論文 Ebola virus-like particles reprogram cellular metabolism. J. Mol. Med.,101:557-568 2023 Author:Tang, H., Abouleila, Y., Saris, A., Shimizu, Y., Ottenhoff, T. H. M., *Mashaghi, A.
ePURE_JSBML: A tool for constructing a deterministic model of a reconstituted Escherichia coli protein translation system with a user-specified nucleic acid sequence. Adv. Biol.,7:e2200177-e2200177 2023 Author:*Shimizu, Y., Tanimura, N., Matsuura, T.
A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer. Cancer Med.,12:7616-7626 2023 Author:Kasahara, K., Narumi, R., Nagayama, S., Masuda, K., Esaki, T., Obama, K., *Tomonaga, T., Sakai, Y., *Shimizu, Y., *Adachi, J.
Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System. ACS Synth. Biol.,11:2791-2799 2022 Author:Miyachi, R., Shimizu, Y., *Ichihashi, N.
A red light-responsive photoswitch for deep tissue optogenetics. Nat. Biotechnol.,40:1672-1679 2022 Author:Kuwasaki, Y., Suzuki, K., Yu, G., Yamamoto, S., Otabe, T., Kakihara, Y., Nishiwaki, M., Miyake, K., Fushimi, K., Bekdash, R., Shimizu, Y., Narikawa, R., Nakajima, T., Yazawa, M., *Sato, M.
Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery. Cancer Biomark.,33:437-447 2022 Author:Abouleila Y., Ali, A., Masuda, K., Mashaghi, A., *Shimizu, Y.
Tracking metabolites at single-cell resolution reveals metabolic dynamics during plant mitosis. Plant Physiol.,189:459-464 2022 Author:Okubo-Kurihara, E., Ali, A., Hiramoto, M., Kurihara, Y., Abouleila, Y., Abdelazem, E. M., Kawai, T., Makita, Y., Kawashima, M., Esaki, T., Shimada, H., Mori, T., Hirai, M. Y., Higaki, T., Hasezawa, S., Shimizu, Y., Masujima, T., *Matsui, M.
Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display. Anal. Chem.,(94):3831-3839 2022 Author:Nakai, H., Isshiki, K., Hattori, M., Maehira, H., Yamaguchi, T., Masuda, K., Shimizu, Y., Watanabe, T., Hohsaka, T., Shihoya, W., Nureki, O., Kato, Y., Watanabe, H., *Matsuura, T.
Efficient and precise protein synthesis in a cell-free system using a set of in vitro transcribed tRNAs with nucleotide modifications. Methods Mol.,2433:151-168 2022 Author:Amikura, K., Hibi, K., *Shimizu, Y.
In vitro reconstitution of the Escherichia coli 70S ribosome with a full set of recombinant ribosomal proteins. J. Biochem.,171:227-237 2022 Author:Aoyama, R., Masuda, K., Shimojo, M., Kanamori, T., Ueda, T., *Shimizu, Y.
Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides. J. Proteomics,251:104393 2022 Author:Masuda, K., Kasahara, K., Narumi, R., Shimojo, M., *Shimizu, Y.
Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization. Chembiochem,22:3437-3442 2021 Author:Hiraoka, H., Shu, Z., Tri Le, B., Masuda, K., Nakamoto, K., Fangjie, L., Abe, N., Hashiya, F., Kimura, Y., Shimizu, Y., Veedu, R. N., *Abe, H.
Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface. ACS Synth. Biol.,10:609-619 2021 Author:Levy, M., Falkovich, R., Vonshak, O., Bracha, D., Tayar, A. M., Shimizu, Y., Daube, S. S., *Bar-Ziv, R. H.
Direct infusion nano-electrospray ionization mass spectrometry for therapeutic drug monitoring of ciprofloxacin and its metabolites in human saliva. J. Pharm. Biomed. Anal.,195(113866) 2021 Author:Demeiry, M. E., Ali, A., Abouleila, Y., Zarad, W., El-Gendy, H, Salam, R. A., Hadad, G., Shimizu, Y., Masujima, T., *Emara, S.
Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew. Chem. Int. Ed. Engl.,59:17403-17407 2020 Author:Kawaguchi, D., Kodama, A., Abe, N., Takebuchi, K., Hashiya, F., Tomoike, F., Nakamoto, K., Kimura, Y., *Shimizu, Y., *Abe, H.
Reconstituted cell-free protein synthesis using in vitro transcribed tRNAs. Commun. Biol.,3:350 2020 Author:Hibi, K., Amikura, K., Sugiura, N., Masuda, K., Ohno, S., Yokogawa, T., Ueda, T., *Shimizu, Y.
Mass spectrometry-based absolute quantification of amyloid proteins in pathology tissue specimens: Merits and limitations. PLoS One,15:e0235143 2020 Author:Ogawa, M., Shintani-Domoto, Y., Nagashima, Y., Ode, K. L., Sato, A., Shimizu, Y., Ohashi, K., Roehrl, M. H. A., Ushiku, T., Ueda, H. R., *Fukayama, M.
Prospects for Comprehensive Analyses of Circulating Tumor Cells in Tumor Biology. Cancers,12:1135 2020 Author:Aoki, M., Shoji, H., Kashiro, A., Takeuchi, K., Shimizu, Y., *Honda, K.
Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation. Chem. Commun.,56:6217-6220 2020 Author:Nakamoto, K., Abe, N., Tsuji, G., Kimura, Y., Tomoike, F., Shimizu, Y., *Abe, H.
Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat. Commun.,11:1982 2020 Author:*Susaki, E. A., Shimizu, C., Kuno, A., Tainaka, K., Li, X., Nishi, K., Morishima, K., Ono, H., Ode, K. L., Saeki, Y., Miyamichi, K., Isa, K., Yokoyama, C., Kitaura, H., Ikemura, M., Ushiku, T., Shimizu, Y., Saito, T., Saido, T. C., Fukayama, M., Onoe, H., Touhara, K., Isa, T., Kakita, A., Shibayama, M., *Ueda, H. R.
In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli. Commun. Biol.,3:142 2020 Author:Shimojo, M., Amikura, K., Masuda, K., Kanamori, T., Ueda, T., *Shimizu, Y.
Quantification and targeted detection of ciprofloxacin in dosage form and human urine by direct injection nano-electrospray ionization multi-stage mass spectrometry. Microchem. J.,153:104534 2020 Author:Demeiry, M. E., Ali, A., Abouleila, Y., Shimizu, Y., Masujima, T., Salam, R. A., Hadad, G., *Emara, S.
Single-cell metabolomics by mass spectrometry: Advances, challenges, and future applications. Trends Analyt. Chem.,120:115436 2019 Author:Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., *Mashaghi, A., *Hankemeier, T.
Phosphorogenic and spontaneous formation of tris(bipyridine)ruthenium in peptide scaffolds. J. Pept. Sci.,25:e3158 2019 Author:Karimiavargania, M., Tada, S., Minagawa, N., Shimizu, Y., Hirose, T., Ito, Y., *Uzawa, T.
Single-cell screening of tamoxifen abundance and effect using mass spectrometry and Raman-spectroscopy. Anal. Chem.,91:2710-2718 2019 Author:Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Watanabe, T. M., Yanagida, T., *Germond, A.
High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus. Proteins,87:226-235 2019 Author:Matsumoto, A., Uehara, Y., Shimizu, Y., Ueda, T., Uchiumi, T., *Ito, K.
Live single cell mass spectrometry reveals cancer-specific metabolic profiles of circulating tumor cells. Cancer Sci.,110:697-706 2019 Author:Abouleila, Y., Onidani, K., Ali, A., Shoji, H., Kawai, T., Lim, C. T., Kumar, V., Okaya, S., Kato, K., Hiyama, E., Yanagida, T., Masujima, T., *Shimizu, Y., *Honda, K.
G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System. Life (Basel),8:E54 2018 Author:Gessesse, B., Nagaike, T., Nagata, K., Shimizu, Y., *Ueda, T.
Reconstitution of 30S ribosomal subunits in vitro using ribosome biogenesis factors. RNA,24:1512-1519 2018 Author:Tamaru, D., *Amikura, K., Shimizu, Y., Nierhaus, K. H., Ueda, T.
Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents. Cell Rep.,24:2196-2210. e9 2018 Author:Tainaka, K., Murakami, T. C., Susaki, E. A., Shimizu, C., Saito, R., Takahashi, K., Hayashi-Takagi, A., Sekiya, H., Arima, Y., Nojima, S., Ikemura, M., Ushiku, T., Shimizu, Y., Murakami, M., Tanaka, K. F., Iino, M., Kasai, H., Sasaoka, T., Kobayashi, K., Miyazono, K., Morii, E., Isa, T., Fukayama, M., Kakita, A., *Ueda, H. R.
Robustness of a reconstituted Escherichia coli protein translation system analyzed by computational modeling. ACS Synth. Biol.,7:1964-1972 2018 Author:*Matsuura, T., Hosoda, K., Shimizu, Y.
Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth. Syst. Biotechnol.,3:97-104 2018 Author:Narumi, R., Masuda, K., Tomonaga, T., Adachi, J., Ueda, H. R., *Shimizu, Y.
Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System. ACS Synth. Biol.,7:1269-1278 2018 Author:Senoussi, A., Lee Tin Wah, J., Shimizu, Y., Robert, J., Jaramillo, A., Findeiss, S., Axmann, I. M., *Estevez-Torres, A.
A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. Nat. Neurosci.,21:625-637 2018 Author:Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., Iino, M., Mochizuki, H., Tainaka, K., *Ueda, H. R.
Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proc. Natl. Acad. Sci. U. S. A.,114:E1336-E1344 2017 Author:*Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T., *Shimizu, Y.
Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc. Natl. Acad. Sci. U. S. A.,113:E3461-E3467 2016 Author:#Narumi, R., #*Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., Sato, A., Matsumoto, K., *Ueda, H. R.
Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene. Cell Rep.,14:662-677 2016 Author:Sunagawa, G. A., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D., Fujishima, H., Ukai, H., Nishimura, O., Shi, S., Ohno, R., Narumi, R., Shimizu, Y., Tone, D., Ode, K. L., Kuraku, S., *Ueda, H. R.
Integration of a reconstituted cell-free protein-synthesis system on a glass microchip. Anal. Sci.,31:67-71 2015 Author:#*Tanaka, Y. #*Shimizu, Y.
Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell,157:726-739 2014 Author:Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., Abe, T., Kiyonari, H., Shimizu, Y., Miyawaki, A., Yokota, H., *Ueda, H. R.
Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front. Microbiol.,5:170 2014 Author:*Shimizu, Y.
The PURE System for Protein Production. Methods Mol. Biol.,1118:275-284 2014 Author:Shimizu, Y., Kuruma, Y., Kanamori, T., *Ueda, T.
Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun.,69:332-335 2013 Author:Matsumoto, A., Shimizu, Y., Takemoto, C., Ueda, T., Uchiumi, T., *Ito, K.
Robust in vitro affinity maturation strategy based on interface-focused high-throughtput mutational scanning. Biochem. Biophys. Res. Commun.,428:395-400 2012 Author:*Fujino, Y., Fujita, R., Wada K., Fujishige, K., Kanamori, T., Hunt, L., Shimizu, Y., *Ueda, T.
Crystal structure analysis of the translation factor RF3 (release factor 3). FEBS Lett.,586:3705-3709 2012 Author:Kihira, K. Shimizu, Y., Shomura, Y., Shibata, N., Kitamura, M., Nakagawa, A, Ueda, T., Ochi, K., *Higuchi, Y.
ArfA recruits RF2 into stalled ribosomes. J. Mol. Biol.,423:624-631 2012 Author:*Shimizu, Y.
Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase. Nucleic Acids Res.,40:10521-10531 2012 Author:*Ito, K., Murakami, R., Mochizuki, M., Qi, H., Shimizu, Y., Miura, K. I., Ueda, T., Uchiumi, T.
Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TYC domain of tRNA. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun.,67:1566-1569 2011 Author:*Ito, K., Qi, H., Shimizu, Y., Murakami, R., Miura, K. I., Ueda, T., Uchiumi, T.
Application of micro-reactor chip technique for millisecond quenching of deuterium incorporation into 70S ribosomal protein complex. Int. J. Mass Spectrom.,302:132-138 2011 Author:Yamamoto, T., Shimizu, Y., Ueda, T., Shiro, Y., *Suematsu, M.
Single molecule imaging of the trans-translation entry process via anchoring of the tagged ribosome. J. Biochem.,149:609-618 2011 Author:Zhou Z. P., Shimizu, Y., *Tadakuma, T., Taguchi, H., Ito, K., Ueda, T.
A highly controllable reconstituted cell-free system -- a breakthrough in protein synthesis research. Curr. Pharm. Biotechnol.,11:267-271 2010 Author:Ohashi, H., Kanamori, T., Shimizu, Y., *Ueda, T.
PURE technology. Methods Mol. Biol.,607:11-21 2010 Author:Shimizu, Y., *Ueda, T.
Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry. J. Biol. Chem.,285:5646-5652 2010 Author:Yamamoto, T., Shimizu, Y., Ueda, T., *Shiro, Y.
Real-time monitoring of cell-free translation on a quartz-crystal microbalance. J. Am. Chem. Soc.,131:9326-9332 2009 Author:Takahashi, S., Iida, M., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
Epitope mapping using ribosome display in a reconstituted cell-free protein synthesis system. J. Biochem.,145:593-700 2009 Author:Osada, E., *Shimizu, Y., Akbar, B. K., Kanamori, T., Ueda, T.
Single molecule imaging of full protein synthesis by immobilized ribosomes. Nucleic Acids Res.,36:e70 2008 Author:Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J. D., *Funatsu, T.
70S ribosomes bind to Shine-Dalgarno sequences without required dissociations. Chembiochem,9:870-873 2008 Author:Takahashi, S., Akita, R., Matsuno, H., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
Kinetic analysis of the effects of translation enhancers in translation initiation. Nucleic Acids Symp. Ser. (Oxf).,51:45-46 2007 Author:Takahashi, S., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
EF-Tu mutants expand amino acid tolerance of protein biosynthesis system. J. Am. Chem. Soc.,129:14458-14462 2007 Author:Doi, Y., *Ohtsuki, T., Shimizu, Y., Ueda, T., *Sisido, M.
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature,449:867-871 2007 Author:Watanabe, K., Toh, Y., Suto, K., Shimizu, Y., Oka, N., Wada, T., *Tomita, K.
Ribosomal protein S1 is not essential for the trans-translation machinery. J. Mol. Biol.,386:845-852 2007 Author:Qi, H., *Shimizu, Y., Ueda, T.
Efficient protein selection based on ribosome display system with purified components. Biochem. Biophys. Res. Commun.,352:270-276 2007 Author:Ohashi, H., *Shimizu, Y., Ying, B. W., Ueda, T.
Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog. EMBO J.,25(5942):5950 2006 Author:#Suto, K., #Shimizu, Y., Watanabe, K., Ueda, T., Fukai, S., Nureki, O. *Tomita, K.
Kinetic analysis of ribosome binding process onto mRNA using a quartz-crystal microbalance. Nucleic Acids Symp. Ser.,50:49-50 2006 Author:Takahashi, S., Akita, R., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
Cell-free translation systems for protein engineering. FEBS J.,273:4133-4140 2006 Author:Shimizu, Y., Kuruma, Y., Ying, B. W., Umekage, S., *Ueda, T.
SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation. J. Biol. Chem.,281:15987-15996 2006 Author:Shimizu, Y., *Ueda, T.
Development of a minimal cell-free translation system for the synthesis of presecretory and integral membrane proteins. Biotechnol. Prog.,21:1243-1251 2005 Author:Kuruma, Y., Nishiyama, K., Shimizu, Y., Muller, M., *Ueda, T.
Protein synthesis by pure translation systems. Methods,36:299-304 2005 Author:Shimizu, Y., Kanamori, T., *Ueda, T.
Esterification of Escherichia coli tRNAs with D-histidine and D-lysine by aminoacyl-tRNA synthetases. Biosci. Biotechnol. Biochem.,69:1040-1041 2005 Author:Takayama, T., Ogawa, T., Hidaka, M., Shimizu, Y., Ueda, T., *Masaki, H.
Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria. J. Biol. Chem.,279:8539-8546 2004 Author:Udagawa, T., Shimizu, Y., *Ueda, T.
A novel screening system for self-mRNA targeting proteins. J. Biochem.,133:485-491 2003 Author:Ying, B. W., Suzuki, T., Shimizu, Y., *Ueda, T.
A point mutation in ribosomal protein L7/L12 reduces its ability to form a compact dimer structure and to assemble into the GTPase center. Biochemistry,42:4691-4698 2003 Author:Nomura, T., Mochizuki, R., Dabbs, E. R., Shimizu, Y., Ueda, T., Hachimori, A., *Uchiumi, T.
The role of SmpB protein in trans-translation. FEBS Lett.,514:74-77 2002 Author:Shimizu, Y., *Ueda, T.
Cell-free translation reconstituted with purified components. Nat. Biotechnol.,19:751-755 2001 Author:Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., *Ueda, T.
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