Murakami Lab

Nagoya University Department of Biomolecular Engineering, Graduate School of Engineering

PUBLICATIONS

  1. K. Endo, S. Umemoto, N. Tsuzuki, H. Okumura, Y. Sato, T. Yoshii*, S. Tsukiji, S. Nagano, H. Murakami*, T. Hino* Crystallization and X-ray structure of a highly aggregation-prone monobody engineered for high-affinity small-molecule recognition. Acta Crystallogr. Sect. F. Struct. Biol. Commun., 2026, F82, 75-82.
    https://doi.org/10.1107/S2053230X26000798
  2. K. Nakatsu, F. Yoshitomi, H. Onoda, R. Shikimachi, K. Arita, A. Okamoto*, H. Murakami*, G. Hayashi* Chemical Protein Synthesis via Direction-Switching One-Pot Peptide Ligation Enabled by Orthogonal Cysteinyl Protection. J. Am. Chem. Soc., 2026, 148, 4622-4634.
    https://doi.org/10.1021/jacs.5c20510
  3. N. Iwamoto, S. Ohno, K. Nakamura, T. Naito, S. Miura, S. Inuki, H. Ohno, G. Hayashi, H. Murakami, S. Oishi* Design and Evaluation of Stable Cysteine-Modified Monobody Scaffolds for Mirror-Image Synthesis. Bioconjug. Chem., 2025, 36, 1504-1515.
    https://doi.org/10.1021/acs.bioconjchem.5c00181
  4. G. Hayashi*, T. Naito, S. Miura, N. Iwamoto, Y. Usui, M. Bando-Shimizu, S. Suzuki, K. Higashi, M. Nonaka*, S. Oishi*, H. Murakami*, Generating a mirror-image monobody targeting MCP-1 via TRAP display and chemical protein synthesis. Nat. Commun., 2024, 15, 10723.
    https://doi.org/10.1038/s41467-024-54902-x
  5. H. Tagawa, R. Saeki, C. Yamamoto, K. Tanito, C. Tanaka, S. Munekawa, T. Nii, A. Kishinuma, H. Murakami, T. Mori*, Y. Katayama*, The effect of Fc region affinity of protein-based antibody-recruiting molecules on antibody-dependent cellular cytotoxicity. RSC Adv., 2024, 14, 22860-22866.
    https://doi.org/10.1039/d4ra03391d
  6. D. Quiroz, S. Oya, D. Lopez-Mateos, K. Zhao, A. Pierce, L. Ortega, A. Ali, P. Carbonell-Bejerano, V. Yarov-Yarovoy, S. Suzuki, G. Hayashi, A. Osakabe, G. Monroe*, H3K4me1 recruits DNA repair proteins in plants. The Plant Cell, 2024, 36, 2426.
    https://doi.org/10.1093/plcell/koae089
  7. T. Fujino, R. Sonoda, T. Higashinagata, E. Mishiro-Sato, K. Kano, H. Murakami*, Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set. Nat. Commun., 2024, 15, 4143.
    https://doi.org/10.1038/s41467-024-48056-z
  8. K. Yamano, M. Sawada, R. Kikuchi, K. Nagataki, W. Kojima, R. Endo, H. Kinefuchi, A. Sugihara, T. Fujino, A. Watanabe, K. Tanaka, G. Hayashi, H. Murakami, N. Matsuda*, Optineurin provides a mitophagy contact site for TBK1 activation. EMBO J., 2024, 43 (5), 754-779.
    https://doi.org/10.1038/s44318-024-00036-1
  9. S. Umemoto, T. Kondo, T. Fujino, G. Hayashi, H. Murakami*, 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 Res., 2023, gkad555.
    https://doi.org/10.1093/nar/gkad555
  10. S. Suzuki, Y. Nakajima, N. Kamo, A. Osakabe, A. Okamoto, G. Hayashi*, H. Murakami*, Thiocholine-Mediated One-Pot Peptide Ligation and Desulfurization. Molecules, 2023, 28, 3655.
    https://doi.org/10.3390/molecules28093655
  11. K. Nakatsu, A. Okamoto*, G. Hayashi*, H. Murakami* Repetitive Thiazolidine Deprotection Using a Thioester-Compatible Aldehyde Scavenger for One-Pot Multiple Peptide Ligation. Angew. Chem. Int. Ed., 2022, 61, 39, e202206240.
    https://doi.org/10.1002/anie.202206240
  12. T. Kondo, K. Matsuoka, S. Umemoto, T. Fujino, G. Hayashi, Y. Iwatani.*, H. Murakami.*, Monobodies with potent neutralizing activity against SARS-CoV-2 Delta and other variants of concern. Life Sci. Alliance, 2022, 5, 6, e202101322.
    https://doi.org/10.26508/lsa.202101322
  13. T. Kondo, M. Eguchi, N. Tsuzuki, N. Murata, T. Fujino, G. Hayashi, H. Murakami.*, Construction of a Highly Diverse mRNA Library for in vitro Selection of Monobodies. Bio-Protocol, 2021, 11(16), e4125.
    https://doi.org/10.21769/BioProtoc.4125
  14. T. Kondo, M. Eguchi, S. Kito, T. Fujino, G. Hayashi, H. Murakami.*, cDNA TRAP display for rapid and stable in vitro selection of antibody-like proteins. Chem. Commun., 2021, 57, 2416 - 2419
    https://doi.org/10.1039/D0CC07541H
  15. N. Kamo, T. Kujirai, H. Kurumizaka, H. Murakami, G. Hayashi.*, A. Okamoto.* Organoruthenium-Catalyzed Chemical Protein Synthesis to Elucidate the Functions of Epigenetic Modifications on Heterochromatin Factors. Chem. Sci., 2021, 12, 5926-5937
    https://doi.org/10.1039/D1SC00731A
  16. T. Kondo, Y. Iwatani, K. Matsuoka, T. Fujino, S. Umemoto, Y. Yokomaku, K. Ishizaki, S. Kito, T. Sezaki, G. Hayashi, H. Murakami*, Antibody-like proteins that capture and neutralize SARS-CoV-2. Sci. Adv., 2020, 6(42), eabd3916.
    https://doi.org/10.1126/sciadv.abd3916
  17. T. Fujino, M. Tozaki, H. Murakami*, An amino acid-swapped genetic code. ACS Synth. Biol., 2020, 9(10), 2703 -13.
    https://doi.org/10.1021/acssynbio.0c00196
    18. 　
  18. T. Fujino, T. Kondo, H. Suga, H. Murakami*, Exploring the Minimal RNA Substrate of Flexizymes. ChemBioChem, 2019, 20(15),1959-1965.
    https://doi.org/10.1002/cbic.201900150
  19. N. Taniguchi, H. Murakami. Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method. Methods Mol. Biol. 2017, 1498, 339-347.
    https://doi.org/10.1007/978-1-4939-6472-7_22
  20. Y. Iwane, A. Hitomi, H. Murakami, T. Katoh, Y. Goto, H. Suga*, Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes. Nat. Chem. 2016, 8, 4, 317-25.
    https://doi.org/10.1038/nchem.2446
  21. T. Fujino, Y. Goto, H. Suga, H. Murakami*, Ribosomal synthesis of peptides with multiple ß-amino acids. J. Am. Chem. Soc., 2016, 138, 6, 1962-9.
    https://doi.org/10.1021/jacs.5b12482
  22. T. Fujino, H. Murakami*, In vitro selection combined with ribosomal translation containing non-proteinogenic amino acids. Chem. Rec., 2016, 16, 1, 365-77. (Review article)
    https://doi.org/10.1002/tcr.201500239
  23. S. Adachi, M. Homoto, R. Tanaka, Y. Hioki, H. Murakami, H. Suga, M. Matsumoto, K. Nakayama, T. Hatta, S. Iemura, T. Natsume*, ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK–RSK pathway. Nucleic Acids Res., 2014, 42, 10037-10049.
    https://doi.org/10.1093/nar/gku652
  24. T. Kawakami*, T. Sasaki, P. C. Reid, H. Murakami*, Incorporation of electrically charged N-alkyl amino acids into ribosomally synthesized peptides via post-translational conversion. Chem. Sci., 2014, 5, 887-893.
    https://doi.org/10.1039/D1SC00731A
  25. Y. Goto, M. Iseki, A. Hitomi, H. Murakami, H. Suga*, Nonstandard Peptide Expression under the Genetic Code Consisting of Reprogrammed Dual Sense Codons. ACS Chem. Biol. 2013, 8, 2630-34.
    https://doi.org/10.1021/cb400549p
  26. N. Taniguchi, S. Nakayama, T. Kawakami, H. Murakami*, Patch cloning method for multiple site-directed and saturation mutagenesis. BMC Biotechnol. 2013, 13:91.
    https://doi.org/10.1186/1472-6750-13-91
  27. T. Kawakami*, T. Ishizawa, H. Murakami*, Extensive reprogramming of the genetic code for genetically encoded synthesis of highly N-alkylated polycyclic peptidomimetics. J. Am. Chem. Soc. 2013, 135, 12297-304.
    https://doi.org/10.1021/ja405044k
  28. T. Kawakami, T. Ishizawa, T. Fujino, P. C. Reid, H. Suga, H. Murakami*, In Vitro Selection of Multiple Libraries Created by Genetic Code Reprogramming To Discover Macrocyclic Peptides That Antagonize VEGFR2 Activity in Living Cells. ACS Chem. Biol. 2013, 8, 1205-14.
    https://doi.org/10.1021/cb300697h
  29. T. Ishizawa, T. Kawakami, P. C. Reid, H. Murakami*, TRAP display: a high-speed selection method for the generation of functional polypeptides. J. Am. Chem. Soc. 2013, 135, 5433-40.
    https://doi.org/10.1021/ja312579u
  30. T. Fujino, Y. Goto, H. Suga, H. Murakami*, Reevaluation of the D-Amino Acid Compatibility with the Elongation Event in Translation. J. Am. Chem. Soc. 2013, 135, 1830-7.
    https://doi.org/10.1021/ja309570x
  31. T. Kawakami, H. Murakami*, Genetically encoded libraries of nonstandard peptides. J. Nucleic Acids 2012, 2012, 713510. (Review article)
    https://doi.org/10.1155/2012/713510
    32. 　
  32. T. Kawakami, A. Ohta, M. Ohuchi, H. Ashigai, H. Murakami, H. Suga*, Diverse backbone-cyclized peptides via codon reprogramming. Nat. Chem. Biol. 2009, 5, 888-90.
    https://doi.org/10.1038/nchembio.259
  33. N. Niwa, Y. Yamagishi, H. Murakami, H. Suga*, A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. Bioorg. Med. Chem. Lett. 2009, 19, 3892-4.
    　https://doi.org/10.1016/j.bmcl.2009.03.114
  34. Y. Yamagishi, H. Ashigai, Y. Goto, H. Murakami, H. Suga*, Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction. Chembiochem 2009, 10, 1469-72.
    https://doi.org/10.1002/cbic.200900021
  35. E. Nakajima, Y. Goto, Y. Sako, H. Murakami, H. Suga*, Ribosomal Synthesis of Peptides with C-Terminal Lactams, Thiolactones, and Alkylamides. Chembiochem 2009, 10, 1186-92
    https://doi.org/10.1002/cbic.200900058
  36. H. Murakami.*, A. Ohta, H. Suga.*, Bases in the anticodon loop of tRNA(Ala)(GGC) prevent misreading. Nat. Struct. Mol. Biol. 2009, 16, 353-8.
    　https://doi.org/10.1038/nsmb.1580
  37. Y. Goto, K. Iwasaki, K. Torikai, H. Murakami, H. Suga.*, Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chem. Commun. 2009, 3419-21.
    　https://pubs.rsc.org/en/content/articlelanding/2009/cc/b904314d
  38. T. Kawakami, H. Murakami, H. Suga.*, Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem. Biol. 2008, 15, 32-42.
    　https://doi.org/10.1016/j.chembiol.2007.12.008
  39. T. Kawakami, H. Murakami, H. Suga.*, Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J. Am. Chem. Soc. 2008, 130, 16861-3.
    　https://pubs.acs.org/doi/10.1021/ja806998v
  40. A. Ohta, H. Murakami, H. Suga.*, Polymerization of alpha-hydroxy acids by ribosomes. ChemBioChem 2008, 9, 2773-8.
    　https://doi.org/10.1002/cbic.200800439
  41. H. Xiao, H. Murakami, H. Suga, A. R. Ferre-D'Amare.*, Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 2008, 454, 358-61.
    　https://doi.org/10.1038/nature07033
  42. Y. Goto, H. Murakami, H. Suga.*, Initiating translation with D-amino acids. RNA 2008, 14, 1390-8.
    　https://doi.org/10.1261/rna.1020708
    43. 　　
  43. Y. Sako, J. Morimoto, H. Murakami, H. Suga., Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions. J. Am. Chem. Soc. 2008, 130, 7232-4.
    　https://doi.org/10.1021/ja800953c
  44. Y. Sako, Y. Goto, H. Murakami, H. Suga.*, Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. ACS Chem. Biol. 2008, 3, 241-9.
    　https://doi.org/10.1021/cb800010p
  45. Y. Goto, A. Ohta, Y. Sako, Y. Yamagishi, H. Murakami, H. Suga.*, Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem. Biol. 2008, 3, 120-9.
    　https://doi.org/10.1021/cb700233t
  46. A. Ohta, H. Murakami, E. Higashimura, H. Suga.*, Synthesis of polyester by means of genetic code reprogramming. Chem. Biol. 2007, 14, 1315-22.
    　https://doi.org/10.1016/j.chembiol.2007.10.015
  47. M. Ohuchi, H. Murakami, H. Suga., The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr. Opin. Chem. Biol. 2007, 11, 537-542. (Review article)
    　https://doi.org/10.1016/j.cbpa.2007.08.011
  48. M. Taki.*, A. Kuno., S. Matoba., Y. Kobayashi., J. Futami., H. Murakami., H. Suga., K. Taira., T. Hasegawa., M. Sisido.*, Leucyl/Phenylalanyl-tRNA-Protein Transferase-Mediated Chemoenzymatic Coupling of N-Terminal Arg/Lys Units in Post-translationally Processed Proteins with Non-natural Amino Acids. ChemBioChem 2006, 7, 1676-1679.
    　https://doi.org/10.1002/cbic.200600181
  49. H. Murakami, A. Ohta, H. Ashigai, H. Suga.*, A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat. Methods 2006, 3, 357-9.
    　https://doi.org/10.1038/nmeth877
  50. D. Kourouklis, H. Murakami, H. Suga.*, Programmable ribozymes for mischarging tRNA with nonnatural amino acids and their applications to translation. Methods 2005, 36, 239-44.
    　https://doi.org/10.1016/j.ymeth.2005.04.001
  51. K. Ramaswamy, H. Saito, H. Murakami, K. Shiba, H. Suga.*, Designer ribozymes: programming the tRNA specificity into flexizyme. J. Am. Chem. Soc. 2004, 126, 11454-5.
    　https://doi.org/10.1021/ja046843y
  52. T. Hohsaka, N. Muranaka, C. Komiyama, K. Matsui, S. Takaura, R. Abe, H. Murakami, M. Sisido.*, Position-specific incorporation of dansylated non-natural amino acids into streptavidin by using a four-base codon. FEBS Lett. 2004, 560, 173-7.
    　https://doi.org/10.1016/s0014-5793(04)00099-7
  53. H. Murakami, D. Kourouklis, H. Suga.*, Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Chem. Biol. 2003, 10, 1077-84.
    　https://doi.org/10.1016/j.chembiol.2003.10.010
  54. H. Murakami, H. Saito, H. Suga.*, A versatile tRNA aminoacylation catalyst based on RNA. Chem. Biol. 2003, 10, 655-62.
    　https://doi.org/10.1016/s1074-5521(03)00145-5
  55. M. Taki.*, T. Hohsaka, H. Murakami, K. Taira, M. Sisido.*, Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/anticodon pairs. J. Am. Chem. Soc. 2002, 124, 14586-90.
    　https://doi.org/10.1021/ja017714+
  56. H. Murakami, N. J. Bonzagni, H. Suga.*, Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme. J. Am. Chem. Soc. 2002, 124, 6834-5.
    　https://doi.org/10.1021/ja025872a
  57. H. Murakami, T. Hohsaka, M. Sisido.*, Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat. Biotechnol. 2002, 20, 76-81.
    　https://doi.org/10.1038/nbt0102-76
  58. M. Taki, T. Hohsaka, H. Murakami, K. Taira, M. Sisido.*, A non-natural amino acid for efficient incorporation into proteins as a sensitive fluorescent probe. FEBS Lett. 2001, 507, 35-8.
    　https://doi.org/10.1016/s0014-5793(01)02935-0
  59. T. Hohsaka, Y. Ashizuka, H. Taira, H. Murakami, M. Sisido.*, 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.
    　https://doi.org/10.1021/bi0108204
  60. T. Hohsaka, Y. Ashizuka, H. Murakami, M. Sisido.*, Five-base codons for incorporation of nonnatural amino acids into proteins. Nucleic Acids Res. 2001, 29, 3646-51.
    　https://doi.org/10.1093/nar/29.17.3646
  61. H. Murakami, T. Hohsaka, Y. Ashizuka, K. Hashimoto, M. Sisido.*, Site-directed incorporation of fluorescent nonnatural amino acids into streptavidin for highly sensitive detection of biotin. Biomacromolecules 2000, 1, 118-25.
    　https://pubs.acs.org/doi/10.1021/bm990012g
  62. M. Taki, H. Murakami, M. Sisido.*, A chiral Eu3+-thienoyltrifluoroacetone complex on an avidin tetramer: luminescence and CD studies on the supramolecular protein-metal chelate complex. Chem. Commun. 2000, 1199-1200.
    　https://doi.org/10.1039/B001908I
  63. T. Hohsaka, D. Kajihara, Y. Ashizuka, H. Murakami, M. Sisido.*, Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems. J. Am. Chem. Soc. 1999, 121, 34-40.
    　https://pubs.acs.org/doi/10.1021/ja9813109
  64. T. Hohsaka, Y. Ashizuka, H. Sasaki, H. Murakami, M. Sisido.*, Incorporation of two different nonnatural amino acids independently into a single protein through extension of the genetic code. J. Am. Chem. Soc. 1999, 121, 12194-12195.
    　https://doi.org/10.1021/ja992204p.s001
  65. H. Murakami, T. Hohsaka, Y. Ashizuka, M. Sisido.*, 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. J. Am. Chem. Soc. 1998, 120, 7520-7529.
    　https://pubs.acs.org/doi/full/10.1021/ja971890u
  66. T. Hohsaka, Y. Ashizuka, H. Murakami, M. Sisido.*, Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression. J. Am. Chem. Soc. 1996, 118, 9778-9779.
    　https://pubs.acs.org/doi/10.1021/ja9614225