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Items: 38

1.

Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib.

Ohbayashi N, Murayama K, Kato-Murayama M, Kukimoto-Niino M, Uejima T, Matsuda T, Ohsawa N, Yokoyoma S, Nojima H, Shirouzu M.

ChemistryOpen. 2018 Sep 10;7(9):721-727. doi: 10.1002/open.201800177. eCollection 2018 Sep.

2.

Cholesterol sulfate is a DOCK2 inhibitor that mediates tissue-specific immune evasion in the eye.

Sakurai T, Uruno T, Sugiura Y, Tatsuguchi T, Yamamura K, Ushijima M, Hattori Y, Kukimoto-Niino M, Mishima-Tsumagari C, Watanabe M, Suematsu M, Fukui Y.

Sci Signal. 2018 Jul 31;11(541). pii: eaao4874. doi: 10.1126/scisignal.aao4874.

PMID:
30065028
3.

Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression.

Katsura K, Tomabechi Y, Matsuda T, Yonemochi M, Mikuni J, Ohsawa N, Terada T, Yokoyama S, Kukimoto-Niino M, Takemoto C, Shirouzu M.

Protein Expr Purif. 2018 Oct;150:92-99. doi: 10.1016/j.pep.2018.05.005. Epub 2018 May 21.

PMID:
29793032
4.

Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction.

Matsuda T, Ito T, Takemoto C, Katsura K, Ikeda M, Wakiyama M, Kukimoto-Niino M, Yokoyama S, Kurosawa Y, Shirouzu M.

PLoS One. 2018 Feb 20;13(2):e0193158. doi: 10.1371/journal.pone.0193158. eCollection 2018.

5.

Identification of pyrrolo[2,3-d]pyrimidines as potent HCK and FLT3-ITD dual inhibitors.

Koda Y, Kikuzato K, Mikuni J, Tanaka A, Yuki H, Honma T, Tomabechi Y, Kukimoto-Niino M, Shirouzu M, Shirai F, Koyama H.

Bioorg Med Chem Lett. 2017 Nov 15;27(22):4994-4998. doi: 10.1016/j.bmcl.2017.10.012. Epub 2017 Oct 7.

PMID:
29037944
6.

Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.

Yuki H, Kikuzato K, Koda Y, Mikuni J, Tomabechi Y, Kukimoto-Niino M, Tanaka A, Shirai F, Shirouzu M, Koyama H, Honma T.

Bioorg Med Chem. 2017 Aug 15;25(16):4259-4264. doi: 10.1016/j.bmc.2017.05.053. Epub 2017 Jun 16.

PMID:
28662963
7.

Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1.

Tajiri H, Uruno T, Shirai T, Takaya D, Matsunaga S, Setoyama D, Watanabe M, Kukimoto-Niino M, Oisaki K, Ushijima M, Sanematsu F, Honma T, Terada T, Oki E, Shirasawa S, Maehara Y, Kang D, Côté JF, Yokoyama S, Kanai M, Fukui Y.

Cell Rep. 2017 May 2;19(5):969-980. doi: 10.1016/j.celrep.2017.04.016.

8.

Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes.

Terasawa K, Tomabechi Y, Ikeda M, Ehara H, Kukimoto-Niino M, Wakiyama M, Podyma-Inoue KA, Rajapakshe AR, Watabe T, Shirouzu M, Hara-Yokoyama M.

Biochem Biophys Res Commun. 2016 Oct 21;479(3):489-495. doi: 10.1016/j.bbrc.2016.09.093. Epub 2016 Sep 20.

PMID:
27663661
9.

TNIK inhibition abrogates colorectal cancer stemness.

Masuda M, Uno Y, Ohbayashi N, Ohata H, Mimata A, Kukimoto-Niino M, Moriyama H, Kashimoto S, Inoue T, Goto N, Okamoto K, Shirouzu M, Sawa M, Yamada T.

Nat Commun. 2016 Aug 26;7:12586. doi: 10.1038/ncomms12586.

10.

A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.

Nishii W, Kukimoto-Niino M, Terada T, Shirouzu M, Muramatsu T, Kojima M, Kihara H, Yokoyama S.

Nat Chem Biol. 2015 Jan;11(1):46-51. doi: 10.1038/nchembio.1688. Epub 2014 Nov 10.

PMID:
25383757
11.

Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5.

Kusano S, Kukimoto-Niino M, Satta Y, Ohsawa N, Uchikubo-Kamo T, Wakiyama M, Ikeda M, Terada T, Yamamoto K, Nishimura Y, Shirouzu M, Sasazuki T, Yokoyama S.

J Mol Biol. 2014 Aug 26;426(17):3016-27. doi: 10.1016/j.jmb.2014.06.020. Epub 2014 Jul 11.

12.

Immune regulatory functions of DOCK family proteins in health and disease.

Nishikimi A, Kukimoto-Niino M, Yokoyama S, Fukui Y.

Exp Cell Res. 2013 Sep 10;319(15):2343-9. doi: 10.1016/j.yexcr.2013.07.024. Epub 2013 Aug 2. Review.

PMID:
23911989
13.

Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.

Terasawa M, Uruno T, Mori S, Kukimoto-Niino M, Nishikimi A, Sanematsu F, Tanaka Y, Yokoyama S, Fukui Y.

PLoS One. 2012;7(9):e46277. doi: 10.1371/journal.pone.0046277. Epub 2012 Sep 26.

14.

Tetrameric interaction of the ectoenzyme CD38 on the cell surface enables its catalytic and raft-association activities.

Hara-Yokoyama M, Kukimoto-Niino M, Terasawa K, Harumiya S, Podyma-Inoue KA, Hino N, Sakamoto K, Itoh S, Hashii N, Hiruta Y, Kawasaki N, Mishima-Tsumagari C, Kaitsu Y, Matsumoto T, Wakiyama M, Shirouzu M, Kasama T, Takayanagi H, Utsunomiya-Tate N, Takatsu K, Katada T, Hirabayashi Y, Yokoyama S, Yanagishita M.

Structure. 2012 Sep 5;20(9):1585-95. doi: 10.1016/j.str.2012.06.017. Epub 2012 Aug 2.

15.

Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.

Sato T, Watanabe H, Tsuganezawa K, Yuki H, Mikuni J, Yoshikawa S, Kukimoto-Niino M, Fujimoto T, Terazawa Y, Wakiyama M, Kojima H, Okabe T, Nagano T, Shirouzu M, Yokoyama S, Tanaka A, Honma T.

Bioorg Med Chem. 2012 Jun 15;20(12):3756-67. doi: 10.1016/j.bmc.2012.04.042. Epub 2012 Apr 27.

PMID:
22607878
16.

Structural basis of interleukin-5 dimer recognition by its α receptor.

Kusano S, Kukimoto-Niino M, Hino N, Ohsawa N, Ikutani M, Takaki S, Sakamoto K, Hara-Yokoyama M, Shirouzu M, Takatsu K, Yokoyama S.

Protein Sci. 2012 Jun;21(6):850-64. doi: 10.1002/pro.2072. Epub 2012 Apr 23.

17.

Blockade of inflammatory responses by a small-molecule inhibitor of the Rac activator DOCK2.

Nishikimi A, Uruno T, Duan X, Cao Q, Okamura Y, Saitoh T, Saito N, Sakaoka S, Du Y, Suenaga A, Kukimoto-Niino M, Miyano K, Gotoh K, Okabe T, Sanematsu F, Tanaka Y, Sumimoto H, Honma T, Yokoyama S, Nagano T, Kohda D, Kanai M, Fukui Y.

Chem Biol. 2012 Apr 20;19(4):488-97. doi: 10.1016/j.chembiol.2012.03.008.

18.

DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses.

Harada Y, Tanaka Y, Terasawa M, Pieczyk M, Habiro K, Katakai T, Hanawa-Suetsugu K, Kukimoto-Niino M, Nishizaki T, Shirouzu M, Duan X, Uruno T, Nishikimi A, Sanematsu F, Yokoyama S, Stein JV, Kinashi T, Fukui Y.

Blood. 2012 May 10;119(19):4451-61. doi: 10.1182/blood-2012-01-407098. Epub 2012 Mar 28.

19.

Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.

Yoshikawa S, Kukimoto-Niino M, Parker L, Handa N, Terada T, Fujimoto T, Terazawa Y, Wakiyama M, Sato M, Sano S, Kobayashi T, Tanaka T, Chen L, Liu ZJ, Wang BC, Shirouzu M, Kawa S, Semba K, Yamamoto T, Yokoyama S.

Oncogene. 2013 Jan 3;32(1):27-38. doi: 10.1038/onc.2012.21. Epub 2012 Feb 20.

PMID:
22349823
20.

Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.

Hanawa-Suetsugu K, Kukimoto-Niino M, Mishima-Tsumagari C, Akasaka R, Ohsawa N, Sekine S, Ito T, Tochio N, Koshiba S, Kigawa T, Terada T, Shirouzu M, Nishikimi A, Uruno T, Katakai T, Kinashi T, Kohda D, Fukui Y, Yokoyama S.

Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3305-10. doi: 10.1073/pnas.1113512109. Epub 2012 Feb 13.

21.

Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding.

Kusano S, Kukimoto-Niino M, Hino N, Ohsawa N, Okuda K, Sakamoto K, Shirouzu M, Shindo T, Yokoyama S.

Protein Sci. 2012 Feb;21(2):199-210. doi: 10.1002/pro.2003. Epub 2011 Dec 28.

22.

Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.

Kukimoto-Niino M, Tokmakov A, Terada T, Ohbayashi N, Fujimoto T, Gomi S, Shiromizu I, Kawamoto M, Matsusue T, Shirouzu M, Yokoyama S.

Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):763-73. doi: 10.1107/S090744491102405X. Epub 2011 Aug 9.

PMID:
21904029
23.

Identification of critical residues in G(alpha)13 for stimulation of p115RhoGEF activity and the structure of the G(alpha)13-p115RhoGEF regulator of G protein signaling homology (RH) domain complex.

Hajicek N, Kukimoto-Niino M, Mishima-Tsumagari C, Chow CR, Shirouzu M, Terada T, Patel M, Yokoyama S, Kozasa T.

J Biol Chem. 2011 Jun 10;286(23):20625-36. doi: 10.1074/jbc.M110.201392. Epub 2011 Apr 20.

24.

Crystal structure of the Ca²⁺/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609.

Kukimoto-Niino M, Yoshikawa S, Takagi T, Ohsawa N, Tomabechi Y, Terada T, Shirouzu M, Suzuki A, Lee S, Yamauchi T, Okada-Iwabu M, Iwabu M, Kadowaki T, Minokoshi Y, Yokoyama S.

J Biol Chem. 2011 Jun 24;286(25):22570-9. doi: 10.1074/jbc.M111.251710. Epub 2011 Apr 19.

25.

Cell-permeable carboxyl-terminal p27(Kip1) peptide exhibits anti-tumor activity by inhibiting Pim-1 kinase.

Morishita D, Takami M, Yoshikawa S, Katayama R, Sato S, Kukimoto-Niino M, Umehara T, Shirouzu M, Sekimizu K, Yokoyama S, Fujita N.

J Biol Chem. 2011 Jan 28;286(4):2681-8. doi: 10.1074/jbc.M109.092452. Epub 2010 Nov 9.

26.

Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.

Shida M, Arakawa A, Ishii R, Kishishita S, Takagi T, Kukimoto-Niino M, Sugano S, Tanaka A, Shirouzu M, Yokoyama S.

Acta Crystallogr D Biol Crystallogr. 2010 Mar;66(Pt 3):223-32. doi: 10.1107/S0907444909053979. Epub 2010 Feb 12.

PMID:
20179333
27.

A Rac GTPase-activating protein, MgcRacGAP, is a nuclear localizing signal-containing nuclear chaperone in the activation of STAT transcription factors.

Kawashima T, Bao YC, Minoshima Y, Nomura Y, Hatori T, Hori T, Fukagawa T, Fukada T, Takahashi N, Nosaka T, Inoue M, Sato T, Kukimoto-Niino M, Shirouzu M, Yokoyama S, Kitamura T.

Mol Cell Biol. 2009 Apr;29(7):1796-813. doi: 10.1128/MCB.01423-08. Epub 2009 Jan 21.

28.

Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases.

Kukimoto-Niino M, Sakamoto A, Kanno E, Hanawa-Suetsugu K, Terada T, Shirouzu M, Fukuda M, Yokoyama S.

Structure. 2008 Oct 8;16(10):1478-90. doi: 10.1016/j.str.2008.07.014.

29.

Crystal structure of the human receptor activity-modifying protein 1 extracellular domain.

Kusano S, Kukimoto-Niino M, Akasaka R, Toyama M, Terada T, Shirouzu M, Shindo T, Yokoyama S.

Protein Sci. 2008 Nov;17(11):1907-14. doi: 10.1110/ps.036012.108. Epub 2008 Aug 25.

30.

Crystal Structure of the interleukin-15.interleukin-15 receptor alpha complex: insights into trans and cis presentation.

Olsen SK, Ota N, Kishishita S, Kukimoto-Niino M, Murayama K, Uchiyama H, Toyama M, Terada T, Shirouzu M, Kanagawa O, Yokoyama S.

J Biol Chem. 2007 Dec 21;282(51):37191-204. Epub 2007 Oct 18.

31.

Structure of the UNC5H2 death domain.

Handa N, Kukimoto-Niino M, Akasaka R, Murayama K, Terada T, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Tanaka A, Hayashizaki Y, Kigawa T, Shirouzu M, Yokoyama S.

Acta Crystallogr D Biol Crystallogr. 2006 Dec;62(Pt 12):1502-9. Epub 2006 Nov 23.

PMID:
17139086
32.

The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain.

Handa N, Kukimoto-Niino M, Akasaka R, Kishishita S, Murayama K, Terada T, Inoue M, Kigawa T, Kose S, Imamoto N, Tanaka A, Hayashizaki Y, Shirouzu M, Yokoyama S.

J Mol Biol. 2006 Oct 13;363(1):114-24. Epub 2006 Aug 3.

PMID:
16962612
33.

Crystal structure of the RUN domain of the RAP2-interacting protein x.

Kukimoto-Niino M, Takagi T, Akasaka R, Murayama K, Uchikubo-Kamo T, Terada T, Inoue M, Watanabe S, Tanaka A, Hayashizaki Y, Kigawa T, Shirouzu M, Yokoyama S.

J Biol Chem. 2006 Oct 20;281(42):31843-53. Epub 2006 Aug 23.

34.

Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.

Arai R, Kukimoto-Niino M, Kuroishi C, Bessho Y, Shirouzu M, Yokoyama S.

Protein Sci. 2006 Feb;15(2):373-7. Epub 2005 Dec 29.

35.

Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Angstroms resolution.

Arai R, Kukimoto-Niino M, Uda-Tochio H, Morita S, Uchikubo-Kamo T, Akasaka R, Etou Y, Hayashizaki Y, Kigawa T, Terada T, Shirouzu M, Yokoyama S.

Protein Sci. 2005 Jul;14(7):1888-93. Epub 2005 Jun 3.

36.

Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 A resolution.

Kukimoto-Niino M, Shibata R, Murayama K, Hamana H, Nishimoto M, Bessho Y, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S.

Protein Sci. 2005 Mar;14(3):823-7. Epub 2005 Feb 2.

37.

Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8.

Kukimoto-Niino M, Murayama K, Kato-Murayama M, Idaka M, Bessho Y, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S.

Protein Sci. 2004 Nov;13(11):3038-42. Epub 2004 Sep 30.

38.

Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.

Kukimoto-Niino M, Murayama K, Inoue M, Terada T, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S.

J Mol Biol. 2004 Mar 26;337(3):761-70.

PMID:
15019792

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