村上研究室

名古屋大学大学院工学研究科 生命分子工学専攻
名古屋大学工学部化学生命工学科 生体分子応用化学

PUBLICATIONS

論文発表

  1. Suzuki, S.; Nakajima, Y.; Kamo, N.; Osakabe, A.; Okamoto, A.; Hayashi, G.*; Murakami, H.*, Thiocholine-Mediated One-Pot Peptide Ligation and Desulfurization. molecules, 2023, 28, 3655.
  2. Umemoto, S.; Kondo, T.; Fujino, T.; Hayashi, G.; Murakami, H.*, Large-scale analysis of mRNA sequences localized near the start and amber codons and their impact on the diversity of mRNA display libraries. Nucleic Acids Research, 2023, gkad555.
  3. Nakatsu, K.; Okamoto, A.*; Hayashi, G.*; Murakami, H.* Repetitive Thiazolidine Deprotection Using a Thioester-Compatible Aldehyde Scavenger for One-Pot Multiple Peptide Ligation. Angewandte Chemie International Edition, 2022, 61, 39, e202206240.
  4. Kondo, T.; Matsuoka, K.; Umemoto, S.;Fujino, T.; Hayashi, G.; Iwatani, Y.*; Murakami, H.*, Monobodies with potent neutralizing activity against SARS-CoV-2 Delta and other variants of concern. Life Science Alliance, 2022, 5, 6, e202101322.
  5. Kondo, T.; Eguchi, M.; Tsuzuki, N.; Murata, N.; Fujino, T.; Hayashi, G.; Murakami, H.*, Construction of a Highly Diverse mRNA Library for in vitro Selection of Monobodies. Bio-Protocol, 2021, 11(16), e4125.
  6. Kamo, N.; Kujirai, T.; Kurumizaka, H.; Murakami, H.; Hayashi, G.* Okamoto, A.* Organoruthenium-Catalyzed Chemical Protein Synthesis to Elucidate the Functions of Epigenetic Modifications on Heterochromatin Factors. Chemical Science, 2021, 12, 5926-5937
  7. Kondo, T.; Eguchi, M.; Kito, S.; Fujino, T.; Hayashi, G.; Murakami, H.*, cDNA TRAP display for rapid and stable in vitro selection of antibody-like proteins. Chemical Communications, 2021, 57, 2416 - 2419
  8. Kondo, T.; Iwatani, Y.; Matsuoka, K.; Fujino, T.; Umemoto, S.; Yokomaku, Y.; Ishizaki, K.; Kito, S.; Sezaki, T.; Hayashi, G.; Murakami, H.*, Antibody-like proteins that capture and neutralize SARS-CoV-2. Science Advances, 2020, 6(42), eabd3916.
  9. Fujino, T.; Tozaki, M.; Murakami, H.*, An amino acid-swapped genetic code. ACS Synthetic Biology, 2020, 9(10), 2703 -13.
  10. Fujino, T.; Kondo, T.; Suga, H.; Murakami, H.*, Exploring the Minimal RNA Substrate of Flexizymes. Chembiochem, 2019, 20(15),1959-1965.
  11. Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method. Methods in Molecular Biology 2017, 1498, 339-347.
  12. Fujino, T.; Goto, Y.; Suga, H.; Murakami, H.*, Ribosomal synthesis of peptides with multiple ß-amino acids. Journal of the American Chemical Society, 2016, 138, 6, 1962-9.
  13. Iwane, Y; Hitomi, A; Murakami, H; Katoh, T; Goto, Y; Suga, H*, Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes. Nature Chemistry 2016, 8, 4, 317-25.
  14. Fujino, T.; Murakami, H.*, In vitro selection combined with ribosomal translation containing non-proteinogenic amino acids. The Chemical Record, 2016, 16, 1, 365-77. (Review article)
  15. Kawakami, T.*; Sasaki, T; Reid, P. C.; Murakami, H.*, Incorporation of electrically charged N-alkyl amino acids into ribosomally synthesized peptides via post-translational conversion. Chemical Science, 2014, 5, 887-893.
  16. Taniguchi, N; Nakayama, S; Kawakami, T.; Murakami, H.*, Patch cloning method for multiple site-directed and saturation mutagenesis. BMC Biotechnology 2013, 13:91.
  17. Goto, Y.; Iseki, M.; Hitomi, A.; Murakami, H.; Suga, H.*, Nonstandard Peptide Expression under the Genetic Code Consisting of Reprogrammed Dual Sense Codons. ACS Chemical Biology 2013, 8, 2630-34.
  18. Kawakami, T.*; Ishizawa, T.; Murakami, H.*, Extensive reprogramming of the genetic code for genetically encoded synthesis of highly N-alkylated polycyclic peptidomimetics. Journal of the American Chemical Society 2013, 135, 12297-304.
  19. Kawakami, T.; Ishizawa, T.; Fujino, T.; Reid, P. C.; Suga, H.; Murakami, H.*, In Vitro Selection of Multiple Libraries Created by Genetic Code Reprogramming To Discover Macrocyclic Peptides That Antagonize VEGFR2 Activity in Living Cells. ACS Chemical Biology 2013, 8, 1205-14.
  20. Ishizawa, T.; Kawakami, T.; Reid, P. C.; Murakami, H.*, TRAP display: a high-speed selection method for the generation of functional polypeptides. Journal of the American Chemical Society 2013, 135, 5433-40.
  21. Fujino, T.; Goto, Y.; Suga, H.; Murakami, H.*, Reevaluation of the D-Amino Acid Compatibility with the Elongation Event in Translation. Journal of the American Chemical Society 2013, 135, 1830-7.
  22. Kawakami, T.; Murakami, H.*, Genetically encoded libraries of nonstandard peptides. Journal of Nucleic Acids 2012, 2012, 713510. (Review article)
  23. Yamagishi, Y.; Ashigai, H.; Goto, Y.; Murakami, H.; Suga, H.*, Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction. Chembiochem 2009, 10, 1469-72.
  24. Niwa, N.; Yamagishi, Y.; Murakami, H.; Suga, H.*, A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. Bioorganic & Medicinal Chemistry Letters 2009, 19, 3892-4.
  25. Nakajima, E.; Goto, Y.; Sako, Y.; Murakami, H.; Suga, H.*, Ribosomal Synthesis of Peptides with C-Terminal Lactams, Thiolactones, and Alkylamides. Chembiochem 2009, 10, 1186-92
  26. Murakami, H.*; Ohta, A.; Suga, H.*, Bases in the anticodon loop of tRNA(Ala)(GGC) prevent misreading. Nature Structural & Molecular Biology 2009, 16, 353-8.
  27. Kawakami, T.; Ohta, A.; Ohuchi, M.; Ashigai, H.; Murakami, H.; Suga, H.*, Diverse backbone-cyclized peptides via codon reprogramming. Nature Chemical Biology 2009, 5, 888-90.
  28. Goto, Y.; Iwasaki, K.; Torikai, K.; Murakami, H.; Suga, H.*, Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chemical Communications 2009, 3419-21.
  29. Xiao, H.; Murakami, H.; Suga, H.; Ferre-D'Amare, A. R.*, Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 2008, 454, 358-61.
  30. Sako, Y.; Morimoto, J.; Murakami, H.; Suga, H., Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions. Journal of the American Chemical Society 2008, 130, 7232-4.
  31. Sako, Y.; Goto, Y.; Murakami, H.; Suga, H.*, Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. ACS Chemical Biology 2008, 3, 241-9.
  32. Ohta, A.; Murakami, H.; Suga, H.*, Polymerization of alpha-hydroxy acids by ribosomes. Chembiochem 2008, 9, 2773-8.
  33. Kawakami, T.; Murakami, H.; Suga, H.*, Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. Journal of the American Chemical Society 2008, 130, 16861-3.
  34. Kawakami, T.; Murakami, H.; Suga, H.*, Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chemistry & Biology 2008, 15, 32-42.
  35. Goto, Y.; Ohta, A.; Sako, Y.; Yamagishi, Y.; Murakami, H.; Suga, H.*, Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chemical Biology 2008, 3, 120-9.
  36. Goto, Y.; Murakami, H.; Suga, H.*, Initiating translation with D-amino acids. RNA 2008, 14, 1390-8.
  37. Ohuchi, M.; Murakami, H.; Suga, H., The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Current Opinion in Chemical Biology 2007, 11, 537-42. (Review article)
  38. Ohta, A.; Murakami, H.; Higashimura, E.; Suga, H.*, Synthesis of polyester by means of genetic code reprogramming. Chemistry & Biology 2007, 14, 1315-22.
  39. Murakami, H.; Ohta, A.; Ashigai, H.; Suga, H.*, A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nature Methods 2006, 3, 357-9.
  40. Kourouklis, D.; Murakami, H.; Suga, H.*, Programmable ribozymes for mischarging tRNA with nonnatural amino acids and their applications to translation. Methods 2005, 36, 239-44.
  41. Ramaswamy, K.; Saito, H.; Murakami, H.; Shiba, K.; Suga, H.*, Designer ribozymes: programming the tRNA specificity into flexizyme. Journal of the American Chemical Society 2004, 126, 11454-5.
  42. Hohsaka, T.; Muranaka, N.; Komiyama, C.; Matsui, K.; Takaura, S.; Abe, R.; Murakami, H.; Sisido, M.*, Position-specific incorporation of dansylated non-natural amino acids into streptavidin by using a four-base codon. FEBS Letters 2004, 560, 173-7.
  43. Murakami, H.; Saito, H.; Suga, H.*, A versatile tRNA aminoacylation catalyst based on RNA. Chemistry & Biology 2003, 10, 655-62.
  44. Murakami, H.; Kourouklis, D.; Suga, H.*, Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Chemistry & Biology 2003, 10, 1077-84.
  45. Taki, M.*; Hohsaka, T.; Murakami, H.; Taira, K.; Sisido, M.*, Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/anticodon pairs. Journal of the American Chemical Society 2002, 124, 14586-90.
  46. Murakami, H.; Hohsaka, T.; Sisido, M.*, Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nature Biotechnology 2002, 20, 76-81.
  47. Murakami, H.; Bonzagni, N. J.; Suga, H.*, Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme. Journal of the American Chemical Society 2002, 124, 6834-5.
  48. Taki, M.; Hohsaka, T.; Murakami, H.; Taira, K.; Sisido, M.*, A non-natural amino acid for efficient incorporation into proteins as a sensitive fluorescent probe. FEBS Letters 2001, 507, 35-8.
  49. Hohsaka, T.; Ashizuka, Y.; Taira, H.; Murakami, H.; Sisido, M.*, Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system. Biochemistry 2001, 40, 11060-4.
  50. Hohsaka, T.; Ashizuka, Y.; Murakami, H.; Sisido, M.*, Five-base codons for incorporation of nonnatural amino acids into proteins. Nucleic Acids Research 2001, 29, 3646-51.
  51. Taki, M.; Murakami, H.; Sisido, M.*, A chiral Eu3+-thienoyltrifluoroacetone complex on an avidin tetramer: luminescence and CD studies on the supramolecular protein-metal chelate complex. Chemical Communications 2000, 1199-1200.
  52. Murakami, H.; Hohsaka, T.; Ashizuka, Y.; Hashimoto, K.; Sisido, M.*, Site-directed incorporation of fluorescent nonnatural amino acids into streptavidin for highly sensitive detection of biotin. Biomacromolecules 2000, 1, 118-25.
  53. Hohsaka, T.; Kajihara, D.; Ashizuka, Y.; Murakami, H.; Sisido, M.*, Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems. Journal of the American Chemical Society 1999, 121, 34-40.
  54. Hohsaka, T.; Ashizuka, Y.; Sasaki, H.; Murakami, H.; Sisido, M.*, Incorporation of two different nonnatural amino acids independently into a single protein through extension of the genetic code. Journal of the American Chemical Society 1999, 121, 12194-12195.
  55. Murakami, H.; Hohsaka, T.; Ashizuka, Y.; Sisido, M.*, Site-directed incorporation of p-nitrophenylalanine into streptavidin and site-to-site photoinduced electron transfer from a pyrenyl group to a nitrophenyl group on the protein framework. Journal of the American Chemical Society 1998, 120, 7520-7529.
  56. Hohsaka, T.; Ashizuka, Y.; Murakami, H.; Sisido, M.*, Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression. Journal of the American Chemical Society 1996, 118, 9778-9779.

日本語の文献

  1. 近藤太志・梅本駿・藤野公茂・林剛介・村上裕 (2022) “6章　進化分子工学を用いた人工抗体創製とその応用”　最先端ナノライフシステム研究　第Ⅰ編 6章　36-41 最先端ナノライフシステム研究編集委員会
  2. 近藤太志・梅本駿・藤野公茂・林剛介・村上裕（2021）“新型コロナウイルスに対する迅速な人工抗体創製”　 創薬研究者がこれだけは知っておきたい最新のウイルス学　第１０章－第７節, 技術情報協会
  3. 藤野公茂, 若手研究者からのメッセージ 日本化学会バイオテクノロジー部会ニュースレター, 2018, 22, 12-16.
  4. 藤野公茂, β-アミノ酸を複数個含むペプチドの翻訳合成 Tracer, 2017, 61, 9-13.
  5. 藤野公茂, 後藤佑樹, 菅裕明, 村上裕, D体アミノ酸の翻訳伸長反応への適合性 ケミカルバイオロジー, 2016, 9, 11-4.
  6. 石沢尭大・川上隆史・村上裕（2013）“高速試験管内進化分子工学法―TRAP displayの開発と血管新生阻害ペプチド創製への応用”　進化分子工学〜高速分子進化によるタンパク質•核酸の開発　第3編−第4章−第4節, 株式会社エヌ・ティー・エス
  7. 村上裕　(2011) “特殊ペプチド増幅法の開発”　日本化学会 生体機能関連化学部会 NEWS LETTER　6月号　26(1), 7-10.
  8. 村上裕・菅裕明　(2008) “新創薬技術RAPIDシステムとマイクロ・ナノディバイスへの期待”　化学工業　6月号　59(6), 463-469.
  9. 村上裕 (2007) “翻訳系を用いた特殊ペプチドの合成”　生命化学研究レター, 23, 14-19
  10. 川上隆史・村上裕・菅裕明 (2007) “遺伝暗号をリプログラミングして特殊ペプチドをつくる”　化学, 62(8), 68-69
  11. 後藤佑樹・太田淳・村上裕・菅裕明 (2007) “特殊ペプチドのコンビナトリアル翻訳合成”　化学工業、４月号　58(4), 255-262
  12. 太田淳・村上裕・菅裕明 (2007) “遺伝暗号のリプログラミングによるポリエステルの翻訳合成”　高分子, 56, 196-198
  13. 村上裕・菅裕明 (2006) “フレキシザイム～遺伝暗号の拡張とリプログラミングへの応用”, バイオテクノロジージャーナル 11•12月号：6(6), 734-737
  14. 村上裕・菅裕明 (2006) “フレキシザイムを用いた遺伝暗号の拡張とリプログラミング”蛋白核酸酵素, 増刊号, 51(16), 2496-2501
  15. 村上裕・菅裕明・平尾一郎 (2006) “合成生物学　セントラルドグマをつくりかえる” Bionics, 3月号, 34-39.
  16. 村上裕・菅裕明 (2003). “人工リボザイム：試験管内分子進化と非天然アミノ酸変異法への応用”蛋白核酸酵素、増刊号 48(11):1511-1518「化学と生物学の接点がつくるニューバイオテクノロジー」
  17. 村上裕・芳坂貴弘・宍戸昌彦 (2002) “新規変異タンパク質創出のためのランダム挿入削除変異法”, Bioベンチャー 2: 94-97