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Class I Polyhydroxyalkanoate Synthase from the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Predominantly Exists as a Functional Dimer in the Absence of a Substrate.

Higuchi-Takeuchi M, Motoda Y, Kigawa T, Numata K.

ACS Omega. 2017 Aug 31;2(8):5071-5078. doi: 10.1021/acsomega.7b00667. Epub 2017 Aug 29.


Impact of cellular health conditions on the protein folding state in mammalian cells.

Inomata K, Kamoshida H, Ikari M, Ito Y, Kigawa T.

Chem Commun (Camb). 2017 Oct 10;53(81):11245-11248. doi: 10.1039/c7cc06004a.


Advances in stable isotope assisted labeling strategies with information science.

Kigawa T.

Arch Biochem Biophys. 2017 Aug 15;628:17-23. doi: 10.1016/ Epub 2017 Jun 20.


Molecular actions of two synthetic brassinosteroids, iso-carbaBL and 6-deoxoBL, which cause altered physiological activities between Arabidopsis and rice.

Nakamura A, Tochio N, Fujioka S, Ito S, Kigawa T, Shimada Y, Matsuoka M, Yoshida S, Kinoshita T, Asami T, Seto H, Nakano T.

PLoS One. 2017 Apr 3;12(4):e0174015. doi: 10.1371/journal.pone.0174015. eCollection 2017.


Corrigendum to "Multiple inhibitory factor removal from an Escherichia coli cell extract improves cell-free protein synthesis" [J Biosci Bioeng 108 (2009) 30-35].

Seki E, Matsuda N, Kigawa T.

J Biosci Bioeng. 2017 Jan;123(1):139. doi: 10.1016/j.jbiosc.2016.10.001. Epub 2016 Oct 27. No abstract available.


Angucycline antibiotic waldiomycin recognizes common structural motif conserved in bacterial histidine kinases.

Eguchi Y, Okajima T, Tochio N, Inukai Y, Shimizu R, Ueda S, Shinya S, Kigawa T, Fukamizo T, Igarashi M, Utsumi R.

J Antibiot (Tokyo). 2017 Mar;70(3):251-258. doi: 10.1038/ja.2016.151. Epub 2016 Dec 21.


Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR.

Konagaya Y, Miyakawa R, Sato M, Matsugami A, Watanabe S, Hayashi F, Kigawa T, Nishimura C.

PLoS One. 2016 Dec 1;11(12):e0167176. doi: 10.1371/journal.pone.0167176. eCollection 2016.


Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.

Kuwasako K, Nameki N, Tsuda K, Takahashi M, Sato A, Tochio N, Inoue M, Terada T, Kigawa T, Kobayashi N, Shirouzu M, Ito T, Sakamoto T, Wakamatsu K, Güntert P, Takahashi S, Yokoyama S, Muto Y.

Protein Sci. 2017 Feb;26(2):280-291. doi: 10.1002/pro.3080. Epub 2016 Nov 27.


Corrigendum to ''Cell-free protein synthesis system from Escherichia coli cells cultured at decreased temperatures improves productivity by decreasing DNA template degradation'' [Anal. Biochem. 377 (2008) 156-161].

Seki E, Matsuda N, Yokoyama S, Kigawa T.

Anal Biochem. 2017 Jan 15;517:22. doi: 10.1016/j.ab.2016.09.023. Epub 2016 Nov 2. No abstract available.


A pre-metazoan origin of the CRK gene family and co-opted signaling network.

Shigeno-Nakazawa Y, Kasai T, Ki S, Kostyanovskaya E, Pawlak J, Yamagishi J, Okimoto N, Taiji M, Okada M, Westbrook J, Satta Y, Kigawa T, Imamoto A.

Sci Rep. 2016 Sep 30;6:34349. doi: 10.1038/srep34349.


A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C.

Makino A, Abe M, Ishitsuka R, Murate M, Kishimoto T, Sakai S, Hullin-Matsuda F, Shimada Y, Inaba T, Miyatake H, Tanaka H, Kurahashi A, Pack CG, Kasai RS, Kubo S, Schieber NL, Dohmae N, Tochio N, Hagiwara K, Sasaki Y, Aida Y, Fujimori F, Kigawa T, Nishibori K, Parton RG, Kusumi A, Sako Y, Anderluh G, Yamashita M, Kobayashi T, Greimel P, Kobayashi T.

FASEB J. 2017 Apr;31(4):1301-1322. doi: 10.1096/fj.201500075R. Epub 2016 Aug 4.


Intracellular Delivery of Proteins via Fusion Peptides in Intact Plants.

Ng KK, Motoda Y, Watanabe S, Sofiman Othman A, Kigawa T, Kodama Y, Numata K.

PLoS One. 2016 Apr 21;11(4):e0154081. doi: 10.1371/journal.pone.0154081. eCollection 2016.


Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution.

Okamura H, Nishimura H, Nagata T, Kigawa T, Watanabe T, Katahira M.

Sci Rep. 2016 Feb 17;6:21742. doi: 10.1038/srep21742.


Stable isotope labeling strategy based on coding theory.

Kasai T, Koshiba S, Yokoyama J, Kigawa T.

J Biomol NMR. 2015 Oct;63(2):213-21. doi: 10.1007/s10858-015-9978-8. Epub 2015 Aug 21.


Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.

Tochio N, Umehara T, Nakabayashi K, Yoneyama M, Tsuda K, Shirouzu M, Koshiba S, Watanabe S, Kigawa T, Sasazuki T, Shirasawa S, Yokoyama S.

J Struct Funct Genomics. 2015 Jun;16(2):55-65. doi: 10.1007/s10969-015-9196-3. Epub 2015 Mar 24.


Co-expression of two polyhydroxyalkanoate synthase subunits from Synechocystis sp. PCC 6803 by cell-free synthesis and their specific activity for polymerization of 3-hydroxybutyryl-coenzyme A.

Numata K, Motoda Y, Watanabe S, Osanai T, Kigawa T.

Biochemistry. 2015 Feb 17;54(6):1401-7. doi: 10.1021/bi501560b. Epub 2015 Feb 6.


Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR.

Ono Y, Miyashita M, Ono Y, Okazaki H, Watanabe S, Tochio N, Kigawa T, Nishimura C.

Biochim Biophys Acta. 2015 Mar;1854(3):229-38. doi: 10.1016/j.bbapap.2014.12.007. Epub 2014 Dec 16.


Molecular level evaluation on HEMA interaction with a collagen model.

Hiraishi N, Tochio N, Kigawa T, Otsuki M, Tagami J.

Dent Mater. 2015 Feb;31(2):88-92. doi: 10.1016/ Epub 2014 Dec 11.


Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3.

Tsuda K, Kuwasako K, Nagata T, Takahashi M, Kigawa T, Kobayashi N, Güntert P, Shirouzu M, Yokoyama S, Muto Y.

Proteins. 2014 Oct;82(10):2879-86. doi: 10.1002/prot.24651. Epub 2014 Aug 11.


Long-range effects of tag sequence on marginally stabilized structure in HIV-1 p24 capsid protein monitored using NMR.

Okazaki H, Kaneko C, Hirahara M, Watanabe S, Tochio N, Kigawa T, Nishimura C.

Biochim Biophys Acta. 2014 Sep;1844(9):1638-47. doi: 10.1016/j.bbapap.2014.06.009. Epub 2014 Jun 21.


Role of 2-hydroxyethyl methacrylate in the interaction of dental monomers with collagen studied by saturation transfer difference NMR.

Hiraishi N, Tochio N, Kigawa T, Otsuki M, Tagami J.

J Dent. 2014 Apr;42(4):484-9. doi: 10.1016/j.jdent.2013.12.016. Epub 2014 Jan 17.


Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR.

Ohori Y, Okazaki H, Watanabe S, Tochio N, Arai M, Kigawa T, Nishimura C.

Biochim Biophys Acta. 2014 Mar;1844(3):520-6. doi: 10.1016/j.bbapap.2013.12.010. Epub 2013 Dec 26.


A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid.

Wang W, Uzawa T, Tochio N, Hamatsu J, Hirano Y, Tada S, Saneyoshi H, Kigawa T, Hayashi N, Ito Y, Taiji M, Aigaki T, Ito Y.

Chem Commun (Camb). 2014 Mar 18;50(22):2962-4. doi: 10.1039/c3cc47624c. Epub 2013 Dec 9.


Aberrant assembly of RNA recognition motif 1 links to pathogenic conversion of TAR DNA-binding protein of 43 kDa (TDP-43).

Shodai A, Morimura T, Ido A, Uchida T, Ayaki T, Takahashi R, Kitazawa S, Suzuki S, Shirouzu M, Kigawa T, Muto Y, Yokoyama S, Takahashi R, Kitahara R, Ito H, Fujiwara N, Urushitani M.

J Biol Chem. 2013 May 24;288(21):14886-905. doi: 10.1074/jbc.M113.451849. Epub 2013 Apr 4.


Reduced native state stability in crowded cellular environment due to protein-protein interactions.

Harada R, Tochio N, Kigawa T, Sugita Y, Feig M.

J Am Chem Soc. 2013 Mar 6;135(9):3696-701. doi: 10.1021/ja3126992. Epub 2013 Feb 20.


Monomer-collagen interactions studied by saturation transfer difference NMR.

Hiraishi N, Tochio N, Kigawa T, Otsuki M, Tagami J.

J Dent Res. 2013 Mar;92(3):284-8. doi: 10.1177/0022034512474310. Epub 2013 Jan 22.


Cell-free synthesis system suitable for disulfide-containing proteins.

Matsuda T, Watanabe S, Kigawa T.

Biochem Biophys Res Commun. 2013 Feb 8;431(2):296-301. doi: 10.1016/j.bbrc.2012.12.107. Epub 2013 Jan 3.


Rapid biochemical synthesis of (11)C-labeled single chain variable fragment antibody for immuno-PET by cell-free protein synthesis.

Matsuda T, Furumoto S, Higuchi K, Yokoyama J, Zhang MR, Yanai K, Iwata R, Kigawa T.

Bioorg Med Chem. 2012 Nov 15;20(22):6579-82. doi: 10.1016/j.bmc.2012.09.038. Epub 2012 Sep 25.


Active intermediates of polyhydroxyalkanoate synthase from Aeromonas caviae in polymerization reaction.

Numata K, Motoda Y, Watanabe S, Tochio N, Kigawa T, Doi Y.

Biomacromolecules. 2012 Nov 12;13(11):3450-5. doi: 10.1021/bm301276k. Epub 2012 Oct 11.


DNA-binding domains of plant-specific transcription factors: structure, function, and evolution.

Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S.

Trends Plant Sci. 2013 May;18(5):267-76. doi: 10.1016/j.tplants.2012.09.001. Epub 2012 Oct 3. Review.


Structural insight into the interaction of ADP-ribose with the PARP WWE domains.

He F, Tsuda K, Takahashi M, Kuwasako K, Terada T, Shirouzu M, Watanabe S, Kigawa T, Kobayashi N, Güntert P, Yokoyama S, Muto Y.

FEBS Lett. 2012 Nov 2;586(21):3858-64. doi: 10.1016/j.febslet.2012.09.009. Epub 2012 Sep 22.


A fluorescent-based high-throughput screening assay for small molecules that inhibit the interaction of MdmX with p53.

Tsuganezawa K, Nakagawa Y, Kato M, Taruya S, Takahashi F, Endoh M, Utata R, Mori M, Ogawa N, Honma T, Yokoyama S, Hashizume Y, Aoki M, Kasai T, Kigawa T, Kojima H, Okabe T, Nagano T, Tanaka A.

J Biomol Screen. 2013 Feb;18(2):191-8. doi: 10.1177/1087057112460729. Epub 2012 Sep 18.


Simplification of the genetic code: restricted diversity of genetically encoded amino acids.

Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D.

Nucleic Acids Res. 2012 Nov 1;40(20):10576-84. doi: 10.1093/nar/gks786. Epub 2012 Aug 21.


Solution structure and siRNA-mediated knockdown analysis of the mitochondrial disease-related protein C12orf65.

Kogure H, Hikawa Y, Hagihara M, Tochio N, Koshiba S, Inoue Y, Güntert P, Kigawa T, Yokoyama S, Nameki N.

Proteins. 2012 Nov;80(11):2629-42. doi: 10.1002/prot.24152. Epub 2012 Aug 10.


An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

Kobayashi N, Harano Y, Tochio N, Nakatani E, Kigawa T, Yokoyama S, Mading S, Ulrich EL, Markley JL, Akutsu H, Fujiwara T.

J Biomol NMR. 2012 Aug;53(4):311-20. doi: 10.1007/s10858-012-9641-6. Epub 2012 Jun 13.


Solution structures of the double-stranded RNA-binding domains from RNA helicase A.

Nagata T, Tsuda K, Kobayashi N, Shirouzu M, Kigawa T, Güntert P, Yokoyama S, Muto Y.

Proteins. 2012 Jun;80(6):1699-706. doi: 10.1002/prot.24059. Epub 2012 Mar 27.


A multiphysics model of in vitro transcription coupling enzymatic reaction and precipitation formation.

Akama S, Yamamura M, Kigawa T.

Biophys J. 2012 Jan 18;102(2):221-30. doi: 10.1016/j.bpj.2011.12.014.


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.


Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor.

Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki T, Seki M, Shinozaki K, Yokoyama S.

J Biol Chem. 2012 Mar 2;287(10):7683-91. doi: 10.1074/jbc.M111.279844. Epub 2012 Jan 4.


Solution structure of the splicing factor motif of the human Prp18 protein.

He F, Inoue M, Kigawa T, Takahashi M, Kuwasako K, Tsuda K, Kobayashi N, Terada T, Shirouzu M, Güntert P, Yokoyama S, Muto Y.

Proteins. 2012 Mar;80(3):968-74. doi: 10.1002/prot.24003. Epub 2011 Dec 28. No abstract available.


RING domain mutations uncouple TRIM5α restriction of HIV-1 from inhibition of reverse transcription and acceleration of uncoating.

Roa A, Hayashi F, Yang Y, Lienlaf M, Zhou J, Shi J, Watanabe S, Kigawa T, Yokoyama S, Aiken C, Diaz-Griffero F.

J Virol. 2012 Feb;86(3):1717-27. doi: 10.1128/JVI.05811-11. Epub 2011 Nov 23.


Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity.

Yaeno T, Li H, Chaparro-Garcia A, Schornack S, Koshiba S, Watanabe S, Kigawa T, Kamoun S, Shirasu K.

Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14682-7. doi: 10.1073/pnas.1106002108. Epub 2011 Aug 5.


ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain.

Nagano M, Hoshino D, Koshiba S, Shuo T, Koshikawa N, Tomizawa T, Hayashi F, Tochio N, Harada T, Akizawa T, Watanabe S, Handa N, Shirouzu M, Kigawa T, Yokoyama S, Seiki M.

J Biol Chem. 2011 Sep 9;286(36):31598-609. doi: 10.1074/jbc.M110.199430. Epub 2011 Jul 15.


Contribution of E3-ubiquitin ligase activity to HIV-1 restriction by TRIM5alpha(rh): structure of the RING domain of TRIM5alpha.

Lienlaf M, Hayashi F, Di Nunzio F, Tochio N, Kigawa T, Yokoyama S, Diaz-Griffero F.

J Virol. 2011 Sep;85(17):8725-37. doi: 10.1128/JVI.00497-11. Epub 2011 Jul 6.


NMR solution structure of human vaccinia-related kinase 1 (VRK1) reveals the C-terminal tail essential for its structural stability and autocatalytic activity.

Shin J, Chakraborty G, Bharatham N, Kang C, Tochio N, Koshiba S, Kigawa T, Kim W, Kim KT, Yoon HS.

J Biol Chem. 2011 Jun 24;286(25):22131-8. doi: 10.1074/jbc.M110.200162. Epub 2011 May 3.


Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP.

Kuratani M, Kasai T, Akasaka R, Higashijima K, Terada T, Kigawa T, Shinkai A, Bessho Y, Yokoyama S.

Proteins. 2011 Jul;79(7):2065-75. doi: 10.1002/prot.23026. Epub 2011 May 2.


A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution.

Yokoyama J, Matsuda T, Koshiba S, Tochio N, Kigawa T.

Anal Biochem. 2011 Apr 15;411(2):223-9. doi: 10.1016/j.ab.2011.01.017. Epub 2011 Jan 20.


Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.

Yamashita S, Nagata T, Kawazoe M, Takemoto C, Kigawa T, Güntert P, Kobayashi N, Terada T, Shirouzu M, Wakiyama M, Muto Y, Yokoyama S.

Protein Sci. 2011 Jan;20(1):118-30. doi: 10.1002/pro.543.


An economical method for producing stable-isotope labeled proteins by the E. coli cell-free system.

Yokoyama J, Matsuda T, Koshiba S, Kigawa T.

J Biomol NMR. 2010 Dec;48(4):193-201. doi: 10.1007/s10858-010-9455-3. Epub 2010 Nov 4.


Structural basis for the dual RNA-recognition modes of human Tra2-β RRM.

Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Güntert P, Yokoyama S, Muto Y.

Nucleic Acids Res. 2011 Mar;39(4):1538-53. doi: 10.1093/nar/gkq854. Epub 2010 Oct 5.

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