Laboratory for Environment and Life Science

From Molecules To Environment

YOHDA Publications

2023

Nishijima R, Endo T, Gankhuyag E, Khin STMM, Jafar SM, Shinohara Y, Tanaka Y, Sawakami K, Yohda M, Furuya T.
Detection of anti-feline infectious peritonitis virus activity of a Chinese herb extract using geneLEAD VIII, a fully automatednucleic acid extraction/quantitative PCR testing system.
J Vet Med Sci. 2023 Mar 30;85(4):443-446.
doi: 10.1292/jvms.22-0185.

2022
Kurata H, Ishino T, Ohshima Y, Yohda M.
CDMOs Play a Critical Role in the Biopharmaceutical Ecosystem.
Front Bioeng Biotechnol. 2022 Mar 21;10:841420.
doi: 10.3389/fbioe.2022.841420.

Yoshii T, Takayama I, Fukutani Y, Ikuta T, Maehashi K, Yohda M.
Development of an odorant sensor with a cell-free synthesized olfactory receptor and a graphene field-effect transistor.
Anal Sci. 2022 Feb;38(2):241-245.
doi: 10.1007/s44211-022-00073-y.

Fukutani Y, Nakamura Y, Muto N, Miyanaga S, Kanemaki R, Ikegami K, Noguchi K, Ohsawa I, Matsunami H, Yohda M.
Hot Spot Mutagenesis Improves the Functional Expression of Unique Mammalian Odorant Receptors.
Int J Mol Sci. 2021 Dec 28;23(1):277.
doi: 10.3390/ijms23010277.

Kurokawa N, Midorikawa R, Nakamura M, Noguchi K, Morishima K, Inoue R, Sugiyama M, Yohda M.
Oligomeric Structural Transition of HspB1 from Chinese Hamster.
Int J Mol Sci. 2021 Oct 6;22(19):10797.
doi: 10.3390/ijms221910797.

Miyagi M, Takiguchi S, Hakamada K, Yohda M, Kawano R.
Single polypeptide detection using a translocon EXP2 nanopore.
Proteomics. 2022 Mar;22(5-6):e2100070.
doi: 10.1002/pmic.202100070.

Terada A, Komatsu D, Ogawa T, Flamandita D, Sahlan M, Nishimura M, Yohda M.
Isolation of cyanide-degrading bacteria and molecular characterization of its cyanide-degrading nitrilase.
Biotechnol Appl Biochem. 2022 Feb;69(1):183-189.
doi: 10.1002/bab.2095.

2021
Inoue Y, Hanazono Y, Noi K, Kawamoto A, Kimatsuka M, Harada R, Takeda K, KitaR, Iwamasa N, Shibata K, Noguchi K, Shigeta Y, Namba K, Ogura T, Miki K,
Shinohara K, Yohda M.
Split conformation of Chaetomium thermophilum Hsp104 disaggregase.
Structure. 2021 Jul 1;29(7):721-730.e6.
doi: 10.1016/j.str.2021.02.002.

2020
Hakamada K, Nakamura M, Midorikawa R, Shinohara K, Noguchi K, Nagaoka H, Takashima E, Morishima K, Inoue R, Sugiyama M, Kawamoto A, Yohda M.
PV1 Protein from
Plasmodium falciparum Exhibits Chaperone-Like Functions and Cooperates with Hsp100s.
Int J Mol Sci. 2020 Nov 16;21(22):8616.
doi:10.3390/ijms21228616.

Matsumura H, Furukawa Y, Nakagaki T, Furutani C, Osanai S, Noguchi K, Odaka M, Yohda M, Ohtani H, Michishita Y, Kawabata Y, Kitabayashi A, Ikeda S, Nara M,
Komatsuda A, Takahashi N, Wakui H. Multiple Myeloma-Associated Ig Light Chain
Crystalline Cast Nephropathy. Kidney Int Rep. 2020 Jul 3;5(9):1595-1602.
doi:10.1016/j.ekir.2020.06.026.

Komatsu K, Kumon K, Arita M, Onitsuka M, Omasa T, Yohda M. Effect of the disulfide isomerase PDIa4 on the antibody production of Chinese hamster ovary cells.
J Biosci Bioeng. 2020 Aug 30:S1389-1723(20)30300-5.
doi: 10.1016/j.jbiosc.2020.08.001.

Odo S, Tanabe K, Yohda M, Yamauchi M. Liver-Oriented Acute Metabolic Effects of A Low Dose of L-Carnitine under Fat-Mobilizing Conditions: Pilot Human
Clinical Trial.
J Nutr Sci Vitaminol (Tokyo). 2020;66(2):136-149.
doi: 10.3177/jnsv.66.136.

3: Hu XS, Ikegami K, Vihani A, Zhu KW, Zapata M, de March CA, Do M, Vaidya N,
Kucera G, Bock C, Jiang Y, Yohda M, Matsunami H. Concentration-Dependent Recruitment of Mammalian Odorant Receptors.
eNeuro. 2020 Apr 23;7(2):ENEURO.0103-19.2019.
doi: 10.1523/ENEURO.0103-19.2019.

Ikegami K, de March CA, Nagai MH, Ghosh S, Do M, Sharma R, Bruguera ES, Lu YE, Fukutani Y, Vaidehi N, Yohda M, Matsunami H.
Structural instability and divergence from conserved residues underlie intracellular retention of mammalian odorant receptors.
Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):2957-2967.
doi: 10.1073/pnas.1915520117.

Perdani MS, Sahlan M, Yohda M, Hermansyah H.
Immobilization of Cholesterol Oxidase from Streptomyces Sp. on Magnetite Silicon Dioxide by Crosslinking Method for Cholesterol Oxidation.
Appl Biochem Biotechnol. 2020 Jul;191(3):968-980.
doi: 10.1007/s12010-020-03241-w.

2019
Sahlan M, Mahira KF, Wiratama I, Mahadewi AG, Yohda M, Hermansyah H, Noguchi K.
Purification and characterization of proteins in multifloral honey from kelulut bee (stingless bee).
Heliyon. 2019 Nov 16;5(11):e02835.
doi: 10.1016/j.heliyon.2019.e02835.

Sahlan M, Devina A, Pratami DK, Situmorang H, Farida S, Munim A, Kusumoputro B, Yohda M, Faried A, Gozan M, Ledyawati M.
Anti-inflammatory activity of Tetragronula species from Indonesia.
Saudi J Biol Sci. 2019 Nov;26(7):1531-1538.
doi: 10.1016/j.sjbs.2018.12.008.

8: Sahlan M, Karwita S, Gozan M, Hermansyah H, Yohda M, Yoo YJ, Pratami DK.
Identification and classification of honey's authenticity by attenuated total reflectance Fourier-transform infrared spectroscopy and chemometric method.
Vet World. 2019 Aug;12(8):1304-1310.
doi: 10.14202/vetworld.2019.1304-1310.

Sha E, Nakamura M, Ankai K, Yamamoto YY, Oka T, Yohda M.
Functional and structural characterization of HspB1/Hsp27 from Chinese hamster ovary cells.
FEBS Open Bio. 2019 Oct;9(10):1826-1834.
doi: 10.1002/2211-5463.12726.

Fukutani Y, Tamaki R, Inoue R, Koshizawa T, Sakashita S, Ikegami K, Ohsawa I, Matsunami H, Yohda M.
The N-terminal region of RTP1S plays important roles in dimer formation and odorant receptor-trafficking.
J Biol Chem. 2019 Oct 4;294(40):14661-14673.
doi: 10.1074/jbc.RA118.007110.

Sonotaki S, Noguchi K, Yohda M, Murakami Y.
A zeolite as a tool for successful refolding of PEGylated proteins and their reassembly with tertiary structures.
Biotechnol Prog. 2019 Sep;35(5):e2853.
doi: 10.1002/btpr.2853.

Kimura M, Sasaki K, Fukutani Y, Yoshida H, Ohsawa I, Yohda M, Sakurai K.
Anticancer saponin OSW-1 is a novel class of selective Golgi stress inducer.
Bioorg Med Chem Lett. 2019 Jul 15;29(14):1732-1736. doi:
10.1016/j.bmcl.2019.05.022. Epub 2019 May 15. PMID: 31126855.

Conway de Macario E, Yohda M, Macario AJL, Robb FT.
Bridging human chaperonopathies and microbial chaperonins.
Commun Biol. 2019 Mar 15;2:103.
doi: 10.1038/s42003-019-0318-5.

Djohan Y , Azukizawa T , Patmawati , Sakai K , Yano Y , Sato F , Takahashi R, Yohda M , Maeda M , Kamiya N , Zako T .
Molecular chaperone prefoldin-assisted biosynthesis of gold nanoparticles with improved size distribution and dispersion.
Biomater Sci. 2019 Apr 23;7(5):1801-1804.
doi: 10.1039/c8bm01026a.

2018
Kida H, Fukutani Y, Mainland JD, de March CA, Vihani A, Li YR, Chi Q, Toyama A, Liu L, Kameda M, Yohda M, Matsunami H.
Vapor detection and discrimination with a panel of odorant receptors.
Nat Commun. 2018 Nov 1;9(1):4556.
doi: 10.1038/s41467-018-06806-w.

Nakamura R, Obata T, Nojima R, Hashimoto Y, Noguchi K, Ogawa T, Yohda M.
Functional Expression and Characterization of Tetrachloroethene Dehalogenase From Geobacter sp.
Front Microbiol. 2018 Aug 10;9:1774.
doi: 10.3389/fmicb.2018.01774.

Morita K, Yamamoto YY, Hori A, Obata T, Uno Y, Shinohara K, Noguchi K, Noi K, Ogura T, Ishii K, Kato K, Kikumoto M, Arranz R, Valpuesta JM, Yohda M.
Expression, Functional Characterization, and Preliminary Crystallization of the
Cochaperone Prefoldin from the Thermophilic Fungus Chaetomium thermophilum.
Int J Mol Sci. 2018 Aug 19;19(8):2452.
doi: 10.3390/ijms19082452.

Ikegami K, Aita Y, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Shinzato M, Ohki S, Nakano K, Teruya K, Satou K, Hirano T, Yohda M. Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp.
Genome Announc. 2018 May 3;6(18):e00384-18.
doi: 10.1128/genomeA.00384-18.

Ogawa N, Yamamoto YY, Abe K, Sekiguchi H, Sasaki YC, Ishikawa A, Frydman J, Yohda M.
Time-Resolved Measurement of the ATP-Dependent Motion of the Group II Chaperonin by Diffracted Electron Tracking.
Int J Mol Sci. 2018 Mar 22;19(4):950.
doi: 10.3390/ijms19040950.

Sahlan M, Zako T, Yohda M.
Prefoldin, a jellyfish-like molecular chaperone: functional cooperation with a group II chaperonin and beyond.
Biophys Rev. 2018 Apr;10(2):339-345.
doi: 10.1007/s12551-018-0400-0.

2017
Asakawa M, Fukutani Y, Savangsuksa A, Noguchi K, Matsunami H, Yohda M.
Modification of the response of olfactory receptors to acetophenone by CYP1a2.
Sci Rep. 2017 Aug 31;7(1):10167.
doi: 10.1038/s41598-017-10862-5.

Yohda M, Ikegami K, Aita Y, Kitajima M, Takechi A, Iwamoto M, Fukuda T, Tamura N, Shibasaki J, Koike S, Komatsu D, Miyagi S, Nishimura M, Uchino Y,
Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Shinzato M, Ohki S, Nakano K, Teruya K, Satou K, Hirano T, Yagi O.
Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.
Sci Rep. 2017 May 22;7(1):2230.
doi: 10.1038/s41598-017-02381-0.

Yamamoto YY, Uno Y, Sha E, Ikegami K, Ishii N, Dohmae N, Sekiguchi H, Sasaki YC, Yohda M.
Asymmetry in the function and dynamics of the cytosolic group II chaperonin CCT/TRiC.
PLoS One. 2017 May 2;12(5):e0176054.
doi: 10.1371/journal.pone.0176054.

Sonotaki S, Takami T, Noguchi K, Odaka M, Yohda M, Murakami Y.
Successful PEGylation of hollow encapsulin nanoparticles from Rhodococcus erythropolis N771 without affecting their disassembly and reassembly properties. Biomater Sci. 2017 May 30;5(6):1082-1089.
doi: 10.1039/c7bm00207f.

Islam MM, Yohda M, Kidokoro SI, Kuroda Y.
Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy.
Sci Rep. 2017 Mar 7;7:41205.
doi: 10.1038/srep41205.

Sharma R, Ishimaru Y, Davison I, Ikegami K, Chien MS, You H, Chi Q, Kubota M, Yohda M, Ehlers M, Matsunami H.
Olfactory receptor accessory proteins play crucial roles in receptor function and gene choice.
Elife. 2017 Mar 6;6:e21895.
doi: 10.7554/eLife.21895.

Hasegawa K, Negishi R, Matsumoto M, Yohda M, Hosokawa K, Maeda M.
Specificity of MicroRNA Detection on a Power-free Microfluidic Chip with Laminar Flow-assisted Dendritic Amplification.
Anal Sci. 2017;33(2):171-177.
doi: 10.2116/analsci.33.171.

Fukutani Y, Ishii J, Kondo A, Ozawa T, Matsunami H, Yohda M.
Split luciferase complementation assay for the analysis of G protein-coupled receptor ligand response in Saccharomyces cerevisiae.
Biotechnol Bioeng. 2017 Jun;114(6):1354-1361.
doi: 10.1002/bit.26255.

Sugimoto C, Takeda K, Kariya Y, Matsumura H, Yohda M, Ohno H, Nakamura N.
A method of expression for an oxygen-tolerant group III alcohol dehydrogenase from Pyrococcus horikoshii OT3.
J Biol Inorg Chem. 2017 Jun;22(4):527-534.
doi: 10.1007/s00775-017-1439-2.

Hakamada K, Watanabe H, Kawano R, Noguchi K, Yohda M.
Expression and characterization of the Plasmodium translocon of the exported proteins component EXP2.
Biochem Biophys Res Commun. 2017 Jan 22;482(4):700-705.
doi: 10.1016/j.bbrc.2016.11.097.

2016
Yamamoto YY, Tsuchida K, Noguchi K, Ogawa N, Sekiguchi H, Sasaki YC, Yohda M.
Characterization of group II chaperonins from an acidothermophilic archaeon Picrophilus torridus.
FEBS Open Bio. 2016 Jun 14;6(7):751-64.
doi: 10.1002/2211-5463.12090.

Watanabe F, Yu F, Ohtaki A, Yamanaka Y, Noguchi K, Odaka M, Yohda M.
Improvement of enantioselectivity of the B-type halohydrin hydrogen-halide-lyase from Corynebacterium sp. N-1074.
J Biosci Bioeng. 2016 Sep;122(3):270-5.
doi: 10.1016/j.jbiosc.2016.02.003.

Aihara T, Ito T, Yamanaka Y, Noguchi K, Odaka M, Sekine M, Homma H, Yohda M.
Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus.
Extremophiles. 2016 Jul;20(4):385-93.
doi: 10.1007/s00792-016-0829-7.

Zako T, Sahlan M, Fujii S, Yamamoto YY, Tai PT, Sakai K, Maeda M, Yohda M.
Contribution of the C-Terminal Region of a Group II Chaperonin to its Interaction with Prefoldin and Substrate Transfer.
J Mol Biol. 2016 Jun 5;428(11):2405-2417.
doi: 10.1016/j.jmb.2016.04.006.

Kayanuma M, Shoji M, Yohda M, Odaka M, Shigeta Y. Catalytic Mechanism of
Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study.
J Phys Chem B. 2016 Apr 7;120(13):3259-66.
doi: 10.1021/acs.jpcb.5b11363.

2015
Watanabe F, Yu F, Ohtaki A, Yamanaka Y, Noguchi K, Yohda M, Odaka M.
Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074.
Proteins. 2015 Dec;83(12):2230-9.
doi: 10.1002/prot.24938.

Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M.
Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10763-7.
doi: 10.1002/anie.201502731.

Arai T, Kimata S, Mochizuki D, Hara K, Zako T, Odaka M, Yohda M, Arisaka F, Kanamaru S, Matsumoto T, Yajima S, Sato J, Kawasaki S, Niimura Y.
NADH oxidase and alkyl hydroperoxide reductase subunit C (peroxiredoxin) from Amphibacillus xylanus form an oligomeric assembly.
FEBS Open Bio. 2015 Feb 7;5:124-31.
doi: 10.1016/j.fob.2015.01.005.

Yohda M, Yagi O, Takechi A, Kitajima M, Matsuda H, Miyamura N, Aizawa T, Nakajima M, Sunairi M, Daiba A, Miyajima T, Teruya M, Teruya K, Shiroma A,
Shimoji M, Tamotsu H, Juan A, Nakano K, Aoyama M, Terabayashi Y, Satou K, Hirano T.
Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.
J Biosci Bioeng. 2015 Jul;120(1):69-77.
doi: 10.1016/j.jbiosc.2014.12.001.

Fukutani Y, Hori A, Tsukada S, Sato R, Ishii J, Kondo A, Matsunami H, Yohda M.
Improving the odorant sensitivity of olfactory receptor-expressing yeast with accessory proteins.
Anal Biochem. 2015 Feb 15;471:1-8.
doi: 10.1016/j.ab.2014.10.012.

Yokoyama Y, Ohtaki A, Jantan I, Yohda M, Nakamoto H.
Goniothalamin enhances the ATPase activity of the molecular chaperone Hsp90 but inhibits its chaperone activity.
J Biochem. 2015 Mar;157(3):161-8.
doi: 10.1093/jb/mvu061.

Tamura A, Fukutani Y, Takami T, Fujii M, Nakaguchi Y, Murakami Y, Noguchi K, Yohda M, Odaka M.
Packaging guest proteins into the encapsulin nanocompartment from Rhodococcus erythropolis N771.
Biotechnol Bioeng. 2015 Jan;112(1):13-20.
doi: 10.1002/bit.25322.

2014
Yamamoto YY, Abe Y, Moriya K, Arita M, Noguchi K, Ishii N, Sekiguchi H, Sasaki YC, Yohda M.
Inter-ring communication is dispensable in the reaction cycle of group II chaperonins.
J Mol Biol. 2014 Jul 15;426(14):2667-78.
doi: 10.1016/j.jmb.2014.05.013.

Hayakawa S, Matsumura H, Nakamura N, Yohda M, Ohno H. Identification of the rate-limiting step of the peroxygenase reactions catalyzed by the thermophilic cytochrome P450 from Sulfolobus tokodaii strain 7.
FEBS J. 2014 Mar;281(5):1409-16.
doi: 10.1111/febs.12712.

Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y. Computational prediction and experimental characterization of a "size switch type repacking"
during the evolution of dengue envelope protein domain III (ED3).
Biochim Biophys Acta. 2014 Mar;1844(3):585-92.
doi: 10.1016/j.bbapap.2013.12.013.

Nakagawa A, Moriya K, Arita M, Yamamoto Y, Kitamura K, Ishiguro N, Kanzaki T, Oka T, Makabe K, Kuwajima K, Yohda M.
Dissection of the ATP-dependent conformational change cycle of a group II chaperonin.
J Mol Biol. 2014 Jan 23;426(2):447-59.
doi: 10.1016/j.jmb.2013.09.034.

2013
Kikuchi M, Iwabuchi S, Kikkou T, Noguchi K, Odaka M, Yohda M, Kawata M, Sato C, Matsumoto O.
Expression, purification, crystallization and preliminary crystallographic analysis of hepatitis B virus core protein dimerized via a peptide linker containing an EGFP insertion.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Aug;69(Pt 8):942-5.
doi: 10.1107/S1744309113019957.

Sekiguchi H, Nakagawa A, Moriya K, Makabe K, Ichiyanagi K, Nozawa S, Sato T, Adachi S, Kuwajima K, Yohda M, Sasaki YC.
ATP dependent rotational motion of group II chaperonin observed by X-ray single molecule tracking.
PLoS One. 2013 May 29;8(5):e64176.
doi: 10.1371/journal.pone.0064176.

Ishida M, Tomomari T, Kanzaki T, Abe T, Oka T, Yohda M.
Biochemical characterization and cooperation with co-chaperones of heat shock protein 90 from Schizosaccharomyces pombe.
J Biosci Bioeng. 2013 Oct;116(4):444-8.
doi: 10.1016/j.jbiosc.2013.04.020.

Yamanaka Y, Arakawa T, Watanabe T, Namima S, Sato M, Hori S, Ohtaki A, Noguchi K, Katayama Y, Yohda M, Odaka M.
Two arginine residues in the substrate pocket predominantly control the substrate selectivity of thiocyanate hydrolase.
J Biosci Bioeng. 2013 Jul;116(1):22-7.
doi: 10.1016/j.jbiosc.2013.01.013.

Ogawa T, Noguchi K, Saito M, Nagahata Y, Kato H, Ohtaki A, Nakayama H, Dohmae N, Matsushita Y, Odaka M, Yohda M, Nyunoya H, Katayama Y.
Carbonyl sulfide hydrolase from Thiobacillus thioparus strain THI115 is one of the β-carbonic anhydrase family enzymes.
J Am Chem Soc. 2013 Mar 13;135(10):3818-25.
doi: 10.1021/ja307735e.

Kikuchi M, Iwabuchi S, Kikkou T, Noguchi K, Odaka M, Yohda M, Kawata M, Sato C, Matsumoto O.
Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):165-9.
doi: 10.1107/S1744309112052074.

Hanazono Y, Takeda K, Oka T, Abe T, Tomonari T, Akiyama N, Aikawa Y, Yohda M, Miki K.
Nonequivalence observed for the 16-meric structure of a small heat shock protein, SpHsp16.0, from Schizosaccharomyces pombe.
Structure. 2013 Feb 5;21(2):220-8.
doi: 10.1016/j.str.2012.11.015.

Sakono M, Utsumi A, Zako T, Abe T, Yohda M, Maeda M.
Formation of non-toxic Aβ fibrils by small heat shock protein under heat-stress conditions.
Biochem Biophys Res Commun. 2013 Jan 25;430(4):1259-64.
doi: 10.1016/j.bbrc.2012.12.059.

Elahi M, Islam MM, Noguchi K, Yohda M, Kuroda Y.
High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition. Proteins. 2013 Jun;81(6):1090-5.
doi: 10.1002/prot.24237.

Hayakawa S, Matsumura H, Nakamura N, Yohda M, Ohno H.
Spectroscopic characterization of the acid-alkaline transition of a thermophilic cytochrome P450.
FEBS Lett. 2013 Jan 4;587(1):94-7.
doi: 10.1016/j.febslet.2012.11.017.

2012
Tanabe M, Ishino S, Yohda M, Morikawa K, Ishino Y, Nishida H. Structure-based mutational study of an archaeal DNA ligase towards improvement of ligation activity.
Chembiochem. 2012 Nov 26;13(17):2575-82.
doi: 10.1002/cbic.201200336.

Fukutani Y, Ishii J, Noguchi K, Kondo A, Yohda M.
An improved bioluminescence-based signaling assay for odor sensing with a yeast expressing a chimeric olfactory receptor.
Biotechnol Bioeng. 2012 Dec;109(12):3143-51.
doi: 10.1002/bit.24589.

Hanazono Y, Takeda K, Yohda M, Miki K.
Structural studies on the oligomeric transition of a small heat shock protein, StHsp14.0.
J Mol Biol. 2012 Sep 7;422(1):100-8.
doi: 10.1016/j.jmb.2012.05.017.

2011
Rathnayaka T, Tawa M, Nakamura T, Sohya S, Kuwajima K, Yohda M, Kuroda Y.
Solubilization and folding of a fully active recombinant Gaussia luciferase with native disulfide bonds by using a SEP-Tag.
Biochim Biophys Acta. 2011 Dec;1814(12):1775-8.
doi: 10.1016/j.bbapap.2011.09.001.

Fukutani Y, Nakamura T, Yorozu M, Ishii J, Kondo A, Yohda M.
The N-terminal replacement of an olfactory receptor for the development of a yeast-based biomimetic odor sensor.
Biotechnol Bioeng. 2012 Jan;109(1):205-12.
doi: 10.1002/bit.23327.

Igari S, Ohtaki A, Yamanaka Y, Sato Y, Yohda M, Odaka M, Noguchi K, Yamada K.
Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8.
PLoS One. 2011;6(8):e23716.
doi: 10.1371/journal.pone.0023716.

Abe T, Oka T, Nakagome A, Tsukada Y, Yasunaga T, Yohda M.
StHsp14.0, a small heat shock protein of Sulfolobus tokodaii strain 7, protects denatured proteins from aggregation in the partially dissociated conformation.
J Biochem. 2011 Oct;150(4):403-9.
doi: 10.1093/jb/mvr074.

Matsumura H, Matsuda K, Nakamura N, Ohtaki A, Yoshida H, Kamitori S, Yohda
M, Ohno H. Monooxygenation by a thermophilic cytochrome P450 via direct electron
donation from NADH. Metallomics. 2011 Apr;3(4):389-95. doi: 10.1039/c0mt00079e.
Epub 2011 Feb 28. PMID: 21359359.

Takeda K, Hayashi T, Abe T, Hirano Y, Hanazono Y, Yohda M, Miki K.
Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0.
J Struct Biol. 2011 Apr;174(1):92-9.
doi: 10.1016/j.jsb.2010.12.006.

2010
Kimura S, Hasegawa S, Kobayashi A, Yamaguchi H, Yohda M, Kubota T.
Novel CYP2C19 629c>a mutant gene detection in Japanese subjects and estimation of its effect on conformation.
Drug Discov Ther. 2010 Dec;4(6):412-7.

Sakurai K, Fukumoto T, Noguchi K, Sato N, Asaka H, Moriyama N, Yohda M.
Three-dimensional structures of OSW-1 and its congener.
Org Lett. 2010 Dec 17;12(24):5732-5.
doi: 10.1021/ol1025519.

Kagawa Y, Hiraoka M, Miyashita-Hatano Y, Shishido-Oki M, Yoshida M, Kondou S, Sugiura M, Sawakami-Kobayashi K, Takahashi M, Tajima H, Yohda M. Automated single nucleotide polymorphism typing using bead array in capillary tube.
J Biosci Bioeng. 2010 Oct;110(4):505-8.
doi: 10.1016/j.jbiosc.2010.05.007.

Rathnayaka T, Tawa M, Sohya S, Yohda M, Kuroda Y.
Biophysical characterization of highly active recombinant Gaussia luciferase expressed in Escherichia coli.
Biochim Biophys Acta. 2010 Sep;1804(9):1902-7.
doi: 10.1016/j.bbapap.2010.04.014.

Sahlan M, Kanzaki T, Zako T, Maeda M, Yohda M.
Analysis of the interaction mode between hyperthermophilic archaeal group II chaperonin and prefoldin using a platform of chaperonin oligomers of various subunit arrangements.
Biochim Biophys Acta. 2010 Sep;1804(9):1810-6.
doi: 10.1016/j.bbapap.2010.04.013.

Sahlan M, Zako T, Tai PT, Ohtaki A, Noguchi K, Maeda M, Miyatake H, Dohmae N, Yohda M.
Thermodynamic characterization of the interaction between prefoldin and group II chaperonin.
J Mol Biol. 2010 Jun 18;399(4):628-36. doi: 10.1016/j.jmb.2010.04.046.

Takenoya M, Ohtaki A, Noguchi K, Endo K, Sasaki Y, Ohsawa K, Yajima S, Yohda M.
Crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase from the hyperthermophile Thermotoga maritima for insights into the coordination of conformational changes and an inhibitor binding.
J Struct Biol. 2010 Jun;170(3):532-9.
doi: 10.1016/j.jsb.2010.03.015.

Yamanaka Y, Hashimoto K, Ohtaki A, Noguchi K, Yohda M, Odaka M.
Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase.
J Biol Inorg Chem. 2010 Jun;15(5):655-65.
doi: 10.1007/s00775-010-0632-3.

Kanzaki T, Ushioku S, Nakagawa A, Oka T, Takahashi K, Nakamura T, Kuwajima K, Yamagishi A, Yohda M.
Adaptation of a hyperthermophilic group II chaperonin to relatively moderate temperatures.
Protein Eng Des Sel. 2010 May;23(5):393-402.
doi: 10.1093/protein/gzq010.

Ginya H, Matsushita R, Yohda M.
Quantification and improvement of error rate during ligase detection reaction.
J Biosci Bioeng. 2010 Feb;109(2):202-4.
doi: 10.1016/j.jbiosc.2009.07.011.

Ginya H, Asahina J, Nakao R, Tamada Y, Takahashi M, Yohda M, Yatsuhashi H.
Semi-quantitative discrimination of HBV mutants using allele-specific oligonucleotide hybridization with Handy Bio-Strand.
J Biosci Bioeng. 2010 Jan;109(1):94-100.
doi: 10.1016/j.jbiosc.2009.06.023.

Tovar V, Ogura M, Kobayashi A, Kimura S, Saito K, Kainuma M, Yohda M, Hasegawa S, Mitsuhashi M.
A dried tofu-supplemented diet affects mRNA expression of inflammatory cytokines in human blood.
J Nutr Sci Vitaminol (Tokyo). 2010;56(6):396-410.
doi: 10.3177/jnsv.56.396.

Ohtaki A, Noguchi K, Yohda M.
Structure and function of archaeal prefoldin, a co-chaperone of group II chaperonin.
Front Biosci (Landmark Ed). 2010 Jan 1;15:708-17.
doi: 10.2741/3641.

Zako T, Banba S, Sahlan M, Sakono M, Terada N, Yohda M, Maeda M.
Hyperthermophilic archaeal prefoldin shows refolding activity at low temperature.
Biochem Biophys Res Commun. 2010 Jan 1;391(1):467-70.
doi: 10.1016/j.bbrc.2009.11.081.

80: Sato Y, Shimizu S, Ohtaki A, Noguchi K, Miyatake H, Dohmae N, Sasaki S, Odaka M, Yohda M.
Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-
8-(1'-D-ribityl) lumazine, and its analogues, riboflavin and flavin mononucleotide, at high resolution.
J Bacteriol. 2010 Jan;192(1):127-33.
doi: 10.1128/JB.01015-09.
Erratum in: J Bacteriol. 2010 Mar;192(6):1749.

2009
Hayashi T, Abe T, Takeda K, Akiyama N, Yohda M, Miki K.
Crystallization and heavy-atom derivatization of StHsp14.0, a small heat-shock protein from Sulfolobus tokodaii.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Oct 1;65(Pt 10):1007-10.
doi: 10.1107/S1744309109032540.

Islam MM, Sohya S, Noguchi K, Kidokoro S, Yohda M, Kuroda Y.
Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations.
Proteins. 2009 Dec;77(4):962-70.
doi: 10.1002/prot.22522.

Ohtaki A, Murata K, Sato Y, Noguchi K, Miyatake H, Dohmae N, Yamada K, Yohda M, Odaka M.
Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition.
Biochim Biophys Acta. 2010 Jan;1804(1):184-92.
doi: 10.1016/j.bbapap.2009.10.001.

Arakawa T, Kawano Y, Katayama Y, Nakayama H, Dohmae N, Yohda M, Odaka M.
Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification.
J Am Chem Soc. 2009 Oct 21;131(41):14838-43.
doi: 10.1021/ja903979s.

Zako T, Nagata H, Terada N, Utsumi A, Sakono M, Yohda M, Ueda H, Soga K, Maeda M.
Cyclic RGD peptide-labeled upconversion nanophosphors for tumor cell- targeted imaging.
Biochem Biophys Res Commun. 2009 Mar 27;381(1):54-8.
doi: 10.1016/j.bbrc.2009.02.004.

Sahlan M, Kanzaki T, Yohda M.
Construction and characterization of the hetero-oligomer of the group II chaperonin from the hyperthermophilic archaeon, Thermococcus sp. strain KS-1.
Extremophiles. 2009 May;13(3):437-45. doi: 10.1007/s00792-009-0229-3.

Hasegawa S, Kato H, Yamaguchi H, Yohda M, Obara K, Izutsu H, Ogura M, Mitsuhashi M.
Trastuzumab-induced CCL20 and interleukin-8 mRNA in human whole blood ex vivo. Invest New Drugs.
2009 Dec;27(6):579-82.
doi: 10.1007/s10637-009-9223-y.

2008
Sakono M, Zako T, Ueda H, Yohda M, Maeda M.
Formation of highly toxic soluble amyloid beta oligomers by the molecular chaperone prefoldin.
FEBS J. 2008 Dec;275(23):5982-93.
doi: 10.1111/j.1742-4658.2008.06727.x.

Hashimoto K, Suzuki H, Taniguchi K, Noguchi T, Yohda M, Odaka M. Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile.
J Biol Chem. 2008 Dec 26;283(52):36617-23.
doi: 10.1074/jbc.M806577200.

Kanzaki T, Iizuka R, Takahashi K, Maki K, Masuda R, Sahlan M, Yébenes H, Valpuesta JM, Oka T, Furutani M, Ishii N, Kuwajima K, Yohda M. Sequential action of ATP-dependent subunit conformational change and interaction between helical protrusions in the closure of the built-in lid of group II chaperonins.
J Biol Chem. 2008 Dec 12;283(50):34773-84.
doi: 10.1074/jbc.M805303200. Epub 2008 Oct

Kita A, Tasaki S, Yohda M, Miki K.
Crystal structure of PH1733, an aspartate racemase homologue, from Pyrococcus horikoshii OT3.
Proteins. 2009 Jan;74(1):240-4.
doi: 10.1002/prot.22244.

Islam MM, Sohya S, Noguchi K, Yohda M, Kuroda Y.
Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.
Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15334-9.
doi: 10.1073/pnas.0802699105.

Taniguchi K, Murata K, Murakami Y, Takahashi S, Nakamura T, Hashimoto K, Koshino H, Dohmae N, Yohda M, Hirose T, Maeda M, Odaka M.
Novel catalytic activity of nitrile hydratase from Rhodococcus sp. N771.
J Biosci Bioeng. 2008 Aug;106(2):174-9.
doi: 10.1263/jbb.106.174.

Kida H, Sugano Y, Iizuka R, Fujihashi M, Yohda M, Miki K.
Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1.
J Mol Biol. 2008 Nov 14;383(3):465-74.
doi: 10.1016/j.jmb.2008.08.041.

Sugino C, Hirose M, Tohda H, Yoshinari Y, Abe T, Giga-Hama Y, Iizuka R, Shimizu M, Kidokoro S, Ishii N, Yohda M.
Characterization of a sHsp of Schizosaccharomyces pombe, SpHsp15.8, and the implication of its functional mechanism by comparison with another sHsp, SpHsp16.0.
Proteins. 2009 Jan;74(1):6-17.
doi: 10.1002/prot.22132.

Okochi M, Kanie K, Kurimoto M, Yohda M, Honda H.
Overexpression of prefoldin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 endowed Escherichia coli with organic solvent tolerance.
Appl Microbiol Biotechnol. 2008 Jun;79(3):443-9.
doi: 10.1007/s00253-008-1450-1.

Matsumura H, Wakatabi M, Omi S, Ohtaki A, Nakamura N, Yohda M, Ohno H.
Modulation of redox potential and alteration in reactivity via the peroxide shunt pathway by mutation of cytochrome P450 around the proximal heme ligand.
Biochemistry. 2008 Apr 22;47(16):4834-42.
doi: 10.1021/bi800142v.

Funakoshi M, Sekine M, Katane M, Furuchi T, Yohda M, Yoshikawa T, Homma H.
Cloning and functional characterization of Arabidopsis thaliana D-amino acid aminotransferase--D-aspartate behavior during germination.
FEBS J. 2008 Mar;275(6):1188-200.
doi: 10.1111/j.1742-4658.2008.06279.x.

Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, Yohda M.
Functional characterization of recombinant prefoldin complexes from a hyperthermophilic archaeon, Thermococcus sp. strain KS-1.
J Mol Biol. 2008 Mar 28;377(3):972-83.
doi: 10.1016/j.jmb.2008.01.070. E

Ohashi-Kunihiro S, Yohda M, Masaki H, Machida M.
A novel vector for positive selection of inserts harboring an open reading frame by translational coupling.
Biotechniques. 2007 Dec;43(6):751-2, 754.
doi: 10.2144/000112629.

Yohda M, Kobayashi A, Ohishi S, Ebisawa M, Sakihara S, Kakihara F, Tojo Y, Tajima H, Nishimura M.
Quantitative discrimination of 16 S rRNA genes of Dehalococcoides species by MagSNiPer, a quantitative single-nucleotide- polymorphism genotyping method.
Biotechnol Appl Biochem. 2008 Oct;51(Pt2):111-7.
doi: 10.1042/BA20070238.

Ohtaki A, Kida H, Miyata Y, Ide N, Yonezawa A, Arakawa T, Iizuka R, Noguchi K, Kita A, Odaka M, Miki K, Yohda M.
Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.
J Mol Biol. 2008 Feb 29;376(4):1130-41.
doi: 10.1016/j.jmb.2007.12.010.

Saji H, Iizuka R, Yoshida T, Abe T, Kidokoro S, Ishii N, Yohda M.
Role of the IXI/V motif in oligomer assembly and function of StHsp14.0, a small heat shock protein from the acidothermophilic archaeon, Sulfolobus tokodaii strain 7.
Proteins. 2008 May 1;71(2):771-82.
doi: 10.1002/prot.21762.

Nishimura M, Ebisawa M, Sakihara S, Kobayashi A, Nakama T, Okochi M, Yohda M.
Detection and identification of Dehalococcoides species responsible for in situ dechlorination of trichloroethene to ethene enhanced by hydrogen-releasing compounds.
Biotechnol Appl Biochem. 2008 Sep;51(Pt 1):1-7.
doi: 10.1042/BA20070171.

Kurimoto E, Nishi Y, Yamaguchi Y, Zako T, Iizuka R, Ide N, Yohda M, Kato K.
Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy.
Proteins. 2008 Mar;70(4):1257-63.
doi: 10.1002/prot.21606.

Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, Yohda M.
Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism.
Proteins. 2008 Mar;70(4):1167-74.
doi: 10.1002/prot.21528.

2007
Matsumoto N, Kakihara F, Kimura S, Kurebayashi Y, Hirai M, Yohda M, Hasegawa S.
Single nucleotide polymorphism genotyping of CYP2C19 using a new automated system.
Anal Biochem. 2007 Nov 1;370(1):121-3.
doi: 10.1016/j.ab.2007.06.006.


Ginya H, Asahina J, Yoshida M, Segawa O, Asano T, Ikeda H, Hatano YM,
Shishido M, Johansson BM, Zhou Q, Hallberg M, Takahashi M, Nyberg F, Tajima H,
Yohda M. Development of the Handy Bio-Strand and its application to genotyping
of OPRM1 (A118G). Anal Biochem. 2007 Aug 1;367(1):79-86. doi:
10.1016/j.ab.2007.04.052. Epub 2007 May 6. PMID: 17570330.

Hagiwara H, Sawakami-Kobayashi K, Yamamoto M, Iwasaki S, Sugiura M, Abe H, Kunihiro-Ohashi S, Takase K, Yamane N, Kato K, Son R, Nakamura M, Segawa O, Yoshida M, Yohda M, Tajima H, Kobori M, Takahama Y, Itakura M, Machida M.
Development of an automated SNP analysis method using a paramagnetic beads handling robot.
Biotechnol Bioeng. 2007 Oct 1;98(2):420-8.
doi: 10.1002/bit.21380.

Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M.
Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center.
J Mol Biol. 2007 Mar 9;366(5):1497-509.
doi: 10.1016/j.jmb.2006.12.011.


2006
Tojo Y, Syou R, Yoshida M, Momose J, Ginya H, Takahashi M, Tajima H, Yohda M.
Pretreatment of polyamide monofilament with hydrochloric acid improves sensitivity of three-dimensional microarray, Bio-Strand.
J Biosci Bioeng. 2006 Nov;102(5):474-7.
doi: 10.1263/jbb.102.474.

Yoshida T, Iizuka R, Itami K, Yasunaga T, Sakuraba H, Ohshima T, Yohda M, Maruyama T.
Comparative analysis of the protein folding activities of two chaperonin subunits of Thermococcus strain KS-1: the effects of beryllium fluoride.
Extremophiles. 2007 Mar;11(2):225-35.
doi: 10.1007/s00792-006-0026-1.

Zako T, Murase Y, Iizuka R, Yoshida T, Kanzaki T, Ide N, Maeda M, Funatsu T, Yohda M.
Localization of prefoldin interaction sites in the hyperthermophilic group II chaperonin and correlations between binding rate and protein transfer rate.
J Mol Biol. 2006 Nov 17;364(1):110-20.
doi: 10.1016/j.jmb.2006.08.088.

Kataoka S, Arakawa T, Hori S, Katayama Y, Hara Y, Matsushita Y, Nakayama H, Yohda M, Nyunoya H, Dohmae N, Maeda M, Odaka M.
Functional expression of thiocyanate hydrolase is promoted by its activator protein, P15K.
FEBS Lett. 2006 Aug 21;580(19):4667-72.
doi: 10.1016/j.febslet.2006.07.051.

Yoshida T, Seko T, Okada O, Iwata K, Liu L, Miki K, Yohda M.
Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature.
Proteins. 2006 Aug 1;64(2):502-12.
doi: 10.1002/prot.21010.

Yoshida T, Kanzaki T, Iizuka R, Komada T, Zako T, Suzuki R, Maruyama T, Yohda M.
Contribution of the C-terminal region to the thermostability of the archaeal group II chaperonin from Thermococcus sp. strain KS-1.
Extremophiles. 2006 Oct;10(5):451-9.
doi: 10.1007/s00792-006-0519-y.

Takarada H, Kawano Y, Hashimoto K, Nakayama H, Ueda S, Yohda M, Kamiya N, Dohmae N, Maeda M, Odaka M.
Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771.
Biosci Biotechnol Biochem. 2006 Apr;70(4):881-9.
doi: 10.1271/bbb.70.881.

Chiba S, Hashimoto R, Hattori S, Yohda M, Lipska B, Weinberger DR, Kunugi H.
Effect of antipsychotic drugs on DISC1 and dysbindin expression in mouse frontal cortex and hippocampus.
J Neural Transm (Vienna). 2006 Sep;113(9):1337-46.
doi: 10.1007/s00702-005-0414-1.

Ohashi-Kunihiro S, Hagiwara H, Yohda M, Masaki H, Machida M.
Construction of a positive selection marker by a lethal gene with the amber stop codon(s) regulator.
Biosci Biotechnol Biochem. 2006 Jan;70(1):119-25.
doi: 10.1271/bbb.70.119.

Katayama Y, Hashimoto K, Nakayama H, Mino H, Nojiri M, Ono TA, Nyunoya H, Yohda M, Takio K, Odaka M.
Thiocyanate hydrolase is a cobalt-containing metalloenzyme with a cysteine-sulfinic acid ligand.
J Am Chem Soc. 2006 Jan 25;128(3):728-9.
doi: 10.1021/ja057010q.

2005
Tojo Y, Asahina J, Miyashita Y, Takahashi M, Matsumoto N, Hasegawa S, Yohda M, Tajima H.
Development of an automation system for single nucleotide polymorphisms genotyping using bio-strand, a new three-dimensional microarray.
J Biosci Bioeng. 2005 Feb;99(2):120-4.
doi: 10.1263/jbb.99.120.

Iizuka R, Yoshida T, Ishii N, Zako T, Takahashi K, Maki K, Inobe T, Kuwajima K, Yohda M.
Characterization of archaeal group II chaperonin-ADP-metal fluoride complexes: implications that group II chaperonins operate as a "two- stroke engine".
J Biol Chem. 2005 Dec 2;280(48):40375-83.
doi: 10.1074/jbc.M506785200.

Akutsu J, Zhang Z, Tsujimura M, Sasaki M, Yohda M, Kawarabayasi Y.
Characterization of a thermostable enzyme with phosphomannomutase/phosphoglucomutase activities from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
J Biochem. 2005 Aug;138(2):159-66.
doi: 10.1093/jb/mvi115.

Hirose M, Tohda H, Giga-Hama Y, Tsushima R, Zako T, Iizuka R, Pack C, Kinjo M, Ishii N, Yohda M.
Interaction of a small heat shock protein of the fission yeast, Schizosaccharomyces pombe, with a denatured protein at elevated temperature.
J Biol Chem. 2005 Sep 23;280(38):32586-93.
doi: 10.1074/jbc.M504121200.

Zako T, Iizuka R, Okochi M, Nomura T, Ueno T, Tadakuma H, Yohda M, Funatsu T.
Facilitated release of substrate protein from prefoldin by chaperonin.
FEBS Lett. 2005 Jul 4;579(17):3718-24.
doi: 10.1016/j.febslet.2005.05.061.

Koshiba M, Yohda M, Nakamura S.
Topological relation of chick thalamofugal visual projections with hyper pallium revealed by three color tracers.
Neurosci Res. 2005 Jul;52(3):235-42.
doi: 10.1016/j.neures.2005.03.017.

Kakihara F, Kurebayashi Y, Tojo Y, Tajima H, Hasegawa S, Yohda M.
MagSNiPer: a new single nucleotide polymorphism typing method based on single base extension, magnetic separation, and chemiluminescence.
Anal Biochem. 2005 Jun 1;341(1):77-82.
doi: 10.1016/j.ab.2005.03.015.

Okochi M, Matsuzaki H, Nomura T, Ishii N, Yohda M. Molecular
characterization of the group II chaperonin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3.
Extremophiles. 2005 Apr;9(2):127-34.
doi: 10.1007/s00792-004-0427-y.

2004
Oku Y, Ohtaki A, Kamitori S, Nakamura N, Yohda M, Ohno H, Kawarabayasi Y.
Structure and direct electrochemistry of cytochrome P450 from the thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7.
J Inorg Biochem. 2004 Jul;98(7):1194-9.
doi: 10.1016/j.jinorgbio.2004.05.002.

Yoshida T, Usui K, Iizuka R, Zako T, Yohda M.
Reaction mechanism of archaeal molecular chaperones.
Tanpakushitsu Kakusan Koso. 2004 May;49(7 Suppl):858-61. Japanese.

Okochi M, Nomura T, Zako T, Arakawa T, Iizuka R, Ueda H, Funatsu T, Leroux M, Yohda M.
Kinetics and binding sites for interaction of the prefoldin with a group II chaperonin: contiguous non-native substrate and chaperonin binding sites in the archaeal prefoldin.
J Biol Chem. 2004 Jul 23;279(30):31788-95.
doi: 10.1074/jbc.M402889200.

Akutsu J, Tojo Y, Segawa O, Obata K, Okochi M, Tajima H, Yohda M.
Development of an integrated automation system with a magnetic bead-mediated nucleic acid purification device for genetic analysis and gene manipulation.
Biotechnol Bioeng. 2004 Jun 20;86(6):667-71.
doi: 10.1002/bit.20049.

Usui K, Hatipoglu OF, Ishii N, Yohda M.
Role of the N-terminal region of the crenarchaeal sHsp, StHsp14.0, in thermal-induced disassembly of the complex and molecular chaperone activity.
Biochem Biophys Res Commun. 2004 Feb 27;315(1):113-8.
doi: 10.1016/j.bbrc.2004.01.031.

Iizuka R, So S, Inobe T, Yoshida T, Zako T, Kuwajima K, Yohda M.
Role of the helical protrusion in the conformational change and molecular chaperone activity of the archaeal group II chaperonin.
J Biol Chem. 2004 Apr 30;279(18):18834-9.
doi: 10.1074/jbc.M400839200.

Shomura Y, Yoshida T, Iizuka R, Maruyama T, Yohda M, Miki K.
Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms.
J Mol Biol. 2004 Jan 30;335(5):1265-78.
doi: 10.1016/j.jmb.2003.11.028.

Usui K, Ishii N, Kawarabayasi Y, Yohda M.
Expression and biochemical characterization of two small heat shock proteins from the thermoacidophilic crenarchaeon Sulfolobus tokodaii strain 7.
Protein Sci. 2004 Jan;13(1):134-44.
doi: 10.1110/ps.03264204.

2003
Iizuka R, Yoshida T, Shomura Y, Miki K, Maruyama T, Odaka M, Yohda M.
ATP binding is critical for the conformational change from an open to closed state in archaeal group II chaperonin.
J Biol Chem. 2003 Nov 7;278(45):44959-65.
doi: 10.1074/jbc.M305484200.

Ishii D, Kinbara K, Ishida Y, Ishii N, Okochi M, Yohda M, Aida T.
Chaperonin-mediated stabilization and ATP-triggered release of semiconductor nanoparticles.
Nature. 2003 Jun 5;423(6940):628-32.
doi: 10.1038/nature01663.

Nimura N, Fujiwara T, Watanabe A, Sekine M, Furuchi T, Yohda M, Yamagishi A, Oshima T, Homma H.
A novel chiral thiol reagent for automated precolumn derivatization and high-performance liquid chromatographic enantioseparation of amino acids and its application to the aspartate racemase assay. Anal Biochem. 2003 Apr 15;315(2):262-9.
doi: 10.1016/s0003-2697(02)00705-4.

Sawakami-Kobayashi K, Segawa O, Obata K, Hornes E, Yohda M, Tajima H,
Machida M. Multipurpose robot for automated cycle sequencing.
Biotechniques. 2003 Mar;34(3):634-7.
doi: 10.2144/03343pf01.

Yoshida T, Yohda M, Maruyama T.
Archael molecular chaperones: protein folding mechanism of the archael chaperonin.
Tanpakushitsu Kakusan Koso. 2003 Jan;48(1):33-9. Japanese.

2002
Fujimura N, Kohara Y, Okano K, Yohda M, Kambara H.
Rapid multiplex single nucleotide polymorphism genotyping based on single base extension reactions and
color-coded beads. J Biosci Bioeng. 2002;94(4):368-70.
doi: 10.1263/jbb.94.368.

Shomura Y, Yoshida T, Maruyama T, Yohda M, Miki K.
Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1.
Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1830-2.
doi: 10.1107/s0907444902013331.

Liu L, Iwata K, Yohda M, Miki K.
Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases.
FEBS Lett. 2002 Sep 25;528(1-3):114-8.
doi: 10.1016/s0014-5793(02)03264-7.

Obata K, Tajima H, Yohda M, Matsunaga T.
Recent developments in laboratory automation using magnetic particles for genome analysis.
Pharmacogenomics. 2002 Sep;3(5):697-708.
doi: 10.1517/14622416.3.5.697.

Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K.
Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization.
J Mol Biol. 2002 May 31;319(2):479-89.
doi: 10.1016/S0022-2836(02)00296-6.

Yoshida T, Ideno A, Suzuki R, Yohda M, Maruyama T.
Two kinds of archaeal group II chaperonin subunits with different thermostability in Thermococcus strain KS-1.
Mol Microbiol. 2002 May;44(3):761-9.
doi: 10.1046/j.1365-2958.2002.02909.x.

Okochi M, Yoshida T, Maruyama T, Kawarabayasi Y, Kikuchi H, Yohda M.
Pyrococcus prefoldin stabilizes protein-folding intermediates and transfers them to chaperonins for correct folding.
Biochem Biophys Res Commun. 2002 Mar 8;291(4):769-74.
doi: 10.1006/bbrc.2002.6523.

Koshiba M, Kikuchi T, Yohda M, Nakamura S. Inversion of the anatomical lateralization of chick thalamofugal visual pathway by light experience.
Neurosci Lett. 2002 Feb 1;318(3):113-6.
doi: 10.1016/s0304-3940(01)02306-0.
Erratum in: Neurosci Lett 2002 Sep 13;330(1):125. PMID: 11803112.

Yoshida T, Kawaguchi R, Taguchi H, Yoshida M, Yasunaga T, Wakabayashi T, Yohda M, Maruyama T.
Archaeal group II chaperonin mediates protein folding in the cis-cavity without a detachable GroES-like co-chaperonin.
J Mol Biol. 2002 Jan 4;315(1):73-85.
doi: 10.1006/jmbi.2001.5220.

2001
Usui K, Yoshida T, Maruyama T, Yohda M.
Small heat shock protein of a hyperthermophilic archaeum, Thermococcus sp. strain KS-1, exists as a spherical 24 mer and its expression is highly induced under heat-stress conditions.
J Biosci Bioeng. 2001;92(2):161-6.
doi: 10.1263/jbb.92.161.

Obata K, Segawa O, Yakabe M, Ishida Y, Kuroita T, Ikeda K, Kawakami B, Kawamura Y, Yohda M, Matsunaga T, Tajima H.
Development of a novel method for operating magnetic particles, Magtration Technology, and its use for automating nucleic acid purification.
J Biosci Bioeng. 2001;91(5):500-3.
doi: 10.1263/jbb.91.500.

Iizuka R, Yoshida T, Maruyama T, Shomura Y, Miki K, Yohda M.
Glycine at the 65th position plays an essential role in ATP-dependent protein folding by Archael group II chaperonin.
Biochem Biophys Res Commun. 2001 Dec 21;289(5):1118-24.
doi: 10.1006/bbrc.2001.6139.

Liu L, Iwata K, Kawarabayasi Y, Kikuchi H, Kita A, Yohda M, Miki K.
Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3.
Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1674-6.
doi: 10.1107/s0907444901012549.

Fukami TA, Yohda M, Taguchi H, Yoshida M, Miki K.
Crystal structure of chaperonin-60 from Paracoccus denitrificans.
J Mol Biol. 2001 Sep 21;312(3):501-9.
doi: 10.1006/jmbi.2001.4961.

Endo I, Nojiri M, Tsujimura M, Nakasako M, Nagashima S, Yohda M, Odaka M.
Fe-type nitrile hydratase.
J Inorg Biochem. 2001 Feb;83(4):247-53.
doi: 10.1016/s0162-0134(00)00171-9.

Yoshida T, Ideno A, Hiyamuta S, Yohda M, Maruyama T.
Natural chaperonin of the hyperthermophilic archaeum, Thermococcus strain KS-1: a hetero-oligomeric chaperonin with variable subunit composition.
Mol Microbiol. 2001 Mar;39(5):1406-13.
doi: 10.1111/j.1365-2958.2001.02334.x.

158: Long Z, Lee JA, Okamoto T, Sekine M, Nimura N, Imai K, Yohda M, Maruyama T, Sumi M, Kamo N, Yamagishi A, Oshima T, Homma H.
Occurrence of D-Amino Acids and a pyridoxal 5'-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, Thermoplasma acidophilum.
Biochem Biophys Res Commun. 2001 Feb 23;281(2):317-21.
doi: 10.1006/bbrc.2001.4353.

2000
Piersma SR, Nojiri M, Tsujimura M, Noguchi T, Odaka M, Yohda M, Inoue Y, Endo I.
Arginine 56 mutation in the beta subunit of nitrile hydratase: importance of hydrogen bonding to the non-heme iron center.
J Inorg Biochem. 2000 Jul 1;80(3-4):283-8.
doi: 10.1016/s0162-0134(00)00076-3.

Murakami T, Nojiri M, Nakayama H, Odaka M, Yohda M, Dohmae N, Takio K, Nagamune T, Endo I.
Post-translational modification is essential for catalytic activity of nitrile hydratase.
Protein Sci. 2000 May;9(5):1024-30.
doi: 10.1110/ps.9.5.1024.

Teshima T, Kohda J, Kondo A, Yohda M, Tamura A, Fukuda H. Affinity purification of fusion chaperonin Cpn60-(His)(6) from thermophilic bacterium Bacillus strain MS and its use in facilitating protein refolding and preventing heat denaturation.
Biotechnol Prog. 2000 May-Jun;16(3):442-6.
doi: 10.1021/bp0000095.

Asahara Y, Atsuta K, Motohashi K, Taguchi H, Yohda M, Yoshida M.
FtsH recognizes proteins with unfolded structure and hydrolyzes the carboxyl side of hydrophobic residues.
J Biochem. 2000 May;127(5):931-7.
doi: 10.1093/oxfordjournals.jbchem.a022689.

Teshima T, Kohda J, Kondo A, Taguchi H, Yohda M, Fukuda H.
Preparation of Thermus thermophilus holo-chaperonin-immobilized microspheres with high ability to facilitate protein refolding.
Biotechnol Bioeng. 2000 Apr 20;68(2):184-90.

Nojiri M, Nakayama H, Odaka M, Yohda M, Takio K, Endo I.
Cobalt-substituted Fe-type nitrile hydratase of Rhodococcus sp. N-771.
FEBS Lett. 2000 Jan 14;465(2-3):173-7.
doi: 10.1016/s0014-5793(99)01746-9.


1999
Matsumoto M, Homma H, Long Z, Imai K, Iida T, Maruyama T, Aikawa Y, Endo I, Yohda M.
Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic archaea.
J Bacteriol. 1999 Oct;181(20):6560-3.
doi: 10.1128/JB.181.20.6560-6563.1999.

Nakasako M, Odaka M, Yohda M, Dohmae N, Takio K, Kamiya N, Endo I. Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme.
Biochemistry. 1999 Aug 3;38(31):9887-98.
doi: 10.1021/bi982753s.

Motohashi K, Watanabe Y, Yohda M, Yoshida M.
Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones.
Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7184-9.
doi: 10.1073/pnas.96.13.7184.

Endo I, Odaka M, Yohda M.
An enzyme controlled by light: the molecular mechanism of photoreactivity in nitrile hydratase.
Trends Biotechnol. 1999 Jun;17(6):244-8.
doi: 10.1016/s0167-7799(99)01303-7.

Nojiri M, Yohda M, Odaka M, Matsushita Y, Tsujimura M, Yoshida T, Dohmae N, Takio K, Endo I.
Functional expression of nitrile hydratase in Escherichia coli: requirement of a nitrile hydratase activator and post-translational modification of a ligand cysteine.
J Biochem. 1999 Apr;125(4):696-704.
doi: 10.1093/oxfordjournals.jbchem.a022339.

1998
Nagashima S, Nakasako M, Dohmae N, Tsujimura M, Takio K, Odaka M, Yohda M, Kamiya N, Endo I.
Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
Nat Struct Biol. 1998 May;5(5):347-51.
doi: 10.1038/nsb0598-347.

1997
Yoshida T, Yohda M, Suzuki M, Yazaki K, Miura K, Endo I.
Characterization of homo-oligomeric complexes of alpha and beta chaperonin subunits from the acidothermophilic archaeon, Sulfolobus sp. strain 7.
Biochem Biophys Res Commun. 1998 Jan 26;242(3):640-7.
doi: 10.1006/bbrc.1997.8026.

Sumi M, Yohda M, Koga Y, Yoshida M.
F0F1-ATPase genes from an archaebacterium, Methanosarcina barkeri.
Biochem Biophys Res Commun. 1997 Dec 18;241(2):427-33.
doi: 10.1006/bbrc.1997.7809.

Tsujimura M, Dohmae N, Odaka M, Chijimatsu M, Takio K, Yohda M, Hoshino M, Nagashima S, Endo I.
Structure of the photoreactive iron center of the nitrile hydratase from Rhodococcus sp. N-771. Evidence of a novel post-translational modification in the cysteine ligand.
J Biol Chem. 1997 Nov 21;272(47):29454-9.
doi: 10.1074/jbc.272.47.29454.

Yoshida T, Yohda M, Iida T, Maruyama T, Taguchi H, Yazaki K, Ohta T, Odaka M, Endo I, Kagawa Y.
Structural and functional characterization of homo-oligomeric complexes of alpha and beta chaperonin subunits from the hyperthermophilic archaeum Thermococcus strain KS-1.
J Mol Biol. 1997 Oct 31;273(3):635-45.
doi: 10.1006/jmbi.1997.1337.
Erratum in: J Mol Biol 2000 Jun 23;299(5):1399-400.

Motohashi K, Yohda M, Odaka M, Yoshida M.
K+ is an indispensable cofactor for GrpE stimulation of ATPase activity of DnaK x DnaJ complex from Thermus thermophilus.
FEBS Lett. 1997 Aug 4;412(3):633-6.
doi: 10.1016/s0014-5793(97)00847-8.

176: Seki M, Hayashida N, Kato N, Yohda M, Shinozaki K.
Rapid construction of a transcription map for a cosmid contig of Arabidopsis thaliana genome using a novel cDNA selection method.
Plant J. 1997 Aug;12(2):481-7.
doi: 10.1046/j.1365-313x.1997.12020481.x.

177: Nakamura N, Taguchi H, Ishii N, Yoshida M, Suzuki M, Endo I, Miura K, Yohda M.
Purification and molecular cloning of the group II chaperonin from the acidothermophilic archaeon, Sulfolobus sp. strain 7.
Biochem Biophys Res Commun. 1997 Jul 30;236(3):727-32.
doi: 10.1006/bbrc.1997.6916.

178: Shibui H, Hamamoto T, Yohda M, Kagawa Y.
The stabilizing residues and the functional domains in the hyperthermophilic V-ATPase of Desulfurococcus.
Biochem Biophys Res Commun. 1997 May 19;234(2):341-5.
doi: 10.1006/bbrc.1997.6644.

1996
Yohda M, Endo I, Abe Y, Ohta T, Iida T, Maruyama T, Kagawa Y.
Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY.
J Biol Chem. 1996 Sep 6;271(36):22017-21.
doi: 10.1074/jbc.271.36.22017.

Motohashi K, Yohda M, Endo I, Yoshida M.
A novel factor required for the assembly of the DnaK and DnaJ chaperones of Thermus thermophilus.
J Biol Chem. 1996 Jul 19;271(29):17343-8.
doi: 10.1074/jbc.271.29.17343.

Odaka M, Noguchi T, Nagashima S, Yohda M, Yabuki S, Hishino M, Inoue Y, Endo I.
Location of the non-heme iron center on the alpha subunit of photoreactive nitrile hydratase from Rhodococcus sp. N-771.
Biochem Biophys Res Commun. 1996 Apr 5;221(1):146-50.
doi: 10.1006/bbrc.1996.0560.

Tsujimura M, Odaka M, Nagashima S, Yohda M, Endo I.
Photoreactive nitrilebhydratase: the photoreaction site is located on the alpha subunit.
J Biochem. 1996 Mar;119(3):407-13.
doi: 10.1093/oxfordjournals.jbchem.a021256.

1995
Kagawa Y, Ohta T, Abe Y, Endo H, Yohda M, Kato N, Endo I, Hamamoto T, Ichida M, Hoaki T, et al.
Gene of heat shock protein of sulfur-dependent archaeal hyperthermophile Desulfurococcus.
Biochem Biophys Res Commun. 1995 Sep 14;214(2):730-6.
doi: 10.1006/bbrc.1995.2346.

Yohda M, Kato N, Endo I.
Solid-phase nested deletion: a new subcloning-less method for generating nested deletions.
DNA Res. 1995 Aug 31;2(4):175-81.
doi: 10.1093/dnares/2.4.175.

Amada K, Yohda M, Odaka M, Endo I, Ishii N, Taguchi H, Yoshida M.
Molecular cloning, expression, and characterization of chaperonin-60 and chaperonin-10 from a thermophilic bacterium, Thermus thermophilus HB8.
J Biochem. 1995 Aug;118(2):347-54.
doi: 10.1093/oxfordjournals.jbchem.a124913.

1994
Manabe T, Chen N, Terabe S, Yohda M, Endo I.
Effects of linear polyacrylamide concentrations and applied voltages on the separation of oligonucleotides and DNA sequencing fragments by capillary electrophoresis.
Anal Chem. 1994 Dec 1;66(23):4243-52.
doi: 10.1021/ac00095a020.

Yohda M, Honda J, Nagamune T, Endo I, Yoshida T, Miura K.
Molecular cloning and nucleotide sequence of the gene coding photosensitive nitrile hydratase.
Ann N Y Acad Sci. 1994 May 2;721:158-9.
doi: 10.1111/j.1749-6632.1994.tb47388.x.

1993
Nakano H, Matsuda K, Yohda M, Nagamune T, Endo I, Yamane T.
High speed polymerase chain reaction in constant flow.
Biosci Biotechnol Biochem. 1994 Feb;58(2):349-52.
doi: 10.1271/bbb.58.349.

1992
Yamauchi T, Choi SY, Okada H, Yohda M, Kumagai H, Esaki N, Soda K.
Properties of aspartate racemase, a pyridoxal 5'-phosphate-independent amino acid racemase.
J Biol Chem. 1992 Sep 15;267(26):18361-4.

1991
Okada H, Yohda M, Giga-Hama Y, Ueno Y, Ohdo S, Kumagai H.
Distribution and purification of aspartate racemase in lactic acid bacteria.
Biochim Biophys Acta. 1991 Jul 12;1078(3):377-82.
doi: 10.1016/0167-4838(91)90159-w.

Yohda M, Okada H, Kumagai H. Molecular cloning and nucleotide sequencing of the aspartate racemase gene from lactic acid bacteria Streptococcus thermophilus.
Biochim Biophys Acta. 1991 Jun 13;1089(2):234-40.
doi: 10.1016/0167-4781(91)90013-c.

Shirakihara Y, Yohda M, Kagawa Y, Yokoyama K, Yoshida M.
Purification by dye-ligand chromatography and a crystallization study of the F1-ATPase and its major subunits, beta and alpha, from a thermophilic bacterium, PS3.
J Biochem. 1991 Mar;109(3):466-71.
doi: 10.1093/oxfordjournals.jbchem.a123405.

1989
Giga-Hama Y, Yohda M, Kumagai H.
Intracellular distribution of a 32-KDa calcium-dependent phospholipid-binding protein from human placenta.
Cell Struct Funct. 1989 Oct;14(5):587-95.
doi: 10.1247/csf.14.587.

1988
Yohda M, Ohta S, Hisabori T, Kagawa Y. Site-directed mutagenesis of stable adenosine triphosphate synthase.
Biochim Biophys Acta. 1988 Mar 30;933(1):156-64.
doi: 10.1016/0005-2728(88)90065-5.

Ohta S, Yohda M, Ishizuka M, Hirata H, Hamamoto T, Otawara-Hamamoto Y, Matsuda K, Kagawa Y.
Sequence and over-expression of subunits of adenosine triphosphate synthase in thermophilic bacterium PS3.
Biochim Biophys Acta. 1988 Mar 30;933(1):141-55.
doi: 10.1016/0005-2728(88)90064-3.

1987
Yohda M, Yoshida M.
Single-site catalysis of F1-ATPase from thermophilic bacterium PS3 and its dominance in steady-state catalysis at low ATP concentration.
J Biochem. 1987 Oct;102(4):875-83.
doi: 10.1093/oxfordjournals.jbchem.a122128.

Konishi J, Yohda M, Hashimoto T, Yoshida M.
Single site catalysis of the F1-ATPase from Saccharomyces cerevisiae and the effect of inorganic phosphate on it.
J Biochem. 1987 Aug;102(2):273-9.
doi: 10.1093/oxfordjournals.jbchem.a122051.

Ohtsubo M, Yoshida M, Ohta S, Kagawa Y, Yohda M, Date T.
In vitro mutated beta subunits from the F1-ATPase of the thermophilic bacterium, PS3, containing glutamine in place of glutamic acid in positions 190 or 201 assembles with the alpha and gamma subunits to produce inactive complexes.
Biochem Biophys Res Commun. 1987 Jul 31;146(2):705-10.
doi: 10.1016/0006-291x(87)90586-9.

1986
Yohda M, Kagawa Y, Yoshida M.
The synthesis of enzyme-bound ATP by the F1-ATPase from the thermophilic bacterium PS3 in the presence of organic solvents
Biochim Biophys Acta. 1986, Jul 23; 850(3):429-43.
doi: 10.1016/0005-2728(86)90111-8