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Items: 1 to 50 of 377

1.

Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR.

Takeuchi K, Imai M, Shimada I.

Proc Natl Acad Sci U S A. 2019 Sep 16. pii: 201906129. doi: 10.1073/pnas.1906129116. [Epub ahead of print]

PMID:
31527244
2.

Decreased conformational stability in the oncogenic N92I mutant of Ras-related C3 botulinum toxin substrate 1.

Toyama Y, Kontani K, Katada T, Shimada I.

Sci Adv. 2019 Aug 7;5(8):eaax1595. doi: 10.1126/sciadv.aax1595. eCollection 2019 Aug.

3.

Frequency selective coherence transfer NMR spectroscopy to study the structural dynamics of high molecular weight proteins.

Toyama Y, Shimada I.

J Magn Reson. 2019 Jul;304:62-77. doi: 10.1016/j.jmr.2019.05.004. Epub 2019 May 15.

PMID:
31129430
4.

In situ structural biology using in-cell NMR.

Nishida N, Ito Y, Shimada I.

Biochim Biophys Acta Gen Subj. 2019 May 16. pii: S0304-4165(19)30128-X. doi: 10.1016/j.bbagen.2019.05.007. [Epub ahead of print]

PMID:
31103749
5.

Function-related conformational dynamics of G protein-coupled receptors revealed by NMR.

Ueda T, Kofuku Y, Okude J, Imai S, Shiraishi Y, Shimada I.

Biophys Rev. 2019 Jun;11(3):409-418. doi: 10.1007/s12551-019-00539-w. Epub 2019 May 17. Review.

6.

Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel.

Kano H, Toyama Y, Imai S, Iwahashi Y, Mase Y, Yokogawa M, Osawa M, Shimada I.

Nat Commun. 2019 May 1;10(1):2008. doi: 10.1038/s41467-019-10038-x.

7.

Derepression of sonic hedgehog signaling upon Gpr161 deletion unravels forebrain and ventricular abnormalities.

Shimada IS, Somatilaka BN, Hwang SH, Anderson AG, Shelton JM, Rajaram V, Konopka G, Mukhopadhyay S.

Dev Biol. 2019 Jun 1;450(1):47-62. doi: 10.1016/j.ydbio.2019.03.011. Epub 2019 Mar 23.

PMID:
30914320
8.

Conformational landscape alternations promote oncogenic activities of Ras-related C3 botulinum toxin substrate 1 as revealed by NMR.

Toyama Y, Kontani K, Katada T, Shimada I.

Sci Adv. 2019 Mar 13;5(3):eaav8945. doi: 10.1126/sciadv.aav8945. eCollection 2019 Mar.

9.

Synthesis and structure-activity relationships of pyrazine-2-carboxamide derivatives as novel echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) inhibitors.

Iikubo K, Kurosawa K, Matsuya T, Kondoh Y, Kamikawa A, Moritomo A, Iwai Y, Tomiyama H, Shimada I.

Bioorg Med Chem. 2019 Apr 15;27(8):1683-1692. doi: 10.1016/j.bmc.2019.03.018. Epub 2019 Mar 7.

PMID:
30878193
10.

GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures.

Shimada I, Ueda T, Kofuku Y, Eddy MT, Wüthrich K.

Nat Rev Drug Discov. 2019 Jan;18(1):59-82. doi: 10.1038/nrd.2018.180. Epub 2018 Nov 9. Review.

11.

Application of C-Terminal 7-Azabicyclo[2.2.1]heptane to Stabilize β-Strand-like Extended Conformation of a Neighboring α-Amino Acid.

Zhai L, Wang S, Nara M, Takeuchi K, Shimada I, Otani Y, Ohwada T.

J Org Chem. 2018 Nov 2;83(21):13063-13079. doi: 10.1021/acs.joc.8b01756. Epub 2018 Oct 16.

PMID:
30284439
12.

Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif.

Sugiki T, Egawa D, Kumagai K, Kojima C, Fujiwara T, Takeuchi K, Shimada I, Hanada K, Takahashi H.

J Biol Chem. 2018 Jul 13;293(28):11206-11217. doi: 10.1074/jbc.RA118.002465. Epub 2018 May 30.

13.

Functional roles of Mg2+ binding sites in ion-dependent gating of a Mg2+ channel, MgtE, revealed by solution NMR.

Maruyama T, Imai S, Kusakizako T, Hattori M, Ishitani R, Nureki O, Ito K, Maturana AD, Shimada I, Osawa M.

Elife. 2018 Apr 3;7. pii: e31596. doi: 10.7554/eLife.31596.

14.

Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy.

Toyama Y, Kano H, Mase Y, Yokogawa M, Osawa M, Shimada I.

Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):3858-3863. doi: 10.1073/pnas.1722257115. Epub 2018 Mar 26.

15.

Deuteration and selective labeling of alanine methyl groups of β2-adrenergic receptor expressed in a baculovirus-insect cell expression system.

Kofuku Y, Yokomizo T, Imai S, Shiraishi Y, Natsume M, Itoh H, Inoue M, Nakata K, Igarashi S, Yamaguchi H, Mizukoshi T, Suzuki EI, Ueda T, Shimada I.

J Biomol NMR. 2018 Jul;71(3):185-192. doi: 10.1007/s10858-018-0174-5. Epub 2018 Mar 8.

PMID:
29520682
16.

Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR.

Mochizuki A, Saso A, Zhao Q, Kubo S, Nishida N, Shimada I.

J Am Chem Soc. 2018 Mar 14;140(10):3784-3790. doi: 10.1021/jacs.8b00426. Epub 2018 Mar 6.

PMID:
29509009
17.
18.

Basal Suppression of the Sonic Hedgehog Pathway by the G-Protein-Coupled Receptor Gpr161 Restricts Medulloblastoma Pathogenesis.

Shimada IS, Hwang SH, Somatilaka BN, Wang X, Skowron P, Kim J, Kim M, Shelton JM, Rajaram V, Xuan Z, Taylor MD, Mukhopadhyay S.

Cell Rep. 2018 Jan 30;22(5):1169-1184. doi: 10.1016/j.celrep.2018.01.018.

19.

Characterization of the multimeric structure of poly(A)-binding protein on a poly(A) tail.

Sawazaki R, Imai S, Yokogawa M, Hosoda N, Hoshino SI, Mio M, Mio K, Shimada I, Osawa M.

Sci Rep. 2018 Jan 23;8(1):1455. doi: 10.1038/s41598-018-19659-6.

20.

Phosphorylation-induced conformation of β2-adrenoceptor related to arrestin recruitment revealed by NMR.

Shiraishi Y, Natsume M, Kofuku Y, Imai S, Nakata K, Mizukoshi T, Ueda T, Iwaï H, Shimada I.

Nat Commun. 2018 Jan 15;9(1):194. doi: 10.1038/s41467-017-02632-8.

21.

Erratum to: Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

Takeuchi K, Arthanari H, Shimada I, Wagner G.

J Biomol NMR. 2017 Dec;69(4):245. doi: 10.1007/s10858-017-0131-8.

PMID:
29230599
22.

Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR.

Minato Y, Ueda T, Machiyama A, Iwaï H, Shimada I.

Sci Rep. 2017 Nov 28;7(1):16462. doi: 10.1038/s41598-017-16755-x.

23.

Nuclear Magnetic Resonance Approaches for Characterizing Protein-Protein Interactions.

Toyama Y, Mase Y, Kano H, Yokogawa M, Osawa M, Shimada I.

Methods Mol Biol. 2018;1684:115-128. doi: 10.1007/978-1-4939-7362-0_10.

PMID:
29058188
24.

A small-molecule compound inhibits a collagen-specific molecular chaperone and could represent a potential remedy for fibrosis.

Ito S, Ogawa K, Takeuchi K, Takagi M, Yoshida M, Hirokawa T, Hirayama S, Shin-Ya K, Shimada I, Doi T, Goshima N, Natsume T, Nagata K.

J Biol Chem. 2017 Dec 8;292(49):20076-20085. doi: 10.1074/jbc.M117.815936. Epub 2017 Oct 12.

25.

Forbidden Coherence Transfer of 19F Nuclei to Quantitatively Measure the Dynamics of a CF₃-Containing Ligand in Receptor-Bound States.

Tokunaga Y, Takeuchi K, Shimada I.

Molecules. 2017 Sep 7;22(9). pii: E1492. doi: 10.3390/molecules22091492.

26.

ATP-dependent modulation of MgtE in Mg2+ homeostasis.

Tomita A, Zhang M, Jin F, Zhuang W, Takeda H, Maruyama T, Osawa M, Hashimoto KI, Kawasaki H, Ito K, Dohmae N, Ishitani R, Shimada I, Yan Z, Hattori M, Nureki O.

Nat Commun. 2017 Jul 27;8(1):148. doi: 10.1038/s41467-017-00082-w.

27.

Prdm16 is required for the maintenance of neural stem cells in the postnatal forebrain and their differentiation into ependymal cells.

Shimada IS, Acar M, Burgess RJ, Zhao Z, Morrison SJ.

Genes Dev. 2017 Jun 1;31(11):1134-1146. doi: 10.1101/gad.291773.116. Epub 2017 Jul 11.

28.

Gilteritinib, a FLT3/AXL inhibitor, shows antileukemic activity in mouse models of FLT3 mutated acute myeloid leukemia.

Mori M, Kaneko N, Ueno Y, Yamada M, Tanaka R, Saito R, Shimada I, Mori K, Kuromitsu S.

Invest New Drugs. 2017 Oct;35(5):556-565. doi: 10.1007/s10637-017-0470-z. Epub 2017 May 17.

29.

Using Primary Neurosphere Cultures to Study Primary Cilia.

Shimada IS, Badgandi H, Somatilaka BN, Mukhopadhyay S.

J Vis Exp. 2017 Apr 14;(122). doi: 10.3791/55315.

30.

Effect of acidity on the physicochemical properties of α- and β-chitin nanofibers.

Suenaga S, Totani K, Nomura Y, Yamashita K, Shimada I, Fukunaga H, Takahashi N, Osada M.

Int J Biol Macromol. 2017 Sep;102:358-366. doi: 10.1016/j.ijbiomac.2017.04.011. Epub 2017 Apr 11.

PMID:
28410951
31.

Dynamic equilibrium on DNA defines transcriptional regulation of a multidrug binding transcriptional repressor, LmrR.

Takeuchi K, Imai M, Shimada I.

Sci Rep. 2017 Mar 21;7(1):267. doi: 10.1038/s41598-017-00257-x.

32.

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

Toyama Y, Kano H, Mase Y, Yokogawa M, Osawa M, Shimada I.

Nat Commun. 2017 Feb 22;8:14523. doi: 10.1038/ncomms14523.

33.

Tubby family proteins are adapters for ciliary trafficking of integral membrane proteins.

Badgandi HB, Hwang SH, Shimada IS, Loriot E, Mukhopadhyay S.

J Cell Biol. 2017 Mar 6;216(3):743-760. doi: 10.1083/jcb.201607095. Epub 2017 Feb 2.

34.

Trafficking to the primary cilium membrane.

Mukhopadhyay S, Badgandi HB, Hwang SH, Somatilaka B, Shimada IS, Pal K.

Mol Biol Cell. 2017 Jan 15;28(2):233-239. doi: 10.1091/mbc.E16-07-0505. Review.

35.

Disulfide mapping the voltage-sensing mechanism of a voltage-dependent potassium channel.

Nozaki T, Ozawa SI, Harada H, Kimura T, Osawa M, Shimada I.

Sci Rep. 2016 Nov 17;6:37303. doi: 10.1038/srep37303.

36.

Improvement of Ligand Affinity and Thermodynamic Properties by NMR-Based Evaluation of Local Dynamics and Surface Complementarity in the Receptor-Bound State.

Mizukoshi Y, Takeuchi K, Arutaki M, Tokunaga Y, Takizawa T, Hanzawa H, Shimada I.

Angew Chem Int Ed Engl. 2016 Nov 14;55(47):14606-14609. doi: 10.1002/anie.201607474. Epub 2016 Oct 20.

PMID:
27762089
37.

G-protein-coupled receptor signaling and neural tube closure defects.

Shimada IS, Mukhopadhyay S.

Birth Defects Res. 2017 Jan 30;109(2):129-139. doi: 10.1002/bdra.23567. Review.

38.

Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin.

Huang S, Umemoto R, Tamura Y, Kofuku Y, Uyeda TQ, Nishida N, Shimada I.

Sci Rep. 2016 Sep 22;6:33690. doi: 10.1038/srep33690.

39.
40.

Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region.

Minato Y, Suzuki S, Hara T, Kofuku Y, Kasuya G, Fujiwara Y, Igarashi S, Suzuki E, Nureki O, Hattori M, Ueda T, Shimada I.

Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4741-6. doi: 10.1073/pnas.1600519113. Epub 2016 Apr 11.

41.

Leptin Receptor Promotes Adipogenesis and Reduces Osteogenesis by Regulating Mesenchymal Stromal Cells in Adult Bone Marrow.

Yue R, Zhou BO, Shimada IS, Zhao Z, Morrison SJ.

Cell Stem Cell. 2016 Jun 2;18(6):782-96. doi: 10.1016/j.stem.2016.02.015. Epub 2016 Mar 24.

42.

Light-up fluorophore--DNA aptamer pair for label-free turn-on aptamer sensors.

Kato T, Shimada I, Kimura R, Hyuga M.

Chem Commun (Camb). 2016 Mar 14;52(21):4041-4. doi: 10.1039/c5cc08816j.

PMID:
26891088
43.

NMR Method for Characterizing Microsecond-to-Millisecond Chemical Exchanges Utilizing Differential Multiple-Quantum Relaxation in High Molecular Weight Proteins.

Toyama Y, Osawa M, Yokogawa M, Shimada I.

J Am Chem Soc. 2016 Feb 24;138(7):2302-11. doi: 10.1021/jacs.5b12954. Epub 2016 Feb 8.

PMID:
26855064
44.

Nitrogen-detected TROSY yields comparable sensitivity to proton-detected TROSY for non-deuterated, large proteins under physiological salt conditions.

Takeuchi K, Arthanari H, Imai M, Wagner G, Shimada I.

J Biomol NMR. 2016 Feb;64(2):143-51. doi: 10.1007/s10858-016-0015-3. Epub 2016 Jan 22.

45.

Hyperoxia causes diffuse alveolar damage through mechanisms involving upregulation of c-Myc/Bax and enhanced production of reactive oxygen species.

Shimada I, Kubota A, Katoh M, Suzuki F.

Respir Investig. 2016 Jan;54(1):59-68. doi: 10.1016/j.resinv.2015.08.006. Epub 2015 Oct 23.

PMID:
26718146
46.

Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ-Opioid Receptor.

Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I.

Angew Chem Int Ed Engl. 2015 Dec 21;54(52):15771-6. doi: 10.1002/anie.201508794. Epub 2015 Nov 16.

47.

Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

Takeuchi K, Arthanari H, Shimada I, Wagner G.

J Biomol NMR. 2015 Dec;63(4):323-331. doi: 10.1007/s10858-015-9991-y. Epub 2015 Oct 23. Erratum in: J Biomol NMR. 2017 Dec 11;:.

48.

Elucidation of the CCR1- and CCR5-binding modes of MIP-1α by application of an NMR spectra reconstruction method to the transferred cross-saturation experiments.

Yoshiura C, Ueda T, Kofuku Y, Matsumoto M, Okude J, Kondo K, Shiraishi Y, Shimada I.

J Biomol NMR. 2015 Dec;63(4):333-340. doi: 10.1007/s10858-015-9992-x. Epub 2015 Oct 15.

49.

Structural basis for the inhibition of voltage-dependent K+ channel by gating modifier toxin.

Ozawa S, Kimura T, Nozaki T, Harada H, Shimada I, Osawa M.

Sci Rep. 2015 Sep 18;5:14226. doi: 10.1038/srep14226.

50.

Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6.

Moriya J, Takeuchi K, Tai K, Arai K, Kobayashi N, Yoneda N, Fukunishi Y, Inoue A, Kihara M, Murakami T, Chiba K, Shimada I.

J Med Chem. 2015 Jul 23;58(14):5674-83. doi: 10.1021/acs.jmedchem.5b00778. Epub 2015 Jul 14.

PMID:
26132273

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