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Items: 1 to 50 of 357

1.

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. doi: 10.1002/1873-3468.13674. [Epub ahead of print]

PMID:
31713840
2.

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. pii: S0022-3549(19)30728-2. doi: 10.1016/j.xphs.2019.10.056. [Epub ahead of print]

PMID:
31682831
3.

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;9(1):15481. doi: 10.1038/s41598-019-50722-y.

4.

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. doi: 10.1007/s12149-019-01408-y. [Epub ahead of print]

PMID:
31605356
5.

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 Oct 8;518(1):183-189. doi: 10.1016/j.bbrc.2019.08.028. Epub 2019 Aug 14.

PMID:
31421830
6.

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 Sep 18;141(37):14612-14623. doi: 10.1021/jacs.9b04371. Epub 2019 Aug 23.

PMID:
31405271
7.

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 Aug 1;14(8):e0220578. doi: 10.1371/journal.pone.0220578. eCollection 2019.

8.

The Isolation of New Pore-Forming Toxins from the Sea Anemone Actinia fragacea Provides 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;11(7). pii: E401. doi: 10.3390/toxins11070401.

9.

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

Katagiri N, Nagatoishi S, Tsumoto K, Endo H.

Biochem Biophys Res Commun. 2019 Sep 3;516(4):1123-1129. doi: 10.1016/j.bbrc.2019.07.006. Epub 2019 Jul 5.

PMID:
31284952
10.

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 Jun 5;14(6):e0217105. doi: 10.1371/journal.pone.0217105. eCollection 2019.

11.

B-cell receptor-based multitargeting method for simultaneous production of novel multiple monoclonal antibodies.

Obata H, Tsumoto K, Tomita M.

J Biosci Bioeng. 2019 Nov;128(5):578-584. doi: 10.1016/j.jbiosc.2019.04.015. Epub 2019 May 28.

PMID:
31147218
12.

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 Jul;116(7):1742-1751. doi: 10.1002/bit.26965. Epub 2019 Mar 29.

PMID:
30883677
13.

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;9(1):4482. doi: 10.1038/s41598-019-40461-5.

14.

Integrative and theoretical research on the architecture of a biological system and its disorder.

Uchida S, Asai Y, Kariya Y, Tsumoto K, Hibino H, Honma M, Abe T, Nin F, Kurata Y, Furutani K, Suzuki H, Kitano H, Inoue R, Kurachi Y.

J Physiol Sci. 2019 May;69(3):433-451. doi: 10.1007/s12576-019-00667-8. Epub 2019 Mar 13. Review.

15.

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;10(1):876. doi: 10.1038/s41467-019-08833-7.

16.

Aqueous/Aqueous Micro Phase Separation: Construction of an Artificial Model of Cellular Assembly.

Sakuta H, Fujimoto T, Yamana Y, Hoda Y, Tsumoto K, Yoshikawa K.

Front Chem. 2019 Feb 1;7:44. doi: 10.3389/fchem.2019.00044. eCollection 2019.

17.

Future perspectives of therapeutic monoclonal antibodies.

Tsumoto K, Isozaki Y, Yagami H, Tomita M.

Immunotherapy. 2019 Feb;11(2):119-127. doi: 10.2217/imt-2018-0130.

18.

Facilitation of I Kr current by some hERG channel blockers suppresses early afterdepolarizations.

Furutani K, Tsumoto K, Chen IS, Handa K, Yamakawa Y, Sack JT, Kurachi Y.

J Gen Physiol. 2019 Feb 4;151(2):214-230. doi: 10.1085/jgp.201812192. Epub 2019 Jan 23.

19.

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 May;108(5):1686-1691. doi: 10.1016/j.xphs.2018.12.023. Epub 2019 Jan 8.

PMID:
30633887
20.

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;58(6):504-508. doi: 10.1021/acs.biochem.8b01194. Epub 2019 Jan 14.

PMID:
30618239
21.

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;663:71-82. doi: 10.1016/j.abb.2019.01.001. Epub 2019 Jan 4.

22.

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. 2019 Mar 5;27(3):519-527.e5. doi: 10.1016/j.str.2018.11.002. Epub 2018 Dec 27.

PMID:
30595454
23.

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.

24.

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.

25.

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
26.

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
27.

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.

28.

[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.

29.

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.

30.

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;107(11):2965-2967. doi: 10.1016/j.xphs.2018.07.001. Epub 2018 Jul 12.

PMID:
30017886
31.

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
32.

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
33.

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;31(7-8):243-247. doi: 10.1093/protein/gzy008.

PMID:
29850878
34.

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
35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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
41.

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.

42.

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
43.

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.

44.

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
45.

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
46.

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
47.

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
48.

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
49.

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.

50.

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

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