S. Nagatoishi

发表

Biophysical characterization of the interaction between heme and proteins responsible for heme transfer in Streptococcus pyogenes.

K. Tsumoto, M. Hoshino, Makoto Nakakido, 2017, Biochemical and biophysical research communications.

Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.

T. Kodama, K. Tsumoto, Makoto Nakakido, 2019, Structure.

Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2022, The Journal of biological chemistry.

Structural basis for binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin

K. Tsumoto, Masaki Yamamoto, S. Nagatoishi, 2020, bioRxiv.

Per-residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions.

K. Tsumoto, D. Kuroda, S. Nagatoishi, 2020, Journal of the American Chemical Society.

PRDM14 directly interacts with heat shock proteins HSP90α and glucose‐regulated protein 78

K. Tsumoto, K. Imai, S. Nagatoishi, 2017, Cancer science.

Thermodynamic analyses of amino acid residues at the interface of an antibody B2212A and its antigen roundabout homolog 1.

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2017, Journal of biochemistry.

An epitope‐directed antibody affinity maturation system utilizing mammalian cell survival as readout

M. Kawahara, K. Tsumoto, D. Kuroda, 2019, Biotechnology and bioengineering.

G Quadruplex‐Based FRET Probes with the Thrombin‐Binding Aptamer (TBA) Sequence Designed for the Efficient Fluorometric Detection of the Potassium Ion

S. Nagatoishi, S. Takenaka, B. Juskowiak, 2006, Chembiochem : a European journal of chemical biology.

Reversible ion transportation switch by a ligand-gated synthetic supramolecular ion channel.

K. Tsumoto, H. Noji, T. Muraoka, 2014, Journal of the American Chemical Society.

Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium.

K. Tsumoto, D. Kuroda, S. Nagatoishi, 2019, Biochemistry.

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses

T. Kodama, K. Tsumoto, Makoto Nakakido, 2015, Protein science : a publication of the Protein Society.

Mitochonic Acid 5 Binds Mitochondria and Ameliorates Renal Tubular and Cardiac Myocyte Damage.

E. Mishima, T. Abe, S. Ito, 2016, Journal of the American Society of Nephrology : JASN.

Biophysical Characterization of the Contribution of the Fab Region to the IgG-FcγRIIIa Interaction

K. Tsumoto, S. Nagatoishi, A. Ishii‐Watabe, 2022, Biochemistry.

A secondary RET mutation in the activation loop conferring resistance to vandetanib

T. Kohno, Y. Okuno, K. Tsumoto, 2018, Nature Communications.

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

K. Tsumoto, H. Shirai, Shinji Soga, 2019, Scientific Reports.

complex: Crystallographic, thermodynamic, and molecular dynamic analyses

T. Kodama, K. Tsumoto, S. Nagatoishi, 2014 .

Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2018, ACS chemical biology.

On-rate modulation of cadherin interactions by chemical fragments

K. Tsumoto, S. Nagatoishi, S. Kudo, 2020, bioRxiv.

Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition

K. Tsumoto, S. Nagatoishi, Tomoya Takahashi, 2018, PloS one.

A Peptoid with Extended Shape in Water.

K. Tsumoto, S. Nagatoishi, S. Sando, 2019, Journal of the American Chemical Society.

A glutamine sensor that directly activates TORC1

K. Tsumoto, K. Nagata, T. Maeda, 2021, Communications Biology.

Experimental Comparison of Bond Lifetime and Viscoelastic Relaxation in Transient Networks with Well-Controlled Structures.

K. Tsumoto, S. Nagatoishi, T. Sakai, 2022, ACS macro letters.

Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival

K. Tsumoto, H. Sugimoto, S. Nagatoishi, 2021, Communications Biology.

Analysis of bovine serum albumin unfolding in the absence and presence of ATP by SYPRO Orange staining of agarose native gel electrophoresis.

K. Tsumoto, T. Arakawa, S. Nagatoishi, 2022, Analytical biochemistry.

Production and characterization of a novel site-specific-modifiable anti-OX40-receptor single-chain variable fragment for targeted drug delivery.

K. Nakano, K. Tsumoto, Yuetsu Tanaka, 2018, Biochemical and biophysical research communications.

Thermodynamic characterization of the interaction between the human Y-box binding protein YB-1 and nucleic acids.

K. Tsumoto, S. Nagatoishi, Yumiko Tanabe, 2015, Molecular bioSystems.

Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2022, bioRxiv.

Control of Protein Adsorption to Cyclo Olefin Polymer by the Hofmeister Effect.

K. Tsumoto, T. Arakawa, S. Nagatoishi, 2019, Journal of pharmaceutical sciences.

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

K. Tsumoto, Ryo Ueta, S. Nagatoishi, 2017, Journal of biochemistry.

Lipid nanodiscs facilitate the identification of a fragment compound inhibiting the enzymatic activity of the bacterial membrane protein MsbA

K. Tsumoto, T. Ueda, S. Nagatoishi, 2021, bioRxiv.

Raman Spectroscopic Analysis of Highly-Concentrated Antibodies under the Acid-Treated Conditions.

K. Tsumoto, S. Nagatoishi, Yusui Sato, 2022, Pharmaceutical research.

Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5

T. Kodama, K. Tsumoto, H. Doi, 2015, The Journal of Biological Chemistry.

Extracellular matrix-inspired hydrogel of hyaluronan and gelatin crosslinked via a Link module with a transglutaminase reactive sequence

K. Tsumoto, S. Nagatoishi, S. Ohta, 2022, Communications Materials.

Use of SpyTag/SpyCatcher to construct bispecific antibodies that target two epitopes of a single antigen

K. Tsumoto, S. Nagatoishi, T. Hamakubo, 2017, Journal of biochemistry.

A DNA Aptamer That Inhibits the Aberrant Signaling of Fibroblast Growth Factor Receptor in Cancer Cells

K. Tsumoto, S. Nagatoishi, S. Sando, 2021, JACS Au.

Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach

K. Tsumoto, Toru Suzuki, S. Nagatoishi, 2015, Protein & Cell.

Corrigendum to “Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions” [Biochem. Biophys. Res. Commun. 352 (2007) 812–817]

K. Tsumoto, Yoshikazu Tanaka, S. Nagatoishi, 2007 .

Nucleic acid–triggered tumoral immunity propagates pH‐selective therapeutic antibodies through tumor‐driven epitope spreading

S. Ishikawa, D. Komura, K. Tsumoto, 2022, Cancer science.

In vitro validation of chromogenic substrate assay for evaluation of surrogate FVIII-activity of emicizumab.

S. Nagatoishi, K. Amano, H. Inaba, 2023, Thrombosis research.

A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications.

Takahiko Nojima, Satoru Nagatoishi, Bernard Juskowiak, 2005, Angewandte Chemie.

Conformational flexibility influences degree of hydration of nucleic acid hybrids.

N. Sugimoto, S. Nagatoishi, Jhimli Bhattacharyya, 2011, The journal of physical chemistry. B.

Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate

H. Nonaka, K. Tsumoto, S. Nagatoishi, 2021, iScience.

A Peptoid with Extended Shape in Water.

K. Tsumoto, S. Nagatoishi, S. Sando, 2019, Journal of the American Chemical Society.

Design strategy for serine hydroxymethyltransferase probes based on retro-aldol-type reaction

H. Nonaka, I. Aoki, K. Tsumoto, 2019, Nature Communications.

Characterization of glycoengineered anti-HER2 monoclonal antibodies produced by using a silkworm–baculovirus expression system

K. Tsumoto, S. Nagatoishi, Masato Kiyoshi, 2018, Journal of biochemistry.

Mechanism of dimerization and structural features of human LI-cadherin

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2021, The Journal of biological chemistry.

Dimerization mechanism and structural features of human LI-cadherin

K. Tsumoto, S. Uchiyama, Makoto Nakakido, 2020, bioRxiv.

Hyperthin nanochains composed of self-polymerizing protein shackles

K. Tsumoto, S. Nagatoishi, S. Yanaka, 2013, Nature Communications.

Affinity Improvement of a Therapeutic Antibody by Structure-Based Computational Design: Generation of Electrostatic Interactions in the Transition State Stabilizes the Antibody-Antigen Complex

Kouhei Tsumoto, Satoru Nagatoishi, Masato Kiyoshi, 2014, PloS one.

Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2022, bioRxiv.

Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion

K. Tsumoto, S. Nagatoishi, S. Kudo, 2021, Communications Biology.

Identification and characterization of the X-dimer of human P-cadherin: implications for homophilic cell adhesion.

T. Kodama, K. Tsumoto, S. Nagatoishi, 2014, Biochemistry.

Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2018, Communications Biology.

Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding.

N. Sugimoto, K. Tsumoto, S. Nagatoishi, 2011, Biochimie.

Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range.

K. Tsumoto, S. Nagatoishi, Daisuke Kuroda, 2021, Biochemical and biophysical research communications.

Discovery of chemical probes that suppress Wnt/β‐catenin signaling through high‐throughput screening

Y. Furukawa, K. Tsumoto, S. Nagatoishi, 2020, Cancer science.

Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.

P. Defossez, K. Tsumoto, M. Ikeguchi, 2021, Bioorganic & medicinal chemistry.

The yields of transcripts for a RNA polymerase regulated by hairpin structures in nascent RNAs.

N. Sugimoto, S. Nagatoishi, Ryoya Ono, 2012, Chemical communications.

B cell–intrinsic TBK1 is essential for germinal center formation during infection and vaccination in mice

Jelena S. Bezbradica, C. Coban, K. Ishii, 2021, The Journal of experimental medicine.

An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes

Kam Y. J. Zhang, Kouhei Tsumoto, Satoru Nagatoishi, 2021, Briefings Bioinform..

DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles.

N. Sugimoto, S. Nagatoishi, S. Pramanik, 2012, Chemical communications.

Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions.

Kouhei Tsumoto, Satoru Nagatoishi, Yoshikazu Tanaka, 2007, Biochemical and biophysical research communications.

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column

K. Tsumoto, S. Nagatoishi, K. Morante, 2018, Scientific Reports.

The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis

T. Hirokawa, K. Tsumoto, S. Nakano, 2021, Nature Communications.

Effects of network connectivity on viscoelastic relaxation in transient networks using experimental approach

K. Tsumoto, S. Nagatoishi, T. Sakai, 2022, Frontiers in Soft Matter.

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

K. Tsumoto, H. Shirai, Shinji Soga, 2019, Scientific Reports.

Highly sensitive HPLC analysis and biophysical characterization of N‐glycans of IgG‐Fc domain in comparison between CHO and 293 cells using FcγRIIIa ligand

K. Tsumoto, S. Nagatoishi, Toru Tanaka, 2020, Biotechnology progress.

Structural features of methionine aminopeptidase2-active core peptide essential for binding with S100A4.

K. Tsumoto, Naohiro Katagiri, S. Nagatoishi, 2019, Biochemical and biophysical research communications.

Osteomodulin regulates diameter and alters shape of collagen fibrils.

K. Tsumoto, S. Nagatoishi, H. Sagara, 2015, Biochemical and biophysical research communications.

Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2021, The Journal of biological chemistry.

Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions

N. Sugimoto, S. Nagatoishi, D. Miyoshi, 2012, Journal of nucleic acids.

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.

K. Tsumoto, Yoshikazu Tanaka, S. Nagatoishi, 2009, Molecular bioSystems.

Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity

O. Nureki, K. Tsumoto, T. Nishizawa, 2017, Nature Plants.

Technical capabilities and limitations of optical spectroscopy and calorimetry using water-miscible solvents: The case of dimethyl sulfoxide, acetonitrile and 1,4-dioxane.

K. Tsumoto, T. Arakawa, S. Nagatoishi, 2019, Journal of pharmaceutical sciences.

Structural and thermodynamical insights into the binding and inhibition of FIH-1 by the N-terminal disordered region of Mint3

K. Tsumoto, Ryo Maeda, S. Nagatoishi, 2021, The Journal of biological chemistry.

Structural basis for amino acid export by DMT superfamily transporter YddG

O. Nureki, K. Tsumoto, Y. Usuda, 2016, Nature.

Inhibition of homophilic dimerization and disruption of cell adhesion by P-cadherin-specific small molecules from SPR-based assays.

K. Tsumoto, S. Nagatoishi, S. Kudo, 2018, Chemical communications.

Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers

N. Sugimoto, K. Tsumoto, F. Sica, 2016, Nucleic acids research.

Assessment of the Protein–Protein Interactions in a Highly Concentrated Antibody Solution by Using Raman Spectroscopy

K. Tsumoto, S. Nagatoishi, Chikashi Ota, 2016, Pharmaceutical Research.

Highly sensitive biomolecular interaction detection method using optical bound/free separation with grating-coupled surface plasmon field-enhanced fluorescence spectroscopy (GC-SPFS)

S. Nagatoishi, T. Kaya, Yukito Nakamura, 2019, PloS one.

Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach

K. Tsumoto, Toru Suzuki, S. Nagatoishi, 2015, Protein & Cell.

Biophysical characterization of the breast cancer-related BIG3-PHB2 interaction: Effect of non-conserved loop region of BIG3 on the structure and the interaction.

T. Katagiri, K. Tsumoto, S. Nagatoishi, 2019, Biochemical and biophysical research communications.

Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus

K. Tsumoto, S. Nagatoishi, J. Caaveiro, 2015, Scientific Reports.

Elaboration of non-naturally occurring helical tripeptides as p53-MDM2/MDMX interaction inhibitors.

K. Tsumoto, R. Ohki, S. Nagatoishi, 2021, Chemical & pharmaceutical bulletin.

Hydration is Required in DNA G‐Quadruplex–Protein Binding

N. Sugimoto, K. Tsumoto, S. Nagatoishi, 2011, Chembiochem : a European journal of chemical biology.

Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer

N. Sugimoto, F. Sica, A. Merlino, 2013, The FEBS journal.

Development of biparatopic bispecific antibody possessing tetravalent scFv-Fc capable of binding to ROBO1 expressed in hepatocellular carcinoma cells.

K. Tsumoto, S. Nagatoishi, T. Hamakubo, 2021, Journal of biochemistry.

Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors.

K. Tsumoto, S. Nagatoishi, S. Ohkubo, 2021, Journal of medicinal chemistry.

Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein.

N. Sugimoto, S. Nagatoishi, 2012, Molecular bioSystems.

Binding mechanism underlying FIH-1 suppression caused by the N-terminal disordered region of Mint3

K. Tsumoto, S. Nagatoishi, M. Seiki, 2021, bioRxiv.

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations.

N. Kunishima, K. Tsumoto, Tomohiko Hayashi, 2022, The journal of physical chemistry. B.

Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin

K. Tsumoto, S. Nagatoishi, J. Caaveiro, 2017, Scientific Reports.

Conformational features and interaction mechanisms of VHH antibodies with β-hairpin-like CDR-H3: A case of Nb8-HigB2 interaction

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2023, bioRxiv.

Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.

T. Umehara, R. Roeder, K. Tsumoto, 2023, Molecular cell.

Protein stabilization by an amphiphilic short monodisperse oligo(ethylene glycol).

K. Tsumoto, T. Muraoka, K. Kinbara, 2015, Chemical communications.

Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex

Y. Furukawa, M. Oyama, S. Imoto, 2023, iScience.

Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate

O. Nureki, K. Tsumoto, T. Nishizawa, 2017 .

Fluorescence energy transfer probes based on the guanine quadruplex formation for the fluorometric detection of potassium ion.

S. Nagatoishi, S. Takenaka, B. Juskowiak, 2007, Analytica chimica acta.

Development of drug discovery screening system by molecular interaction kinetics-mass spectrometry.

K. Tsumoto, S. Nagatoishi, T. Nishimura, 2018, Rapid communications in mass spectrometry : RCM.

mRNA Delivery: Polymeric Nanocarriers with Controlled Chain Flexibility Boost mRNA Delivery In Vivo through Enhanced Structural Fastening (Adv. Healthcare Mater. 16/2020)

K. Tsumoto, S. Fukushima, K. Kataoka, 2020 .

Polymeric Nanocarriers with Controlled Chain Flexibility Boost mRNA Delivery In Vivo through Enhanced Structural Fastening

K. Tsumoto, S. Fukushima, K. Kataoka, 2020, Advanced healthcare materials.

Design of single-domain VHH antibodies to increase the binding activity in SPR amine coupling.

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2023, Biochemical and biophysical research communications.

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column

K. Tsumoto, S. Nagatoishi, K. Morante, 2018, Scientific Reports.

One-pot preparation of mannan-coated antigen nanoparticles using human serum albumin as a matrix for tolerance induction.

K. Tsumoto, S. Nagatoishi, Takeshi Mori, 2023, Journal of colloid and interface science.

Temperature and salt concentration alter base-sequence selectivity of a duplex DNA-binding protein.

K. Tsumoto, Yoshikazu Tanaka, S. Nagatoishi, 2010, Molecular bioSystems.

Megalin is involved in angiotensinogen-induced, angiotensin II-mediated ERK1/2 signaling to activate Na+-H+ exchanger 3 in proximal tubules

K. Tsumoto, S. Nagatoishi, A. Saito, 2023, Journal of hypertension.

Structural basis for binding and transfer of heme in bacterial heme‐acquisition systems

K. Tsumoto, H. Sugimoto, Y. Naoe, 2017, Proteins.

Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained

Kouhei Tsumoto, Satoshi Yasuda, Tomoki Akiyama, 2020, J. Chem. Inf. Model..

Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2018, Communications Biology.

Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.

K. Tsumoto, S. Nagatoishi, M. Ohue, 2020, Journal of medicinal chemistry.

Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2023, Protein science : a publication of the Protein Society.

Differential binding of prohibitin-2 to estrogen receptor α and to drug-resistant ERα mutants.

K. Tsumoto, S. Nagatoishi, Takeru Chigira, 2015, Biochemical and biophysical research communications.

Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes

J. Tame, Makoto Nakakido, S. Nagatoishi, 2024, Scientific reports.

Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes

K. Tsumoto, Makoto Nakakido, S. Nagatoishi, 2023, The Journal of biological chemistry.

Safe and efficient oral allergy immunotherapy using one-pot-prepared mannan-coated allergen nanoparticles.

K. Tsumoto, S. Nagatoishi, Y. Fujioka, 2023, Biomaterials.

A combination of 19F 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.

K. Tsumoto, E. Katoh, S. Nagatoishi, 2018, Bioorganic & medicinal chemistry.

Agarose native gel electrophoresis analysis of thermal aggregation controlled by Hofmeister series.

K. Tsumoto, T. Arakawa, S. Nagatoishi, 2023, Biophysical chemistry.