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Items: 46


ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system.

Yunoki Y, Ishii K, Yagi-Utsumi M, Murakami R, Uchiyama S, Yagi H, Kato K.

Life Sci Alliance. 2019 Jun 3;2(3). pii: e201900368. doi: 10.26508/lsa.201900368. Print 2019 Jun.


NMR Characterization of Conformational Dynamics and Molecular Assemblies of Proteins.

Yagi-Utsumi M.

Biol Pharm Bull. 2019;42(6):867-872. doi: 10.1248/bpb.b19-00115.


Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer.

Satoh T, Yagi-Utsumi M, Okamoto K, Kurimoto E, Tanaka K, Kato K.

Int J Mol Sci. 2019 May 7;20(9). pii: E2231. doi: 10.3390/ijms20092231.


Effects of a Hydrophilic/Hydrophobic Interface on Amyloid-β Peptides Studied by Molecular Dynamics Simulations and NMR Experiments.

Itoh SG, Yagi-Utsumi M, Kato K, Okumura H.

J Phys Chem B. 2019 Jan 10;123(1):160-169. doi: 10.1021/acs.jpcb.8b11609. Epub 2019 Jan 2.


The immunostimulatory effects and chemical characteristics of heated honey.

Ota M, Ishiuchi K, Xu X, Minami M, Nagachi Y, Yagi-Utsumi M, Tabuchi Y, Cai SQ, Makino T.

J Ethnopharmacol. 2019 Jan 10;228:11-17. doi: 10.1016/j.jep.2018.09.019. Epub 2018 Sep 13.


Stable isotope labeling approaches for NMR characterization of glycoproteins using eukaryotic expression systems.

Yanaka S, Yagi H, Yogo R, Yagi-Utsumi M, Kato K.

J Biomol NMR. 2018 Jul;71(3):193-202. doi: 10.1007/s10858-018-0169-2. Epub 2018 Feb 28.


Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation.

Yagi-Utsumi M, Sikdar A, Kozai T, Inoue R, Sugiyama M, Uchihashi T, Yagi H, Satoh T, Kato K.

Protein Eng Des Sel. 2018 Jan 1;31(1):29-36. doi: 10.1093/protein/gzx066.


Formation of the chaperonin complex studied by 2D NMR spectroscopy.

Takenaka T, Nakamura T, Yanaka S, Yagi-Utsumi M, Chandak MS, Takahashi K, Paul S, Makabe K, Arai M, Kato K, Kuwajima K.

PLoS One. 2017 Oct 23;12(10):e0187022. doi: 10.1371/journal.pone.0187022. eCollection 2017.


Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin.

Kitazawa S, Yagi-Utsumi M, Kato K, Kitahara R.

Molecules. 2017 Aug 28;22(9). pii: E1414. doi: 10.3390/molecules22091414.


Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation.

Kurimoto E, Satoh T, Ito Y, Ishihara E, Okamoto K, Yagi-Utsumi M, Tanaka K, Kato K.

Protein Sci. 2017 May;26(5):1080-1085. doi: 10.1002/pro.3153. Epub 2017 Mar 16.


Mass Spectrometric Characterization of HIV-1 Reverse Transcriptase Interactions with Non-nucleoside Reverse Transcriptase Inhibitors.

Thammaporn R, Ishii K, Yagi-Utsumi M, Uchiyama S, Hannongbua S, Kato K.

Biol Pharm Bull. 2016;39(3):450-4. doi: 10.1248/bpb.b15-00880.


An anticancer drug suppresses the primary nucleation reaction that initiates the production of the toxic Aβ42 aggregates linked with Alzheimer's disease.

Habchi J, Arosio P, Perni M, Costa AR, Yagi-Utsumi M, Joshi P, Chia S, Cohen SI, Müller MB, Linse S, Nollen EA, Dobson CM, Knowles TP, Vendruscolo M.

Sci Adv. 2016 Feb 12;2(2):e1501244. doi: 10.1126/sciadv.1501244. eCollection 2016 Feb.


Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase.

Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K.

ChemMedChem. 2016 Feb 17;11(4):363-6. doi: 10.1002/cmdc.201500554. Epub 2016 Jan 25.


Membrane-Induced Dichotomous Conformation of Amyloid β with the Disordered N-Terminal Segment Followed by the Stable C-Terminal β Structure.

Yagi-Utsumi M, Kato K, Nishimura K.

PLoS One. 2016 Jan 5;11(1):e0146405. doi: 10.1371/journal.pone.0146405. eCollection 2016.


NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities.

Thammaporn R, Yagi-Utsumi M, Yamaguchi T, Boonsri P, Saparpakorn P, Choowongkomon K, Techasakul S, Kato K, Hannongbua S.

Sci Rep. 2015 Oct 29;5:15806. doi: 10.1038/srep15806.


Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins.

Newby FN, De Simone A, Yagi-Utsumi M, Salvatella X, Dobson CM, Vendruscolo M.

Biochemistry. 2015 Nov 24;54(46):6876-86. doi: 10.1021/acs.biochem.5b00670. Epub 2015 Nov 11.


Conformational Effects of the A21G Flemish Mutation on the Aggregation of Amyloid β Peptide.

Yagi-Utsumi M, Dobson CM.

Biol Pharm Bull. 2015;38(10):1668-72. doi: 10.1248/bpb.b15-00466.


Structural basis of redox-dependent substrate binding of protein disulfide isomerase.

Yagi-Utsumi M, Satoh T, Kato K.

Sci Rep. 2015 Sep 9;5:13909. doi: 10.1038/srep13909.


Redox-coupled structural changes of the catalytic a' domain of protein disulfide isomerase.

Inagaki K, Satoh T, Yagi-Utsumi M, Le Gulluche AC, Anzai T, Uekusa Y, Kamiya Y, Kato K.

FEBS Lett. 2015 Sep 14;589(19 Pt B):2690-4. doi: 10.1016/j.febslet.2015.07.041. Epub 2015 Aug 10.


A Self-Assembled Spherical Complex Displaying a Gangliosidic Glycan Cluster Capable of Interacting with Amyloidogenic Proteins.

Sato S, Yoshimasa Y, Fujita D, Yagi-Utsumi M, Yamaguchi T, Kato K, Fujita M.

Angew Chem Int Ed Engl. 2015 Jul 13;54(29):8435-9. doi: 10.1002/anie.201501981. Epub 2015 May 27.


Structural and dynamic views of GM1 ganglioside.

Yagi-Utsumi M, Kato K.

Glycoconj J. 2015 May;32(3-4):105-12. doi: 10.1007/s10719-015-9587-5. Epub 2015 May 1. Review.


Structural basis for amyloidogenic peptide recognition by sorLA.

Kitago Y, Nagae M, Nakata Z, Yagi-Utsumi M, Takagi-Niidome S, Mihara E, Nogi T, Kato K, Takagi J.

Nat Struct Mol Biol. 2015 Mar;22(3):199-206. doi: 10.1038/nsmb.2954. Epub 2015 Feb 2.


A self-assembled, π-stacked complex as a finely-tunable magnetic aligner for biomolecular NMR applications.

Sato S, Takeuchi R, Yagi-Utsumi M, Yamaguchi T, Yamaguchi Y, Kato K, Fujita M.

Chem Commun (Camb). 2015 Feb 14;51(13):2540-3. doi: 10.1039/c4cc09354b.


Mode of substrate recognition by the Josephin domain of ataxin-3, which has an endo-type deubiquitinase activity.

Satoh T, Sumiyoshi A, Yagi-Utsumi M, Sakata E, Sasakawa H, Kurimoto E, Yamaguchi Y, Li W, Joazeiro CA, Hirokawa T, Kato K.

FEBS Lett. 2014 Nov 28;588(23):4422-30. doi: 10.1016/j.febslet.2014.10.013. Epub 2014 Oct 19.


Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.

Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y, Sakae Y, Okamoto Y, Kato K.

Adv Exp Med Biol. 2015;842:217-30. doi: 10.1007/978-3-319-11280-0_14. No abstract available.


Backbone (1)H, (13)C, and (15)N resonance assignments of the Fc fragment of human immunoglobulin G glycoprotein.

Yagi H, Zhang Y, Yagi-Utsumi M, Yamaguchi T, Iida S, Yamaguchi Y, Kato K.

Biomol NMR Assign. 2015 Oct;9(2):257-60. doi: 10.1007/s12104-014-9586-7. Epub 2014 Oct 8.


Structural basis for proteasome formation controlled by an assembly chaperone nas2.

Satoh T, Saeki Y, Hiromoto T, Wang YH, Uekusa Y, Yagi H, Yoshihara H, Yagi-Utsumi M, Mizushima T, Tanaka K, Kato K.

Structure. 2014 May 6;22(5):731-43. doi: 10.1016/j.str.2014.02.014. Epub 2014 Mar 27.


Close identity between alternatively folded state N2 of ubiquitin and the conformation of the protein bound to the ubiquitin-activating enzyme.

Kitazawa S, Kameda T, Kumo A, Yagi-Utsumi M, Baxter NJ, Kato K, Williamson MP, Kitahara R.

Biochemistry. 2014 Jan 28;53(3):447-9. doi: 10.1021/bi401617n. Epub 2014 Jan 10.


Backbone ¹H, ¹³C and ¹⁵N assignments of yeast Ump1, an intrinsically disordered protein that functions as a proteasome assembly chaperone.

Uekusa Y, Okawa K, Yagi-Utsumi M, Serve O, Nakagawa Y, Mizushima T, Yagi H, Saeki Y, Tanaka K, Kato K.

Biomol NMR Assign. 2014 Oct;8(2):383-6. doi: 10.1007/s12104-013-9523-1. Epub 2013 Sep 25.


NMR characterization of the interaction of GroEL with amyloid β as a model ligand.

Yagi-Utsumi M, Kunihara T, Nakamura T, Uekusa Y, Makabe K, Kuwajima K, Kato K.

FEBS Lett. 2013 Jun 5;587(11):1605-9. doi: 10.1016/j.febslet.2013.04.007. Epub 2013 Apr 18.


Structural and functional mosaic nature of MHC class I molecules in their peptide-free form.

Kurimoto E, Kuroki K, Yamaguchi Y, Yagi-Utsumi M, Igaki T, Iguchi T, Maenaka K, Kato K.

Mol Immunol. 2013 Oct;55(3-4):393-9. doi: 10.1016/j.molimm.2013.03.014. Epub 2013 Apr 8.


Nuclear magnetic resonance approaches for characterizing interactions between the bacterial chaperonin GroEL and unstructured proteins.

Nishida N, Yagi-Utsumi M, Motojima F, Yoshida M, Shimada I, Kato K.

J Biosci Bioeng. 2013 Aug;116(2):160-4. doi: 10.1016/j.jbiosc.2013.02.012. Epub 2013 Apr 6.


Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin.

Kitazawa S, Kameda T, Yagi-Utsumi M, Sugase K, Baxter NJ, Kato K, Williamson MP, Kitahara R.

Biochemistry. 2013 Mar 19;52(11):1874-85. doi: 10.1021/bi301420m. Epub 2013 Mar 7.


The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments.

Chandak MS, Nakamura T, Takenaka T, Chaudhuri TK, Yagi-Utsumi M, Chen J, Kato K, Kuwajima K.

Protein Sci. 2013 Apr;22(4):486-91. doi: 10.1002/pro.2221. Epub 2013 Feb 11.


Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide.

Yagi-Utsumi M, Yamaguchi Y, Boonsri P, Iguchi T, Okemoto K, Natori S, Kato K.

Biochem Biophys Res Commun. 2013 Feb 8;431(2):136-40. doi: 10.1016/j.bbrc.2013.01.009. Epub 2013 Jan 10.


Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins.

Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K.

Chem Commun (Camb). 2013 Feb 11;49(12):1235-7. doi: 10.1039/c2cc38016a.


NMR and mutational identification of the collagen-binding site of the chaperone Hsp47.

Yagi-Utsumi M, Yoshikawa S, Yamaguchi Y, Nishi Y, Kurimoto E, Ishida Y, Homma T, Hoseki J, Nishikawa Y, Koide T, Nagata K, Kato K.

PLoS One. 2012;7(9):e45930. doi: 10.1371/journal.pone.0045930. Epub 2012 Sep 25.


Protein encapsulation within synthetic molecular hosts.

Fujita D, Suzuki K, Sato S, Yagi-Utsumi M, Yamaguchi Y, Mizuno N, Kumasaka T, Takata M, Noda M, Uchiyama S, Kato K, Fujita M.

Nat Commun. 2012;3:1093. doi: 10.1038/ncomms2093.


Reversed assembly of dyes in an RNA duplex compared with those in DNA.

Fujii T, Urushihara M, Kashida H, Ito H, Liang X, Yagi-Utsumi M, Kato K, Asanuma H.

Chemistry. 2012 Oct 15;18(42):13304-13. doi: 10.1002/chem.201201956. Epub 2012 Sep 20.


A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex.

Yagi H, Ishimoto K, Hiromoto T, Fujita H, Mizushima T, Uekusa Y, Yagi-Utsumi M, Kurimoto E, Noda M, Uchiyama S, Tokunaga F, Iwai K, Kato K.

EMBO Rep. 2012 May 1;13(5):462-8. doi: 10.1038/embor.2012.24.


Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution.

Hirano T, Serve O, Yagi-Utsumi M, Takemoto E, Hiromoto T, Satoh T, Mizushima T, Kato K.

J Biol Chem. 2011 Oct 28;286(43):37496-502. doi: 10.1074/jbc.M111.256354. Epub 2011 Sep 7.


Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets.

Kamiya Y, Yagi-Utsumi M, Yagi H, Kato K.

Curr Pharm Des. 2011;17(17):1672-84.


Spectroscopic Characterization of Intermolecular Interaction of Amyloid β Promoted on GM1 Micelles.

Yagi-Utsumi M, Matsuo K, Yanagisawa K, Gekko K, Kato K.

Int J Alzheimers Dis. 2010 Dec 28;2011:925073. doi: 10.4061/2011/925073.


Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates.

Sakata E, Satoh T, Yamamoto S, Yamaguchi Y, Yagi-Utsumi M, Kurimoto E, Tanaka K, Wakatsuki S, Kato K.

Structure. 2010 Jan 13;18(1):138-47. doi: 10.1016/j.str.2009.11.007.


NMR characterization of the interactions between lyso-GM1 aqueous micelles and amyloid beta.

Yagi-Utsumi M, Kameda T, Yamaguchi Y, Kato K.

FEBS Lett. 2010 Feb 19;584(4):831-6. doi: 10.1016/j.febslet.2010.01.005. Epub 2010 Jan 12.


Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface.

Serve O, Kamiya Y, Maeno A, Nakano M, Murakami C, Sasakawa H, Yamaguchi Y, Harada T, Kurimoto E, Yagi-Utsumi M, Iguchi T, Inaba K, Kikuchi J, Asami O, Kajino T, Oka T, Nakasako M, Kato K.

J Mol Biol. 2010 Feb 19;396(2):361-74. doi: 10.1016/j.jmb.2009.11.049. Epub 2009 Nov 26.


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