J. Caaveiro

发表

Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4 E 10

Jamie K. Scott, K. Tsumoto, J. L. Nieva, 2015 .

Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10

Jamie K. Scott, K. Tsumoto, J. L. Nieva, 2015, Journal of Virology.

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.

Identification of a Membrane-bound Prepore Species Clarifies the Lytic Mechanism of Actinoporins * ♦

M. Valle, K. Tsumoto, S. Scheuring, 2016, The Journal of Biological Chemistry.

Mapping Ultra-weak Protein-Protein Interactions between Heme Transporters of Staphylococcus aureus

M. Oyama, K. Tsumoto, H. Kozuka-Hata, 2012, The Journal of Biological Chemistry.

Reply to “The Broadly Neutralizing, Anti-HIV Antibody 4E10: an Open and Shut Case?”

Jamie K. Scott, K. Tsumoto, J. L. Nieva, 2016, Journal of Virology.

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

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

Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.

K. Tsumoto, J. Caaveiro, Q. Q. Hoang, 2014, Biochemistry.

Binding of hydrophobic hydroxamic acids enhances peroxidase's stereoselectivity in nonaqueous sulfoxidations.

P. Das, A. Klibanov, J. Caaveiro, 2002, Journal of the American Chemical Society.

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.

Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3

K. Tsumoto, Makoto Nakakido, J. Caaveiro, 2022, Protein science : a publication of the Protein Society.

Incorporation of rapid thermodynamic data in fragment-based drug discovery.

K. Tsumoto, J. Caaveiro, S. Tashiro, 2013, Journal of medicinal chemistry.

Molecular recognition of a membrane-anchored HIV-1 pan-neutralizing epitope

J. L. Nieva, I. de la Arada, J. Torralba, 2022, Communications Biology.

Functional Delineation of a Protein–Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8

J. L. Nieva, C. Eggeling, I. de la Arada, 2022, International journal of molecular sciences.

VARIANTS AGONIST AND ANTAGONIST Signaling Activity: GENERATION OF Non-core Region Modulates Interleukin-11 Protein Structure and Folding:

K. Tsumoto, K. Miura, J. Caaveiro, 2014 .

Asymmetric sulfoxidations mediated by α‐chymotrypsin

P. Das, A. Klibanov, J. Caaveiro, 2002 .

Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.

Daniel Herschlag, Gregory A Petsko, Jose M M Caaveiro, 2008, Journal of the American Chemical Society.

Selective binding of antimicrobial porphyrins to the heme‐receptor IsdH‐NEAT3 of Staphylococcus aureus

K. Tsumoto, T. Terada, K. Shimizu, 2013, Protein science : a publication of the Protein Society.

Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus

K. Tsumoto, Yoshikazu Tanaka, J. Caaveiro, 2013, Bioscience reports.

Structural and thermodynamic characterization of the self-adhesive properties of human P-cadherin.

T. Kodama, K. Tsumoto, J. Caaveiro, 2012, Molecular bioSystems.

Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains.

K. Tsumoto, Yoshikazu Tanaka, J. Caaveiro, 2012, The Biochemical journal.

Hydrogen bond coupling in the ketosteroid isomerase active site.

G. Petsko, D. Ringe, D. Herschlag, 2009, 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.

Differential Effect of Membrane Composition on the Pore-Forming Ability of Four Different Sea Anemone Actinoporins.

J. Slotte, J. Gavilanes, K. Tsumoto, 2016, Biochemistry.

Haemolytic actinoporins interact with carbohydrates using their lipid-binding module

K. Tsumoto, K. Morante, J. Caaveiro, 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

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.

Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism.

K. Tsumoto, J. Caaveiro, S. Kudo, 2016, Structure.

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.

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface

Jamie K. Scott, K. Tsumoto, N. Gulzar, 2016, Scientific Reports.

Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody

K. Tsumoto, K. Sugase, J. Caaveiro, 2019, Scientific Reports.

Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI

K. Tsumoto, J. Caaveiro, Masato Kiyoshi, 2015, Nature Communications.

Molecular basis for the activation of actinoporins by lipids.

K. Tsumoto, J. Caaveiro, 2021, Methods in enzymology.

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, J. Comput. Aided Mol. Des..

Structural basis for antigen recognition by methylated lysine–specific antibodies

K. Tsumoto, Makoto Nakakido, J. Caaveiro, 2020, The Journal of biological chemistry.

Structural analysis of Fc/FcγR complexes: a blueprint for antibody design

K. Tsumoto, J. Caaveiro, Masato Kiyoshi, 2015, Immunological reviews.

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.

Computer-guided library generation applied to the optimization of single-domain antibodies.

K. Tsumoto, J. Caaveiro, Hiroki Akiba, 2019, Protein engineering, design & selection : PEDS.

Antibody recognition of complement factor H reveals a flexible loop involved in atypical hemolytic uremic syndrome pathogenesis

K. Tsumoto, M. Nangaku, Makoto Nakakido, 2022, The Journal of biological chemistry.

Glycosylation of IgG-Fc: a molecular perspective

Akiko Ishii-Watabe, Kouhei Tsumoto, Masato Kiyoshi, 2017, International immunology.

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

K. Tsumoto, T. Ueda, Makoto Nakakido, 2018, Biochemistry.

Selective and reversible modification of kinase cysteines with chlorofluoroacetamides

M. Ono, A. Ojida, I. Hamachi, 2019, Nature Chemical Biology.

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody

K. Tsumoto, Makoto Nakakido, J. Caaveiro, 2018, Journal of biochemistry.

Unfolding is the driving force for mitochondrial import and degradation of the Parkinson's disease-related protein DJ-1

T. Hirokawa, C. Motono, K. Tsumoto, 2021, Journal of cell science.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

G. Petsko, D. Ringe, D. Herschlag, 2013, Proceedings of the National Academy of Sciences.

In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis.

D. Goldberg, K. Tsumoto, K. Morante, 2016, Biochemistry.

Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus.

Kouhei Tsumoto, Yoshitaka Moriwaki, Jose M M Caaveiro, 2011, Biochemistry.

Structural basis for self-assembly of a cytolytic pore lined by protein and lipid

K. Tsumoto, K. Morante, J. Caaveiro, 2015, Nature Communications.

Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile

J. Julien, C. Eggeling, D. Leaman, 2021, iScience.

Affinity for the Interface Underpins Potency of Antibodies Operating In Membrane Environments

J. Julien, C. Eggeling, C. Domene, 2020, Cell reports.

Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane.

K. Tsumoto, E. Rujas, J. Caaveiro, 2017, Journal of molecular biology.

Peripheral Membrane Interactions Boost the Engagement by an Anti-HIV-1 Broadly Neutralizing Antibody*

K. Tsumoto, E. Rujas, J. Caaveiro, 2017, The Journal of Biological Chemistry.

The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region*♦

K. Tsumoto, Beatriz Apellániz, E. Rujas, 2015, The Journal of Biological Chemistry.

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.

A Pore-Forming Toxin Requires a Specific Residue for Its Activity in Membranes with Particular Physicochemical Properties*

K. Tsumoto, K. Morante, J. Caaveiro, 2015, The Journal of Biological Chemistry.

The Isolation of New Pore-Forming Toxins from the Sea Anemone Actinia fragacea Provides Insights into the Mechanisms of Actinoporin Evolution

K. Tsumoto, A. Viguera, K. Morante, 2019, Toxins.

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.

Functional characterization of Val60, a key residue involved in the membrane‐oligomerization of fragaceatoxin C, an actinoporin from Actinia fragacea

K. Tsumoto, A. Viguera, K. Morante, 2015, FEBS letters.

Contributions of interfacial residues of human Interleukin15 to the specificity and affinity for its private alpha-receptor.

K. Tsumoto, Yoshikazu Tanaka, J. Caaveiro, 2009, Journal of molecular biology.

Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide‐synthesizing enzyme from Staphylococcus aureus

K. Tsumoto, Yoshikazu Tanaka, J. Caaveiro, 2013, FEBS letters.

Solubilization of membrane proteins with novel N-acylamino acid detergents.

K. Tsumoto, J. Caaveiro, Ryota Abe, 2010, Molecular bioSystems.

Catalytic activity of MsbA reconstituted in nanodisc particles is modulated by remote interactions with the bilayer

T. Katagiri, K. Tsumoto, J. Caaveiro, 2011, FEBS letters.

The Isolation of New Pore-Forming Toxins from the Sea Anemone Actinia fragacea Provides Insights into the Mechanisms of Actinoporin Evolution

K. Tsumoto, A. Viguera, K. Morante, 2019, Toxins.

Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States.

K. Tsumoto, J. Caaveiro, Koji Tanaka, 2015, Biochemistry.

Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth

K. Tsumoto, Makoto Nakakido, Chihiro Aikawa, 2023, The Journal of biological chemistry.

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.

In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis.

D. Goldberg, K. Tsumoto, K. Morante, 2016, Biochemistry.

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

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

Structural analysis of Fc/FcγR complexes: a blueprint for antibody design

K. Tsumoto, J. Caaveiro, Masato Kiyoshi, 2015, Immunological reviews.

Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.

K. Tsumoto, T. Terada, K. Shimizu, 2013, Biochemistry.

Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab.

Makoto Nakakido, J. Caaveiro, Satoshi Nagata, 2024, 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.

Liposome-based peptide vaccines to elicit immune responses against the membrane active domains of the HIV-1 Env glycoprotein.

Shixia Wang, J. Torralba, Beatriz Apellániz, 2023, Biochimica et biophysica acta. Biomembranes.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

G. Petsko, D. Ringe, D. Herschlag, 2013, Proceedings of the National Academy of Sciences.

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface

Jamie K. Scott, N. Gulzar, Beatriz Apellániz, 2016, Scientific Reports.