Nagoya University Department of Biomolecular Engineering, Graduate School of Engineering

PUBLICATIONS

  1. 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.
  2. 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.
  3. 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.
  4. 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 in press
  5. 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
  6. 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.
  7. Fujino, T.; Tozaki, M.; Murakami, H.*, An amino acid-swapped genetic code. ACS Synthetic Biology, 2020, 9(10), 2703 -13.
  8. Fujino, T.; Kondo, T.; Suga, H.; Murakami, H.*, Exploring the Minimal RNA Substrate of Flexizymes. Chembiochem, 2019, 20(15),1959-1965.
  9. Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method. Methods in Molecular Biology 2017, 1498, 339-347.
  10. 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.
  11. 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.
  12. Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method. Methods in Molecular Biology 2017, 1498, 339-347.
  13. 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)
  14. 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.
  15. Taniguchi, N; Nakayama, S; Kawakami, T.; Murakami, H.*, Patch cloning method for multiple site-directed and saturation mutagenesis. BMC Biotechnology 2013, 13:91.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Kawakami, T.; Murakami, H.*, Genetically encoded libraries of nonstandard peptides. Journal of Nucleic Acids 2012, 2012, 713510. (Review article)
  22. 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.
  23. 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.
  24. 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
  25. 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.
  26. 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.
  27. Goto, Y.; Iwasaki, K.; Torikai, K.; Murakami, H.; Suga, H.*, Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chemical Communications 2009, 3419-21.
  28. 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.
  29. 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.
  30. 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.
  31. Ohta, A.; Murakami, H.; Suga, H.*, Polymerization of alpha-hydroxy acids by ribosomes. Chembiochem 2008, 9, 2773-8.
  32. Kawakami, T.; Murakami, H.; Suga, H.*, Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. Journal of the American Chemical Society 2008, 130, 16861-3.
  33. 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.
  34. 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.
  35. Goto, Y.; Murakami, H.; Suga, H.*, Initiating translation with D-amino acids. RNA 2008, 14, 1390-8.
  36. 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)
  37. Ohta, A.; Murakami, H.; Higashimura, E.; Suga, H.*, Synthesis of polyester by means of genetic code reprogramming. Chemistry & Biology 2007, 14, 1315-22.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. Murakami, H.; Saito, H.; Suga, H.*, A versatile tRNA aminoacylation catalyst based on RNA. Chemistry & Biology 2003, 10, 655-62.
  43. Murakami, H.; Kourouklis, D.; Suga, H.*, Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Chemistry & Biology 2003, 10, 1077-84.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.