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Items: 1 to 50 of 335

1.

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 Oct 11;13(10):e0204856. doi: 10.1371/journal.pone.0204856. eCollection 2018.

2.

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 Apr 19;1:33. doi: 10.1038/s42003-018-0038-2. eCollection 2018.

3.

Antibody Affinity Maturation by Computational Design.

Kuroda D, Tsumoto K.

Methods Mol Biol. 2018;1827:15-34. doi: 10.1007/978-1-4939-8648-4_2.

PMID:
30196490
4.

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;204(2):207-214. doi: 10.1016/j.jsb.2018.08.011. Epub 2018 Aug 18.

PMID:
30125694
5.

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 Jul 14;15:81-85. doi: 10.1016/j.bbrep.2018.07.005. eCollection 2018 Sep.

6.

[Biophysical Analysis of the Protein-Small Molecule Interactions to Develop Small Molecule Drug Discovery].

Nagatoishi S, Caaveiro JMM, Tsumoto K.

Yakugaku Zasshi. 2018;138(8):1033-1041. doi: 10.1248/yakushi.17-00211-2. Review. Japanese.

7.

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;13(9):2783-2793. doi: 10.1021/acschembio.8b00701. Epub 2018 Aug 15.

PMID:
30063823
8.

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 Jul 12. pii: S0022-3549(18)30399-X. doi: 10.1016/j.xphs.2018.07.001. [Epub ahead of print]

PMID:
30017886
9.

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;57(28):4177-4185. doi: 10.1021/acs.biochem.8b00592. Epub 2018 Jul 5.

PMID:
29936828
10.

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;164(1):65-76. doi: 10.1093/jb/mvy032.

PMID:
29924367
11.

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 May 30. doi: 10.1093/protein/gzy008. [Epub ahead of print]

PMID:
29850878
12.

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;54(42):5350-5353. doi: 10.1039/c8cc01964a.

PMID:
29741543
13.

Specific Spatial Localization of Actin and DNA in a Water/Water Microdroplet: Self-Emergence of a Cell-Like Structure.

Nakatani N, Sakuta H, Hayashi M, Tanaka S, Takiguchi K, Tsumoto K, Yoshikawa K.

Chembiochem. 2018 Jul 4;19(13):1370-1374. doi: 10.1002/cbic.201800066. Epub 2018 Jun 1.

14.

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 Mar 2;9:413. doi: 10.3389/fimmu.2018.00413. eCollection 2018.

15.

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.

Nagatoishi S, Yamaguchi S, Katoh E, Kajita K, Yokotagawa T, Kanai S, Furuya T, Tsumoto K.

Bioorg Med Chem. 2018 May 1;26(8):1929-1938. doi: 10.1016/j.bmc.2018.02.041. Epub 2018 Feb 22.

PMID:
29510947
16.

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;8(1):3955. doi: 10.1038/s41598-018-22199-8.

17.

Opposite effect of polyamines on In vitro gene expression: Enhancement at low concentrations but inhibition at high concentrations.

Kanemura A, Yoshikawa Y, Fukuda W, Tsumoto K, Kenmotsu T, Yoshikawa K.

PLoS One. 2018 Mar 1;13(3):e0193595. doi: 10.1371/journal.pone.0193595. eCollection 2018.

18.

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;37(1):1-11. doi: 10.1089/mab.2017.0043.

PMID:
29474162
19.

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;115(10):2496-2501. doi: 10.1073/pnas.1718957115. Epub 2018 Feb 20.

20.

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;32(8):665-671. doi: 10.1002/rcm.8083.

PMID:
29441684
21.

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;9(1):625. doi: 10.1038/s41467-018-02994-7.

22.

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;163(6):481-488. doi: 10.1093/jb/mvy021.

PMID:
29415204
23.

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;54(15):1913-1916. doi: 10.1039/c7cc05814d.

PMID:
29393938
24.

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;496(2):614-620. doi: 10.1016/j.bbrc.2018.01.051. Epub 2018 Jan 9.

PMID:
29330050
25.

Introduction: Antibody-Mediated Therapy Special Issue Part 2.

Nakamura A, Tsumoto K, Takai T.

Int Immunol. 2017 Dec 30;29(11):487-489. doi: 10.1093/intimm/dxx069. No abstract available.

PMID:
29300959
26.

Huntingtin Polyglutamine-Dependent Protein Aggregation in Reconstituted Cells.

Machida K, Kanzawa K, Shigeta T, Yamamoto Y, Tsumoto K, Imataka H.

ACS Synth Biol. 2018 Feb 16;7(2):377-383. doi: 10.1021/acssynbio.7b00372. Epub 2017 Dec 14.

PMID:
29232946
27.

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;109(2):373-383. doi: 10.1111/cas.13458. Epub 2017 Dec 28.

28.

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;162(4):255-258. doi: 10.1093/jb/mvx050.

PMID:
28981752
29.

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;89(21):11269-11277. doi: 10.1021/acs.analchem.7b01550. Epub 2017 Oct 23.

PMID:
28980803
30.

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;3(10):825-832. doi: 10.1038/s41477-017-0022-8. Epub 2017 Oct 2.

PMID:
28970497
31.

Polymeric SpyCatcher Scaffold Enables Bioconjugation in a Ratio-Controllable Manner.

Jia L, Minamihata K, Ichinose H, Tsumoto K, Kamiya N.

Biotechnol J. 2017 Dec;12(12). doi: 10.1002/biot.201700195. Epub 2017 Oct 20.

PMID:
28960874
32.

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;493(2):1109-1114. doi: 10.1016/j.bbrc.2017.09.055. Epub 2017 Sep 14.

PMID:
28919415
33.

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;85(12):2217-2230. doi: 10.1002/prot.25386. Epub 2017 Sep 26.

PMID:
28913898
34.
35.

Elucidation of potential sites for antibody engineering by fluctuation editing.

Yanaka S, Moriwaki Y, Tsumoto K, Sugase K.

Sci Rep. 2017 Aug 30;7(1):9597. doi: 10.1038/s41598-017-10246-9.

36.

Integrative Approach with Electrophysiological and Theoretical Methods Reveals a New Role of S4 Positively Charged Residues in PKD2L1 Channel Voltage-Sensing.

Numata T, Tsumoto K, Yamada K, Kurokawa T, Hirose S, Nomura H, Kawano M, Kurachi Y, Inoue R, Mori Y.

Sci Rep. 2017 Aug 29;7(1):9760. doi: 10.1038/s41598-017-10357-3.

37.

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;137(7):815-816. doi: 10.1248/yakushi.16-00252-F. Japanese. No abstract available.

38.

Glycosylation of IgG-Fc: a molecular perspective.

Kiyoshi M, Tsumoto K, Ishii-Watabe A, Caaveiro JMM.

Int Immunol. 2017 Jul 1;29(7):311-317. doi: 10.1093/intimm/dxx038. Review.

PMID:
28655198
39.

HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research.

Furutani K, Tsumoto K, Kurachi Y; for HD physiology project investigators.

NPJ Syst Biol Appl. 2017 Jan 16;3:1. doi: 10.1038/s41540-016-0001-0. eCollection 2017.

40.

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;162(3):203-210. doi: 10.1093/jb/mvx023.

PMID:
28637250
41.

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;372(1726). pii: 20160216. doi: 10.1098/rstb.2016.0216.

42.

Membrane fusion between baculovirus budded virus-enveloped particles and giant liposomes generated using a droplet-transfer method for the incorporation of recombinant membrane proteins.

Nishigami M, Mori T, Tomita M, Takiguchi K, Tsumoto K.

Colloids Surf B Biointerfaces. 2017 Jul 1;155:248-256. doi: 10.1016/j.colsurfb.2017.04.027. Epub 2017 Apr 13.

PMID:
28432958
43.

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;429(8):1213-1226. doi: 10.1016/j.jmb.2017.03.008. Epub 2017 Mar 11.

44.

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;292(13):5571-5583. doi: 10.1074/jbc.M117.775429. Epub 2017 Feb 17.

45.

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;161(3):269-277. doi: 10.1093/jb/mvw073.

PMID:
28069867
46.

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;7:39518. doi: 10.1038/srep39518.

47.

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;55(48):6630-6641. Epub 2016 Nov 22.

PMID:
27933793
48.

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;6:38177. doi: 10.1038/srep38177.

49.

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;45(1):461-469. doi: 10.1093/nar/gkw1113. Epub 2016 Nov 28.

50.

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;1861(2):205-217. doi: 10.1016/j.bbagen.2016.11.028. Epub 2016 Nov 22.

PMID:
27884519

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