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Items: 41

1.

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 Feb 28. doi: 10.1007/s10858-018-0169-2. [Epub ahead of print]

PMID:
29492730
2.

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.

PMID:
29301037
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

PMID:
26804978
9.

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.

10.

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.

11.

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.

PMID:
26479087
12.

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.

13.

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.

14.

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.

15.

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.

PMID:
26015171
16.

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.

PMID:
25931034
17.

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.

PMID:
25643321
18.

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.

PMID:
25567666
19.

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.

20.

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.

PMID:
25408346
21.

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.

22.

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.

23.

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.

PMID:
24401037
24.

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.

PMID:
24065419
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.

26.

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.

PMID:
23578712
27.

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.

PMID:
23567152
28.

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.

PMID:
23421577
29.

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.

30.

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.

PMID:
23313507
31.

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.

PMID:
23296043
32.

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.

33.

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.

PMID:
23033069
34.

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.

PMID:
22996355
35.

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.

36.

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.

37.

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.

PMID:
21619528
38.

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.

39.

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.

40.

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.

41.

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.

PMID:
19944705

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