Electron microscopy and computational studies of Ebh, a giant cell-wall-associated protein from Staphylococcus aureus.
Sakamoto S, Tanaka Y, Tanaka I, Takei T, Yu J, Kuroda M, Yao M, Ohta T, Tsumoto K
Biochem Biophys Res Commun 2008 Nov 14

Structure-based analysis reveals hydration changes induced by arginine hydrochloride.
Nakakido M, Tanaka Y, Mitsuhori M, Kudou M, Ejima D, Arakawa T, Tsumoto K
Biophys Chem 2008 Oct

Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus.
Watanabe M, Tanaka Y, Suenaga A, Kuroda M, Yao M, Watanabe N, Arisaka F, Ohta T, Tanaka I, Tsumoto K
J Biol Chem 2008 Oct 17

Staphylococcus aureus giant protein Ebh is involved in tolerance to transient hyperosmotic pressure.
Kuroda M, Tanaka Y, Aoki R, Shu D, Tsumoto K, Ohta T
Biochem Biophys Res Commun 2008 Sep 19

Selective expansion of genetically modified T cells using an antibody/interleukin-2 receptor chimera.
Sogo T, Kawahara M, Tsumoto K, Kumagai I, Ueda H, Nagamune T
J Immunol Methods 2008 Aug 20

Expression, purification, crystallization and preliminary diffraction analysis of CapF, a capsular polysaccharide-synthesis enzyme from Staphylococcus aureus.
Miyafusa T, Tanaka Y, Kuroda M, Ohta T, Tsumoto K
Acta Crystallogr Sect F Struct Biol Cryst Commun 2008 Jun 1

How protein recognizes ladder-like polycyclic ethers. Interactions between ciguatoxin (CTX3C) fragments and its specific antibody 10C9.
Ui M, Tanaka Y, Tsumuraya T, Fujii I, Inoue M, Hirama M, Tsumoto K
J Biol Chem 2008 Jul 11

Thermodynamic analysis reveals that GTP binding affects the interaction between the alpha- and gamma-subunits of translation initiation factor 2.
Nakakido M, Tanaka Y, Sokabe M, Tsumoto K
Biochem Biophys Res Commun 2008 Jul 11

A helical string of alternately connected three-helix bundles for the cell wall-associated adhesion protein Ebh from Staphylococcus aureus.
Tanaka Y, Sakamoto S, Kuroda M, Goda S, Gao YG, Tsumoto K, Hiragi Y, Yao M, Watanabe N, Ohta T, Tanaka I
Structure 2008 Mar

Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49.
Tsumoto K, Yokota A, Tanaka Y, Ui M, Tsumuraya T, Fujii I, Kumagai I, Nagumo Y, Oguri H, Inoue M, Hirama M
J Biol Chem 2008 May 2

[Solvent modulation of chromatography].
Arakawa T, Ejima D, Tsumoto K, Gagnon P
Seikagaku 2008 Jan

Effect of an amyloidogenic sequence attached to yellow fluorescent protein.
Hamada D, Tsumoto K, Sawara M, Tanaka N, Nakahira K, Shiraki K, Yanagihara I
Proteins 2008 Aug 15

Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10.
Nakanishi T, Tsumoto K, Yokota A, Kondo H, Kumagai I
Protein Sci 2008 Feb

Grafting of material-binding function into antibodies Functionalization by peptide grafting.
Hattori T, Umetsu M, Nakanishi T, Tsumoto K, Ohara S, Abe H, Naito M, Asano R, Adschiri T, Kumagai I
Biochem Biophys Res Commun 2008 Jan 25

Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528.
Makabe K, Nakanishi T, Tsumoto K, Tanaka Y, Kondo H, Umetsu M, Sone Y, Asano R, Kumagai I
J Biol Chem 2008 Jan 11

Human CD4+ central and effector memory T cells produce IL-21: effect on cytokine-driven proliferation of CD4+ T cell subsets.
Onoda T, Rahman M, Nara H, Araki A, Makabe K, Tsumoto K, Kumagai I, Kudo T, Ishii N, Tanaka N, Sugamura K, Hayasaka K, Asao H
Int Immunol 2007 Oct

Crystal structure analysis reveals a novel forkhead-associated domain of ESAT-6 secretion system C protein in Staphylococcus aureus.
Tanaka Y, Kuroda M, Yasutake Y, Yao M, Tsumoto K, Watanabe N, Ohta T, Tanaka I
Proteins 2007 Nov 15

The N-terminal domain of elastin-binding protein of Staphylococcus aureus changes its secondary structure in a membrane-mimetic environment.
Nakakido M, Tanaka Y, Tsumoto K
J Biochem 2007 Aug

Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii.
Tanaka Y, Sasaki T, Kumagai I, Yasutake Y, Yao M, Tanaka I, Tsumoto K
Proteins 2007 Aug 1

Arginine improves protein elution in hydrophobic interaction chromatography. The cases of human interleukin-6 and activin-A.
Tsumoto K, Ejima D, Nagase K, Arakawa T
J Chromatogr A 2007 Jun 22

Mimicry of erythropoietin and interleukin-6 signalling by an antibody/cytokine receptor chimera in murine myeloid 32D cells.
Kawahara M, Ueda H, Tsumoto K, Kumagai I, Nagamune T
J Biochem 2007 Apr

The effects of arginine on protein binding and elution in hydrophobic interaction and ion-exchange chromatography.
Arakawa T, Tsumoto K, Nagase K, Ejima D
Protein Expr Purif 2007 Jul

A human antibody fragment with high affinity for biodegradable polymer film.
Watanabe H, Tsumoto K, Taguchi S, Yamashita K, Doi Y, Nishimiya Y, Kondo H, Umetsu M, Kumagai I
Bioconjug Chem 2007 May-Jun

Suppression of protein interactions by arginine: a proposed mechanism of the arginine effects.
Arakawa T, Ejima D, Tsumoto K, Obeyama N, Tanaka Y, Kita Y, Timasheff SN
Biophys Chem 2007 Apr

Effects of salts on protein-surface interactions: applications for column chromatography.
Tsumoto K, Ejima D, Senczuk AM, Kita Y, Arakawa T
J Pharm Sci 2007 Jul

Induced binding of proteins by ammonium sulfate in affinity and ion-exchange column chromatography.
Arakawa T, Tsumoto K, Ejima D, Kita Y, Yonezawa Y, Tokunaga M
J Biochem Biophys Methods 2007 Apr 10

Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.
Tanaka Y, Morikawa K, Ohki Y, Yao M, Tsumoto K, Watanabe N, Ohta T, Tanaka I
J Biol Chem 2007 Feb 23

Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.
Shiroishi M, Tsumoto K, Tanaka Y, Yokota A, Nakanishi T, Kondo H, Kumagai I
J Biol Chem 2007 Mar 2

Effects of acid exposure on the conformation, stability, and aggregation of monoclonal antibodies.
Ejima D, Tsumoto K, Fukada H, Yumioka R, Nagase K, Arakawa T, Philo JS
Proteins 2007 Mar 1

Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions.
Nagatoishi S, Tanaka Y, Tsumoto K
Biochem Biophys Res Commun 2007 Jan 19

Improved performance of column chromatography by arginine: dye-affinity chromatography.
Arakawa T, Ejima D, Tsumoto K, Ishibashi M, Tokunaga M
Protein Expr Purif 2007 Apr

Aggregation suppression of proteins by arginine during thermal unfolding.
Arakawa T, Kita Y, Ejima D, Tsumoto K, Fukada H
Protein Pept Lett 2006

Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d).
Shiroishi M, Kuroki K, Rasubala L, Tsumoto K, Kumagai I, Kurimoto E, Kato K, Kohda D, Maenaka K
Proc Natl Acad Sci U S A 2006 Oct 31

Small molecule pharmacological chaperones: From thermodynamic stabilization to pharmaceutical drugs.
Arakawa T, Ejima D, Kita Y, Tsumoto K
Biochim Biophys Acta 2006 Nov

Humanization of the bispecific epidermal growth factor receptor x CD3 diabody and its efficacy as a potential clinical reagent.
Asano R, Sone Y, Makabe K, Tsumoto K, Hayashi H, Katayose Y, Unno M, Kudo T, Kumagai I
Clin Cancer Res 2006 Jul 1

Imaging by atomic force microscopy of the plasma membrane of prestin-transfected Chinese hamster ovary cells.
Murakoshi M, Gomi T, Iida K, Kumano S, Tsumoto K, Kumagai I, Ikeda K, Kobayashi T, Wada H
J Assoc Res Otolaryngol 2006 Sep

[Dissection of specificity and affinity of an antibody for its specific antigen].
Tsumoto K
Seikagaku 2006 Feb

Characterization of arginine as a solvent additive: a halophilic enzyme as a model protein.
Ishibashi M, Tsumoto K, Ejima D, Arakawa T, Tokunaga M
Protein Pept Lett 2005 Oct

Review: Why is arginine effective in suppressing aggregation?
Tsumoto K, Ejima D, Kita Y, Arakawa T
Protein Pept Lett 2005 Oct

Efficient leukocyte Ig-like receptor signaling and crystal structure of disulfide-linked HLA-G dimer.
Shiroishi M, Kuroki K, Ose T, Rasubala L, Shiratori I, Arase H, Tsumoto K, Kumagai I, Kohda D, Maenaka K
J Biol Chem 2006 Apr 14

Entropically driven MHC class I recognition by human inhibitory receptor leukocyte Ig-like receptor B1 (LILRB1/ILT2/CD85j).
Shiroishi M, Kuroki K, Tsumoto K, Yokota A, Sasaki T, Amano K, Shimojima T, Shirakihara Y, Rasubala L, van der Merwe PA, Kumagai I, Kohda D, Maenaka K
J Mol Biol 2006 Jan 13

Arginine as an effective additive in gel permeation chromatography.
Ejima D, Yumioka R, Arakawa T, Tsumoto K
J Chromatogr A 2005 Nov 11

Selection of highly productive mammalian cells based on an inducible growth advantage using an antibody/receptor chimera.
Kawahara M, Ueda H, Tsumoto K, Kumagai I, Mahoney W, Nagamune T
J Biosci Bioeng 2002

A novel “reverse screening” to identify refolding additives for activin-A.
Ejima D, Ono K, Tsumoto K, Arakawa T, Eto Y
Protein Expr Purif 2006 May

Crystal structure of the hypothetical protein ST2072 from Sulfolobus tokodaii.
Tanaka Y, Tsumoto K, Tanabe E, Yasutake Y, Sakai N, Yao M, Tanaka I, Kumagai I
Proteins 2005 Dec 1

Effective elution of antibodies by arginine and arginine derivatives in affinity column chromatography.
Ejima D, Yumioka R, Tsumoto K, Arakawa T
Anal Biochem 2005 Oct 15

Construction of an expression system for the motor protein prestin in Chinese hamster ovary cells.
Iida K, Tsumoto K, Ikeda K, Kumagai I, Kobayashi T, Wada H
Hear Res2 005 Jul

Kinetics of ultrasonic disinfection of Escherichia coli in the presence of titanium dioxide particles.
Kubo M, Onodera R, Shibasaki-Kitakawa N, Tsumoto K, Yonemoto T
Biotechnol Prog 2005 May-Jun

Is arginine a protein-denaturant?
Ishibashi M, Tsumoto K, Tokunaga M, Ejima D, Kita Y, Arakawa T
Protein Expr Purif 2005 Jul

Herpes simplex virus targeting to the EGF receptor by a gD-specific soluble bridging molecule.
Nakano K, Asano R, Tsumoto K, Kwon H, Goins WF, Kumagai I, Cohen JB, Glorioso JC
Mol Ther 2005 Apr

Nondenaturing solubilization of beta2 microglobulin from inclusion bodies by L-arginine.
Umetsu M, Tsumoto K, Nitta S, Adschiri T, Ejima D, Arakawa T, Kumagai I
Biochem Biophys Res Commun 2005 Mar 4

Tumor-directed lymphocyte-activating cytokines: refolding-based preparation of recombinant human interleukin-12 and an antibody variable domain-fused protein by additive-introduced stepwise dialysis.
Makabe K, Asano R, Ito T, Tsumoto K, Kudo T, Kumagai I
Biochem Biophys Res Commun 2005 Mar 4

Role of arginine in protein refolding, solubilization, and purification.
Tsumoto K, Umetsu M, Kumagai I, Ejima D, Philo JS, Arakawa T
Biotechnol Prog 2004 Sep-Oct

Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride.
Tanaka Y, Tsumoto K, Umetsu M, Nakanishi T, Yasutake Y, Sakai N, Yao M, Tanaka I, Arakawa T, Kumagai I
Biochem Biophys Res Commun 2004 Oct 8

Phage-display selection of antibodies to the left end of CTX3C using synthetic fragments.
Nagumo Y, Oguri H, Tsumoto K, Shindo Y, Hirama M, Tsumuraya T, Fujii I, Tomioka Y, Mizugaki M, Kumagai I
J Immunol Methods 2004 Jun

Elution of antibodies from a Protein-A column by aqueous arginine solutions.
Arakawa T, Philo JS, Tsumoto K, Yumioka R, Ejima D
Protein Expr Purif 2004 Aug

Reversal of antigen-dependent signaling by two mutations in antibody/receptor chimera: implication of inverse agonism in cytokine receptor superfamily.
Kawahara M, Ishii S, Tsumoto K, Kumagai I, Ueda H, Nagamune T
Biochem Pharmacol 2004 Aug 1

How oligomerization contributes to the thermostability of an archaeon protein. Protein L-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii.
Tanaka Y, Tsumoto K, Yasutake Y, Umetsu M, Yao M, Fukada H, Tanaka I, Kumagai I
J Biol Chem 2004 Jul 30

Fucose depletion from human IgG1 oligosaccharide enhances binding enthalpy and association rate between IgG1 and FcgammaRIIIa.
Okazaki A, Shoji-Hosaka E, Nakamura K, Wakitani M, Uchida K, Kakita S, Tsumoto K, Kumagai I, Shitara K
J Mol Biol 2004 Mar 5

Engineering amyloidogenicity towards the development of nanofibrillar materials.
Hamada D, Yanagihara I, Tsumoto K
Trends Biotechnol 2004 Feb

Structural characteristics and refolding of in vivo aggregated hyperthermophilic archaeon proteins.
Umetsu M, Tsumoto K, Ashish K, Nitta S, Tanaka Y, Adschiri T, Kumagai I
FEBS Lett 2004 Jan 16

AMEGA: antigen-mediated genetically modified cell amplification.
Kawahara M, Ueda H, Tsumoto K, Kumagai I, Nagamune T
J Immunol Methods 2004 Jan

Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA.
Tanaka Y, Tsumoto K, Nakanishi T, Yasutake Y, Sakai N, Yao M, Tanaka I, Kumagai I
FEBS Lett 2004 Jan 2

[A magic agent in protein refolding: arginine].
Arakawa T, Katsuyama I, Kumagai I, Tsumoto K
Tanpakushitsu Kakusan Koso 2003 Dec

Solubilization of active green fluorescent protein from insoluble particles by guanidine and arginine.
Tsumoto K, Umetsu M, Kumagai I, Ejima D, Arakawa T
Biochem Biophys Res Commun 2003 Dec 26

A highly effective and stable bispecific diabody for cancer immunotherapy: cure of xenografted tumors by bispecific diabody and T-LAK cells.
Hayashi H, Asano R, Tsumoto K, Katayose Y, Suzuki M, Unno M, Kodama H, Takemura S, Yoshida H, Makabe K, Imai K, Matsuno S, Kumagai I, Kudo T
Cancer Immunol Immunother 2004 Jun

An optimized homogeneous noncompetitive immunoassay based on the antigen-driven enzymatic complementation.
Ueda H, Yokozeki T, Arai R, Tsumoto K, Kumagai I, Nagamune T
J Immunol Methods 2003 Aug

On-column refolding and characterization of soluble human interleukin-15 receptor alpha-chain produced in Escherichia coli.
Matsumoto M, Misawa S, Tsumoto K, Kumagai I, Hayashi H, Kobayashi Y
Protein Expr Purif 2003 Sep

Immobilized oxidoreductase as an additive for refolding inclusion bodies: application to antibody fragments.
Tsumoto K, Umetsu M, Yamada H, Ito T, Misawa S, Kumagai I
Protein Eng 2003 Jul

Human inhibitory receptors Ig-like transcript 2 (ILT2) and ILT4 compete with CD8 for MHC class I binding and bind preferentially to HLA-G.
Shiroishi M, Tsumoto K, Amano K, Shirakihara Y, Colonna M, Braud VM, Allan DS, Makadzange A, Rowland-Jones S, Willcox B, Jones EY, van der Merwe PA, Kumagai I, Maenaka K
Proc Natl Acad Sci U S A 2003 Jul 22

Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10.
Kumagai I, Nishimiya Y, Kondo H, Tsumoto K
J Biol Chem 2003 Jul 4

The effects of arginine on refolding of aggregated proteins: not facilitate refolding, but suppress aggregation.
Arakawa T, Tsumoto K
Biochem Biophys Res Commun 2003 Apr 25

Bypassing antibiotic selection: positive screening of genetically modified cells with an antigen-dependent proliferation switch.
Kawahara M, Ueda H, Morita S, Tsumoto K, Kumagai I, Nagamune T
Nucleic Acids Res 2003 Apr 1

Practical considerations in refolding proteins from inclusion bodies.
Tsumoto K, Ejima D, Kumagai I, Arakawa T
Protein Expr Purif 2003 Mar

A morphologic study of filamentous phage infection of Escherichia coli using biotinylated phages.
Nakamura M, Tsumoto K, Kumagai I, Ishimura K
FEBS Lett 2003 Feb 11

How additives influence the refolding of immunoglobulin-folded proteins in a stepwise dialysis system. Spectroscopic evidence for highly efficient refolding of a single-chain Fv fragment.
Umetsu M, Tsumoto K, Hara M, Ashish K, Goda S, Adschiri T, Kumagai I
J Biol Chem 2003 Mar 14

Efficient construction of a diabody using a refolding system: anti-carcinoembryonic antigen recombinant antibody fragment.
Asano R, Kudo T, Nishimura Y, Makabe K, Hayashi H, Suzuki M, Tsumoto K, Kumagai I
J Biochem 2002 Dec

The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction.
Yokota A, Tsumoto K, Shiroishi M, Kondo H, Kumagai I
J Biol Chem 2003 Feb 14

Antitumor activity of interleukin-21 prepared by novel refolding procedure from inclusion bodies expressed in Escherichia coli.
Asano R, Kudo T, Makabe K, Tsumoto K, Kumagai I
FEBS Lett 2002 Sep 25

Inhibition of hepatitis C virus NS3 protease by peptides derived from complementarity-determining regions (CDRs) of the monoclonal antibody 8D4: tolerance of a CDR peptide to conformational changes of a target.
Tsumoto K, Misawa S, Ohba Y, Ueno T, Hayashi H, Kasai N, Watanabe H, Asano R, Kumagai I
FEBS Lett 2002 Aug 14

Chiral recognition in the binding of helicenediamine to double strand DNA: interactions between low molecular weight helical compounds and a helical polymer.
Honzawa S, Okubo H, Anzai S, Yamaguchi M, Tsumoto K, Kumagai I
Bioorg Med Chem 2002 Oct

Selection of human antibody fragments on the basis of stabilization of the variable domain in the presence of target antigens.
Watanabe H, Tsumoto K, Asano R, Nishimiya Y, Kumagai I
Biochem Biophys Res Commun 2002 Jul 5

The effect of an agglutogen on virus infection: biotinylated filamentous phages and avidin as a model.
Nakamura M, Tsumoto K, Ishimura K, Kumagai I
FEBS Lett 2002 Jun 5

T-cell immunotherapy for human MK-1-expressing tumors using a fusion protein of the superantigen SEA and anti-MK-1 scFv antibody.
Ueno A, Arakawa F, Abe H, Matsumoto H, Kudo T, Asano R, Tsumoto K, Kumagai I, Kuroki M, Kuroki M
Anticancer Res 2002 Mar-Apr

Detection of biotinylated proteins in polyacrylamide gels using an avidin-fluorescein conjugate.
Nakamura M, Tsumoto K, Ishimura K, Kumagai I
Anal Biochem 2002 May 15

Phage library panning against cytosolic fraction of cells using quantitative dot blotting assay: application of selected VH to histochemistry.
Nakamura M, Tsumoto K, Ishimura K, Kumagai I
J Immunol Methods 2002 Mar 1

A mutated superantigen SEA D227A fusion diabody specific to MUC1 and CD3 in targeted cancer immunotherapy for bile duct carcinoma.
Takemura S, Kudo T, Asano R, Suzuki M, Tsumoto K, Sakurai N, Katayose Y, Kodama H, Yoshida H, Ebara S, Saeki H, Imai K, Matsuno S, Kumagai I
Cancer Immunol Immunother 2002 Mar

Mutated SEA-D227A-conjugated antibodies greatly enhance antitumor activity against MUC1-expressing bile duct carcinoma.
Kodama H, Suzuki M, Katayose Y, Shinoda M, Sakurai N, Takemura S, Yoshida H, Saeki H, Ichiyama M, Tsumoto K, Asano R, Kumagai I, Imai K, Hinoda Y, Matsuno S, Kudo T
Cancer Immunol Immunother 2001 Dec

A visualization method of filamentous phage infection and phage-derived proteins in Escherichia coli using biotinylated phages.
Nakamura M, Tsumoto K, Ishimura K, Kumagai I
Biochem Biophys Res Commun 2001 Nov 23

Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches.
Horii K, Saito M, Yoda T, Tsumoto K, Matsushima M, Kuwajima K, Kumagai I
Proteins 2001 Oct 1

[Refolding of proteins from inclusion bodies].
Tsumoto K, Kumagai I, Misawa S
Tanpakushitsu Kakusan Koso 2001 Jul

A growth signal with an artificially induced erythropoietin receptor-gp130 cytoplasmic domain heterodimer.
Kawahara M, Ueda H, Tsumoto K, Kumagai I, Mahoney W, Nagamune T
J Biochem 2001 Aug

Replacing factor-dependency with that for lysozyme: affordable culture of IL-6-dependent hybridoma by transfecting artificial cell surface receptor.
Kawahara M, Natsume A, Terada S, Kato K, Tsumoto K, Kumagai I, Miki M, Mahoney W, Ueda H, Nagamune T
Biotechnol Bioeng 2001 Sep 5

Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.
Shiroishi M, Yokota A, Tsumoto K, Kondo H, Nishimiya Y, Horii K, Matsushima M, Ogasahara K, Yutani K, Kumagai I
J Biol Chem 2001 Jun 22

Inhibition of the hepatitis C virus NS3 protease activity by Fv fragment of antibody 8D4.
Kasai N, Tsumoto K, Niwa S, Misawa S, Ueno T, Hayashi H, Kumagai I
Biochem Biophys Res Commun 2001 Feb 23

Panning of a phage VH library using nitrocellulose membranes: application to selection of a human VH library.
Nakamura M, Watanabe H, Nishimiya Y, Tsumoto K, Ishimura K, Kumagai I
J Biochem 2001 Feb

Demonstration of a homogeneous noncompetitive immunoassay based on bioluminescence resonance energy transfer.
Arai R, Nakagawa H, Tsumoto K, Mahoney W, Kumagai I, Ueda H, Nagamune T
Anal Biochem 2001 Feb 1

Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations.
Yoda T, Saito M, Arai M, Horii K, Tsumoto K, Matsushima M, Kumagai I, Kuwajima K
Proteins 2001 Jan 1

Construction of a diabody (small recombinant bispecific antibody) using a refolding system.
Takemura S, Asano R, Tsumoto K, Ebara S, Sakurai N, Katayose Y, Kodama H, Yoshida H, Suzuki M, Imai K, Matsuno S, Kudo T, Kumagai I
Protein Eng 2000 Aug

Cell-growth control by monomeric antigen: the cell surface expression of lysozyme-specific Ig V-domains fused to truncated Epo receptor.
Ueda H, Kawahara M, Aburatani T, Tsumoto K, Todokoro K, Suzuki E, Nishimura H, Schueler PA, Winter G, Mahoney WC, Kumagai I, Nagamune T
J Immunol Methods 2000 Jul 31

Functional Fv fragment of an antibody specific for CD28: Fv-mediated co-stimulation of T cells.
Takemura S, Asano R, Tsumoto K, Arai T, Sakurai N, Kodama H, Yoshida H, Katayose Y, Suzuki M, Matsuno S, Kudo T, Kumagai I
FEBS Lett 2000 Jul 7

Isolation and characterization of monoclonal antibodies that inhibit hepatitis C virus NS3 protease.
Ueno T, Misawa S, Ohba Y, Matsumoto M, Mizunuma M, Kasai N, Tsumoto K, Kumagai I, Hayashi H
J Virol 2000 Jul

Fluorolabeling of antibody variable domains with green fluorescent protein variants: application to an energy transfer-based homogeneous immunoassay.
Arai R, Ueda H, Tsumoto K, Mahoney WC, Kumagai I, Nagamune T
Protein Eng 2000 May

Thermodynamic consequences of grafting enhanced affinity toward the mutated antigen onto an antibody. The case of anti-lysozyme antibody, HyHEL-10.
Nishimiya Y, Tsumoto K, Shiroishi M, Yutani K, Kumagai I
J Biol Chem 2000 Apr 28

Functional construction of the anti-mucin core protein (MUC1) antibody MUSE11 variable regions in a bacterial expression system.
Asano R, Takemura S, Tsumoto K, Sakurai N, Teramae A, Ebara S, Katayose Y, Shinoda M, Suzuki M, Imai K, Matsuno S, Kudo T, Kumagai I
J Biochem 2000 Apr

Homogeneous noncompetitive immunoassay based on the energy transfer between fluorolabeled antibody variable domains (open sandwich fluoroimmunoassay).
Ueda H, Kubota K, Wang Y, Tsumoto K, Mahoney W, Kumagai I, Nagamune T
Biotechniques 1999 Oct

Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces.
Kondo H, Shiroishi M, Matsushima M, Tsumoto K, Kumagai I
J Biol Chem 1999 Sep 24

[Antibody production by phage library].
Kumagai I, Tsumoto K
Nihon Seirigaku Zasshi 1999

Open sandwich ELISA with V(H)-/V(L)-alkaline phosphatase fusion proteins.
Suzuki C, Ueda H, Tsumoto K, Mahoney WC, Kumagai I, Nagamune T
J Immunol Methods 1999 Apr 22

SEA-scFv as a bifunctional antibody: construction of a bacterial expression system and its functional analysis.
Sakurai N, Kudo T, Suzuki M, Tsumoto K, Takemura S, Kodama H, Ebara S, Teramae A, Katayose Y, Shinoda M, Kurokawa T, Hinoda Y, Imai K, Matsuno S, Kumagai I
Biochem Biophys Res Commun 1999 Mar 5

Cell-free expression of two single-chain monoclonal antibodies against lysozyme: effect of domain arrangement on the expression.
Merk H, Stiege W, Tsumoto K, Kumagai I, Erdmann VA
J Biochem 1999 Feb

Effect of the extra n-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli.
Chaudhuri TK, Horii K, Yoda T, Arai M, Nagata S, Terada TP, Uchiyama H, Ikura T, Tsumoto K, Kataoka H, Matsushima M, Kuwajima K, Kumagai I
J Mol Biol 1999 Jan 22

Highly efficient recovery of functional single-chain Fv fragments from inclusion bodies overexpressed in Escherichia coli by controlled introduction of oxidizing reagent–application to a human single-chain Fv fragment.
Tsumoto K, Shinoki K, Kondo H, Uchikawa M, Juji T, Kumagai I
J Immunol Methods 1998 Oct 1

Calorimetric study of mutant human lysozymes with partially introduced Ca2+ binding sites and its efficient refolding system from inclusion bodies.
Koshiba T, Tsumoto K, Masaki K, Kawano K, Nitta K, Kumagai I
Protein Eng 1998 Aug

Construction of mono- and bivalent human single-chain Fv fragments against the D antigen in the Rh blood group: multimerization effect on cell agglutination and application to blood typing.
Furuta M, Uchikawa M, Ueda Y, Yabe T, Taima T, Tsumoto K, Kojima S, Juji T, Kumagai I
Protein Eng 1998 Mar

Novel selection method for engineered antibodies using the mechanism of Fv fragment stabilization in the presence of antigen.
Tsumoto K, Nishimiya Y, Kasai N, Ueda H, Nagamune T, Ogasahara K, Yutani K, Tokuhisa K, Matsushima M, Kumagai I
Protein Eng 1997 Nov

[Generation of novel functional antibody molecules by in vitro selection system].
Kumagai I, Tsumoto K
Tanpakushitsu Kakusan Koso 1998 Feb

Role of salt bridge formation in antigen-antibody interaction. Entropic contribution to the complex between hen egg white lysozyme and its monoclonal antibody HyHEL10.
Tsumoto K, Ogasahara K, Ueda Y, Watanabe K, Yutani K, Kumagai I
J Biol Chem 1996 Dec 20

Open sandwich ELISA: a novel immunoassay based on the interchain interaction of antibody variable region.
Ueda H, Tsumoto K, Kubota K, Suzuki E, Nagamune T, Nishimura H, Schueler PA, Winter G, Kumagai I, Mohoney WC
Nat Biotechnol 1996 Dec

A stable phage-display system using a phagemid vector: phage display of hen egg-white lysozyme (HEL), Escherichia coli alkaline, phosphatase, and anti-HEL monoclonal antibody, HyHEL10.
Maenaka K, Furuta M, Tsumoto K, Watanabe K, Ueda Y, Kumagai I
Biochem Biophys Res Commun 1996 Jan 26

Role of Tyr residues in the contact region of anti-lysozyme monoclonal antibody HyHEL10 for antigen binding.
Tsumoto K, Ogasahara K, Ueda Y, Watanabe K, Yutani K, Kumagai I
J Biol Chem 1995 Aug 4

Contribution to antibody-antigen interaction of structurally perturbed antigenic residues upon antibody binding.
Tsumoto K, Ueda Y, Maenaka K, Watanabe K, Ogasahara K, Yutani K, Kumagai I
J Biol Chem 1994 Nov 18

Effect of the order of antibody variable regions on the expression of the single-chain HyHEL10 Fv fragment in E. coli and the thermodynamic analysis of its antigen-binding properties.
Tsumoto K, Nakaoki Y, Ueda Y, Ogasahara K, Yutani K, Watanabe K, Kumagai I
Biochem Biophys Res Commun 1994 Jun 15

Synthesis and expression of a DNA encoding the Fv domain of an anti-lysozyme monoclonal antibody, HyHEL10, in Streptomyces lividans.
Ueda Y, Tsumoto K, Watanabe K, Kumagai I
Gene 1993 Jul 15

A protease inhibitor produced by Streptomyces lividans 66 exhibits inhibitory activities toward both subtilisin BPN’ and trypsin.
Ueda Y, Kojima S, Tsumoto K, Takeda S, Miura K, Kumagai I
J Biochem 1992 Aug