Nonnatural Amino Acid Technology Team _Publication List

Nonnatural Amino Acid Technology Team

Incorporation of a Doubly Functionalized Synthetic Amino Acid into Proteins for Creating Chemical and Light-Induced Conjugates

Yamaguchi A, Matsuda T, Ohtake K, Yanagisawa T, Yokoyama S, Fujiwara Y, Watanabe T, Hohsaka T, Sakamoto K
Bioconjug Chem, 27(1), 198-206 (2016).

Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon

Mukai T, Hoshi H, Ohtake K, Takahashi M, Yamaguchi A, Hayashi A, Yokoyama S, Sakamoto K.
Sci Rep, 5, 9699 (2015).

Protein stabilization utilizing a redefined codon.

Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N, Haruki M, Kohashi S, Yamagishi K, Murayama K, Tomabechi Y, Itagaki T, Akasaka R, Kawazoe M, Takemoto C, Shirouzu M, Yokoyama S, Sakamoto K.
Sci Rep, 5, 9762 (2015).

Tetrameric interaction of the ectoenzyme CD38 on the cell surface enables its catalytic and raft-association activities.

Hara-Yokoyama M, Kukimoto-Niino M, Terasawa K, Harumiya S, Podyma-Inoue KA, Hino N, Sakamoto K, Itoh S, Hashii N, Hiruta Y, Kawasaki N, Mishima-Tsumagari C, Kaitsu Y, Matsumoto T, Wakiyama M, Shirouzu M, Kasama T, Takayanagi H, Utsunomiya-Tate N, Takatsu K, Katada T, Hirabayashi Y, Yokoyama S, Yanagishita M.
Structure, 20(9), 1585-1595 (2012).

Structural basis of interleukin-5 dimer recognition by its α receptor.

Kusano S, Kukimoto-Niino M, Hino N, Ohsawa N, Ikutani M, Takaki S, Sakamoto K, Hara-Yokoyama M, Shirouzu M, Takatsu K, Yokoyama S.
Protein Sci, 21(6), 850-864 (2012).

Wide-range protein photo-crosslinking achieved by a genetically encoded N^ε-(benzyloxycarbonyl)lysine derivative with a diazirinyl moiety.

Yanagisawa T, Hino N, Iraha F, Mukai T, Sakamoto K, Yokoyama S.
Mol Biosyst, 8(4), 1131-1135 (2012).

Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding.

Kusano S, Kukimoto-Niino M, Hino N, Ohsawa N, Okuda K, Sakamoto K, Shirouzu M, Shindo T, Yokoyama S.
Protein Sci, 21(2), 199-210 (2012).

Site-specific incorporation of unnatural amino acids into proteins in mammalian cells.

Hino N, Sakamoto K, Yokoyama S.
Methods Mol Biol, 794, 215-28 (2012).

Genetic-code evolution for protein synthesis with non-natural amino acids.

Mukai T, Yanagisawa T, Ohtake K, Wakamori M, Adachi J, Hino N, Sato A, Kobayashi T, Hayashi A, Shirouzu M, Umehara T, Yokoyama S, Sakamoto K.
Biochem Biophys Res Commun, 411(4), 757-761 (2011).

Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells.

Hino N, Oyama M, Sato A, Mukai T, Iraha F, Hayashi A, Kozuka-Hata H, Yamamoto T, Yokoyama S, Sakamoto K.
J Mol Biol, 406(2), 343-353 (2011).

Site-specific incorporation of 4-iodo-L-phenylalanine through opal suppression.

Kodama K, Nakayama H, Sakamoto K, Fukuzawa S, Kigawa T, Yabuki T, Kitabatake M, Takio K, Yokoyama S.
J Biochem, 148(2), 179-187 (2010).

Genetic encoding of non-natural amino acids in Drosophila melanogaster Schneider 2 cells.

Mukai T, Wakiyama M, Sakamoto K, Yokoyama S.
Protein Sci, 19(3), 440-448 (2010).

Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.

Sakamoto K, Murayama K, Oki K, Iraha F, Kato-Murayama M, Takahashi M, Ohtake K, Kobayashi T, Kuramitsu S, Shirouzu M, Yokoyama S.
Structure, 17(3), 335-344 (2009).

Recognition of non-alpha-amino substrates by pyrrolysyl-tRNA synthetase.

Kobayashi T, Yanagisawa T, Sakamoto K, Yokoyama S.
J Mol Biol, 385(5), 1352-1360 (2009).

Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.

Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S.
Chem Biol, 15(11), 1187-1197 (2008).

Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases.

Mukai T, Kobayashi T, Hino N, Yanagisawa T, Sakamoto K, Yokoyama S.
Biochem Biophys Res Commun, 371(4), 818-822 (2008).

Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.

Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S.
J Mol Biol, 378(3), 634-652 (2008).

Site-specific functionalization of proteins by organopalladium reactions.

Kodama K, Fukuzawa S, Nakayama H, Sakamoto K, Kigawa T, Yabuki T, Matsuda N, Shirouzu M, Takio K, Yokoyama S, Tachibana K.
Chembiochem, 8(2), 232-238 (2007).

A new protein engineering approach combining chemistry and biology, part I; site-specific incorporation of 4-iodo-L-phenylalanine in vitro by using misacylated suppressor tRNAPhe.

Kodama K, Fukuzawa S, Sakamoto K, Nakayama H, Kigawa T, Yabuki T, Matsuda N, Shirouzu M, Takio K, Tachibana K, Yokoyama S.
Chembiochem, 7(10), 1577-1581 (2006).

Cation−π Interaction in the Polyolefin Cyclization Cascade Uncovered by Incorporating Unnatural Amino Acids into the Catalytic Sites of Squalene Cyclase

Morikubo N, Fukuda Y, Ohtake K, Shinya N, Kiga D, Sakamoto K, Asanuma M, Hirota H, Yokoyama S, Hoshino T.
J Am Chem Soc, 128(40), 13184–13194 (2006).

Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli.

Chumpolkulwong N, Sakamoto K, Hayashi A, Iraha F, Shinya N, Matsuda N, Kiga D, Urushibata A, Shirouzu M, Oki K, Kigawa T, Yokoyama S.
J Struct Funct Genomics, 7(1), 31-36 (2006).

DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing.

Komiya K, Sakamoto K, Kameda A, Yamamoto M, Ohuchi A, Kiga D, Yokoyama S, Hagiya M.
Biosystems, 83(1), 18-25 (2006).

Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry.

Kodama K, Fukuzawa S, Nakayama H, Kigawa T, Sakamoto K, Yabuki T, Matsuda N, Shirouzu M, Takio K, Tachibana K, Yokoyama S.
Chembiochem, 7(1), 134-139 (2006).

Development of an in vivo computer based on Escherichia coli

Nakagawa H, Sakamoto K, Sakakibara Y.
Proceedings of DNA11: the 11th International Workshop on DNA based computers (London, Ontario, Canada),, 68-77 (2005).

Hairpin-based state machine and conformational addressing: Design and experiment

Kameda K, Yamamoto M, Uejima H, Hagiya M, Sakamoto K, Ohuchi A.
Nat Comput, 4(2), 103-126 (2005).

Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.

Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S.
J Mol Biol, 346(1), 105-117 (2005).

Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.

Kobayashi T, Sakamoto K, Takimura T, Sekine R, Kelly VP, Kamata K, Nishimura S, Yokoyama S.
Proc Natl Acad Sci U S A, 102(5), 1366-1371 (2005).

Toward “Wet” Implementation of Genetic Algorithm for Protein Engineering

Sakamoto K, Yamamura M, Someya H.
Lecture Note in Computer Science, 3384, 308-318 (2005).

The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG.

Sakamoto K, Ishimaru S, Kobayashi T, Walker JR, Yokoyama S.
J Bacteriol, 186(17), 5899-5905 (2004).

Conformational Addressing Using the Hairpin Structure of Single-Strand DNA

Kameda A, Yamamoto M, Uejima H, Hagiya M, Sakamoto K, Ohuchi A.
Lecture Notes in Computer Science, 2943, 219-224 (2004).

Branching DNA machines based on transitions of hairpin structures

Kubota M, Ohtake K, Komiya K, Sakamoto K, Hagiya M.
Proceedings of the 2003 Congress on Evolutionary Computation (CEC'03), 4, 2542-2548 (2003).

Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.

Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S.
Nat Struct Biol, 10(6), 425-432 (2003).

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system.

Kiga D, Sakamoto K, Kodama K, Kigawa T, Matsuda T, Yabuki T, Shirouzu M, Harada Y, Nakayama H, Takio K, Hasegawa Y, Endo Y, Hirao I, Yokoyama S.
Proc Natl Acad Sci U S A, 99(15), 9715-9720 (2002).

Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases.

Kitabatake M, Ali K, Demain A, Sakamoto K, Yokoyama S, Söll D.
J Biol Chem, 277(26), 23882-23887 (2002).

Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.

Kitamura A, Muto Y, Watanabe S, Kim I, Ito T, Nishiya Y, Sakamoto K, Ohtsuki T, Kawai G, Watanabe K, Hosono K, Takaku H, Katoh E, Yamazaki T, Inoue T, Yokoyama S.
RNA, 8(4), 440-451 (2002).

Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase.

Kiga D, Sakamoto K, Sato S, Hirao I, Yokoyama S.
Eur J Biochem, 268(23), 6207-6213 (2001).

Successive state transitions with I/O interface by molecules

Komiya K, Sakamoto K, Gouzu H, Yokoyama S, Arita M, Nishikawa A, Hagiya M.
Lecture Notes in Computer Science, 2054, 17-26 (2001).

Synthesis of N-labeled peptidyl AMP.

Narita H, Moriguchi T, Seio K, Sekine M, Miyaguchi H, Sakamoto K, Yokoyama S.
Nucleosides Nucleotides Nucleic Acids, 19(10-12), 1993-2003 (2000).

Molecular Computation by DNA Hairpin Formation

Sakamoto K, Gouzu H, Komiya K, Kiga D, Yokoyama S, Yokomori T, Hagiya M.
Science, 288(5469), 1223-1226 (2000).

Improving sequence design for DNA computing

Arita M, Nisikawa A, Hagiya M, Komiya K, Gouzu H, Sakamoto K.
in Proceedings of Genetic and Evolutionary Computation Conference 2000,, 875-890 (2000).

State transitions by molecules.

Sakamoto K, Kiga D, Komiya K, Gouzu H, Yokoyama S, Ikeda S, Sugiyama H, Hagiya M.
Biosystems, 52(1-3), 82-91 (1999).

Towards parallel evaluation and learning of Boolean µ-formulas with molecules

Hagiya, M., Arita, M., Kiga, D., Sakamoto, K., Yokoyama, S.
DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 48, 57-72 (1999).

RNA aptamers that specifically bind to the Ras-binding domain of Raf-1.

Kimoto M, Sakamoto K, Shirouzu M, Hirao I, Yokoyama S.
FEBS Lett, 441(2), 322-326 (1998).

An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition.

Kiga D, Futamura Y, Sakamoto K, Yokoyama S.
Nucleic Acids Res, 26(7), 1755-1760 (1998).

Chemical Synthesis and Properties of Conformationally Fixed Diuridine Monophosphates as Building Blocks of the RNA Turn Motif

Seio K, Wada T, Sakamoto K, Yokoyama S, Sekine M.
J Org Chem, 63(5), 1429-1443 (1998).

Cleavage effect of oligoribonucleotides substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides.

Hosono K, Gozu H, Hosaka H, Sakamoto K, Yokoyama S, Takai K, Takaku H.
Biochim Biophys Acta, 1354(3), 211-218 (1997).

Study on site specific cleavage of RNA.

Shirakura H, Hosono K, Kawai G, Takai K, Ohtsuki T, Watanabe K, Sakamoto K, Yokoyama S, Takaku H.
Nucleic Acids Symp Ser, 37, 217-218 (1997).

Synthesis and Properties of Conformationally Rigid Cyclouridylic Acids Having Covalent Bonding Linkers Between the Uracil 5-Position and the 5′-Phosphate Group

Seio K, Kurasawa O, Wada T, Sakamoto K, Yokoyama S, Sekine, M.
Nuclosides Nucleotides, 16(7-9), 1023-1032 (1997).

An antibiotic-binding motif of an RNA fragment derived from the A-site-related region of Escherichia coli 16S rRNA.

Miyaguchi H, Narita H, Sakamoto K, Yokoyama S.
Nucleic Acids Res, 24(19), 3700-3706 (1996).

NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA₄^Arg.

Sakamoto K, Kawai G, Watanabe S, Niimi T, Hayashi N, Muto Y, Watanabe K, Satoh T, Sekine M, Yokoyama S.
Biochemistry, 35(21), 6533-6538 (1996).

Major identity determinants in the "augmented D helix" of tRNA^Glu from Escherichia coli.

Sekine S, Nureki O, Sakamoto K, Niimi T, Tateno M, Go M, Kohno T, Brisson A, Lapointe J, Yokoyama S.
J Mol Biol, 256(4), 685-700 (1996).

Properties of RNAs containing modified bases at cleavage sites

Gozu H, Hosono K, Hosaka H, Sakamoto K, Yokoyama S, Takai K, Takaku H.
Nucleic Acids Symposium Series, 35, 201-202 (1996).

Sequence-specific cleavage of oligoribonucleotide capable of forming a stem and loop structure.

Hosaka H, Sakabe I, Sakamoto K, Yokoyama S, Takaku H.
J Biol Chem, 269(31), 20090-20094 (1994).

Characterization of the secondary structure of an oligonucleotide corresponding to the autocleavage site of a precursor RNA from bacteriophage T4.

Hosaka H, Sakabe I, Sakamoto K, Niimi T, Yokoyama S, Takaku H.
Biochim Biophys Acta, 1218(3), 351-356 (1994).

Chemical Synthesis and Properties of an Interresidually Cyclized Uridylyl(3'-5')uridine as a model of tRNA U-Turn Structure Having a Sharp Bend

Sekine M, Seio K, Wada T, Sakamoto K, Yokoyama S.
J Am Chem Soc, 116(10), 4469-4470 (1994).

Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides.

Hatta T, Kim SG, Nakashima H, Yamamoto N, Sakamoto K, Yokoyama S, Takaku H.
FEBS Lett, 330(2), 161-164 (1993).

A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene product, from Escherichia coli.

Sakamoto K, Kawai G, Niimi T, Satoh T, Sekine M, Yamaizumi Z, Nishimura S, Miyazawa T, Yokoyama S.
Eur J Biochem, 216(2), 369-375 (1993).

Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases.

Nureki O, Kohno T, Sakamoto K, Miyazawa T, Yokoyama S.
J Biol Chem, 268(21), 15368-15373 (1993).

Synthesis of Uridylyl (3′-5′) Uridine Derivatives Containing 5-(Methylamino-Methyl) Uridine as A Modified Nucleoside Found from E. COLI Minor tRNA^Arg

Sekine M, Seio K, Satoh T, Sakamoto K, Yokoyama S.
Nuclosides Nucleotides, 12(3-4), 305-321 (1993).

Cleavage reaction of a synthetic oligoribonucleotide corresponding to the autocleavage site of a precursor RNA from bacteriophage T4.

Hosaka H, Ogawa T, Sakamoto K, Yokoyama S, Takaku H.
FEBS Lett, 293(1-2), 204-206 (1991).

Nonnatural Amino Acid Technology Team

Properties of RNAs containing modified bases at cleavage sites

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