K. Sakamoto

发表

Biologically-implemented genetic algorithm for protein engineering

Masayuki Yamamura, Hiroshi Someya, Kensaku Sakamoto, 2009, GECCO.

M. Hagiya, S. Yokoyama, K. Sakamoto, 1999, Bio Systems.

Branching DNA machines based on transitions of hairpin structures

Masami Hagiya, Ken Komiya, Kensaku Sakamoto, 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

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

M. Sekine, S. Yokoyama, K. Sakamoto, 1993, European journal of biochemistry.

Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.

S. Yokoyama, K. Sakamoto, E. Seki, 2019, Cell chemical biology.

Innovative Technology for Recombinant Protein Production Using Engineered E. coli Genetic Codes

K. Sakamoto, 2016 .

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

S. Yokoyama, K. Sakamoto, T. Yanagisawa, 2009, Journal of molecular biology.

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

O. Nureki, S. Yokoyama, K. Sakamoto, 1993, The Journal of biological chemistry.

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

C. Hon, T. Umehara, B. Kaczkowski, 2017, bioRxiv.

The two-domain architecture of LAMP2A regulates its interaction with Hsc70.

S. Yokoyama, K. Sakamoto, T. Watabe, 2021, Experimental cell research.

Direct homophilic interaction of LAMP2A with the two-domain architecture revealed by site-directed photo-crosslinks and steric hindrances in mammalian cells

S. Yokoyama, K. Sakamoto, J. Guan, 2021, Autophagy.

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

S. Yokoyama, K. Sakamoto, T. Mukai, 2008, Biochemical and biophysical research communications.

Incorporation of Halogenated Amino Acids into Antibody Fragments at Multiple Specific Sites Enhances Antigen Binding

K. Sakamoto, Takuhiro Ito, Akiko Hayashi, 2020, Chembiochem : a European journal of chemical biology.

Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits

S. Yokoyama, K. Sakamoto, T. Terada, 2016, Scientific Reports.

Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid.

T. Umehara, S. Yokoyama, K. Sakamoto, 2011, Biochemistry.

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

S. Yokoyama, K. Sakamoto, T. Mukai, 2010, Protein science : a publication of the Protein Society.

Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase.

S. Yokoyama, K. Sakamoto, E. Seki, 2020, ACS synthetic biology.

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

S. Yokoyama, K. Sakamoto, H. Takaku, 1993, FEBS letters.

Dissecting Cell Signaling Pathways with Genetically Encoded 3‐Iodo‐L‐tyrosine

K. Sakamoto, M. Shirouzu, Akiko Hayashi, 2011, Chembiochem : a European journal of chemical biology.

Site-speci ® c incorporation of an unnatural amino acid into proteins in mammalian cells

Kazuki Saito, S. Yokoyama, K. Sakamoto, 2022 .

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

S. Yokoyama, K. Sakamoto, T. Mukai, 2012, Molecular bioSystems.

Site‐Specific Functionalization of Proteins by Organopalladium Reactions

T. Kigawa, S. Yokoyama, K. Sakamoto, 2006, Chembiochem : a European journal of chemical biology.

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

Ryohei Ishii, Shigeyuki Yokoyama, Kensaku Sakamoto, 2008, Chemistry & biology.

Synthetic Tyrosine tRNA Molecules with Noncanonical Secondary Structures

K. Sakamoto, Akiko Hayashi, 2018, International journal of molecular sciences.

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

S. Yokoyama, K. Sakamoto, H. Takaku, 1997, Biochimica et biophysica acta.

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

Daisuke Kiga, Yoko Harada, Takanori Kigawa, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Pyrrolysyl-tRNA Synthetase with a Unique Architecture Enhances the Availability of Lysine Derivatives in Synthetic Genetic Codes

A. Yamaguchi, K. Sakamoto, Kazumasa Ohtake, 2018, Molecules.

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein

Masaki Yamamoto, Shigeyuki Yokoyama, Thirumananseri Kumarevel, 2010, Nature.

Covalently Capturing Protein Interactions in Living Cells by Site-Specific Incorporation of Photo-Cross-Linkable Amino Acids

K. Sakamoto, Nobumasa Hino, 2017 .

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

A. Yamaguchi, S. Yokoyama, K. Sakamoto, 2015, Scientific Reports.

Codon reassignment in the Escherichia coli genetic code

Shigeyuki Yokoyama, Fumie Iraha, Kensaku Sakamoto, 2010, Nucleic acids research.

Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid

S. Yokoyama, K. Sakamoto, Akiko Hayashi, 2005, Nature Methods.

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

M. Oyama, S. Yokoyama, K. Sakamoto, 2011, Journal of molecular biology.

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

S. Yokoyama, K. Sakamoto, H. Takaku, 1994, Biochimica et biophysica acta.

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

D Kiga, S. Yokoyama, K. Sakamoto, 1998, Nucleic acids research.

Synthesis and properties of conformationally rigid cyclouridylic acid having a covalent bonding linker between the uracil 5-position and the 5′-phosphate group

M. Sekine, S. Yokoyama, K. Sakamoto, 1995 .

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

S. Yokoyama, K. Sakamoto, K. Seio, 1997 .

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

T. Kigawa, S. Yokoyama, K. Sakamoto, 2010, Journal of biochemistry.

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

M. Sekine, S. Yokoyama, K. Sakamoto, 1993 .

A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis

Mikako Shirouzu, Kensaku Sakamoto, K. Sakamoto, 2017, Journal of biochemistry.

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

K. Sakamoto, H. Takaku, S. Yokoyama, 1991, FEBS letters.

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

M. Sekine, S. Yokoyama, K. Sakamoto, 1998 .

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 tRNA(Arg)4.

M. Sekine, S. Yokoyama, K. Sakamoto, 1996, Biochemistry.

Relation between functions and conformational characteristics of modified nucleosides found in tRNAs.

S. Yokoyama, K. Sakamoto, G. Kawai, 1991, Nucleic acids symposium series.

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

Shigeyuki Yokoyama, Osamu Nureki, Ryuichiro Ishitani, 2003, Nature Structural Biology.

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

T. Katada, S. Yokoyama, H. Takayanagi, 2012, Structure.

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

S. Yokoyama, K. Sakamoto, R. Fukunaga, 2008, Journal of molecular biology.

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

S. Yokoyama, K. Sakamoto, S. Ishimaru, 2004, Journal of bacteriology.

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

Shigeyuki Yokoyama, Ryo Sekine, Kensaku Sakamoto, 2005, Journal of molecular biology.

Expanded Genetic Code Technologies for Incorporating Modified Lysine at Multiple Sites

T. Umehara, S. Yokoyama, K. Sakamoto, 2014, Chembiochem : a European journal of chemical biology.

Functional replacement of the endogenous tyrosyl-tRNA synthetase–tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion

S. Yokoyama, K. Sakamoto, S. Ohno, 2010, Nucleic acids research.

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

S. Yokoyama, K. Sakamoto, M. Shirouzu, 2009, Structure.

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

S. Yokoyama, K. Sakamoto, D. Kiga, 2002, Nucleic acids research.

An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes

Kam Y. J. Zhang, Kouhei Tsumoto, Satoru Nagatoishi, 2021, Briefings Bioinform..

Structural basis of interleukin‐5 dimer recognition by its α receptor

S. Yokoyama, K. Sakamoto, M. Shirouzu, 2012, Protein science : a publication of the Protein Society.

Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli

Atsushi Yamaguchi, Shigeyuki Yokoyama, Satoshi Kira, 2015, Nucleic acids research.

Efficient Decoding of the UAG Triplet as a Full-Fledged Sense Codon Enhances the Growth of a prfA-Deficient Strain of Escherichia coli

Shigeyuki Yokoyama, Nobumasa Hino, Kensaku Sakamoto, 2012, Journal of bacteriology.

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

S. Yokoyama, K. Sakamoto, D. Kiga, 2001, European journal of biochemistry.

Translation of ‘rare’ Codons in a Cell-free Protein Synthesis System from Escherichia coli

T. Kigawa, S. Yokoyama, K. Sakamoto, 2006, Journal of Structural and Functional Genomics.

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

S. Yokoyama, K. Sakamoto, M. Shirouzu, 2012, Protein science : a publication of the Protein Society.

Adenovirus vector-based incorporation of a photo-cross-linkable amino acid into proteins in human primary cells and cancerous cell lines

Takeshi Tomonaga, Kenji Ishimoto, Hiroyuki Mizuguchi, 2016, Scientific Reports.

Crystal structure of eukaryotic translation initiation factor 2B

T. Umehara, S. Yokoyama, K. Sakamoto, 2016, Nature.

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

S. Yokoyama, K. Sakamoto, M. Shirouzu, 1998, FEBS letters.

Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code

Shigeyuki Yokoyama, Nobumasa Hino, Kensaku Sakamoto, 2006, Nature Protocols.

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

S. Yokoyama, K. Sakamoto, H. Miyaguchi, 1996, Nucleic acids research.

Indolmycin Resistance of Streptomyces coelicolor A3(2) by Induced Expression of One of Its Two Tryptophanyl-tRNA Synthetases*

D. Söll, S. Yokoyama, K. Sakamoto, 2002, The Journal of Biological Chemistry.

Cation-pi interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase.

S. Yokoyama, K. Sakamoto, D. Kiga, 2006, Journal of the American Chemical Society.

Multiple Site‐Specific Installations of Nε‐Monomethyl‐L‐Lysine into Histone Proteins by Cell‐Based and Cell‐Free Protein Synthesis

T. Umehara, S. Yokoyama, K. Sakamoto, 2014, Chembiochem : a European journal of chemical biology.

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation

T. Umehara, S. Yokoyama, K. Sakamoto, 2015, Scientific Reports.

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation

T. Umehara, S. Yokoyama, K. Sakamoto, 2015, Scientific Reports.

Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog

S. Yokoyama, K. Sakamoto, K. Oki, 2008, Proceedings of the National Academy of Sciences.

Synthesis Of N-Labeled Peptidyl AMP

M. Sekine, S. Yokoyama, K. Sakamoto, 2000, Nucleosides, Nucleotides & Nucleic Acids.

Ubiquitin acetylation inhibits polyubiquitin chain elongation

J. Kanno, T. Ohta, K. Sakamoto, 2015, EMBO reports.

Engineering an Automaturing Transglutaminase with Enhanced Thermostability by Genetic Code Expansion with Two Codon Reassignments.

K. Sakamoto, T. Mukai, K. Yokoyama, 2018, ACS synthetic biology.

Protein stabilization utilizing a redefined codon

A. Yamaguchi, S. Yokoyama, K. Sakamoto, 2015, Scientific Reports.

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

T. Umehara, S. Yokoyama, K. Sakamoto, 2011, Biochemical and biophysical research communications.

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

S. Yokoyama, K. Sakamoto, R. Sekine, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Site-specific Incorporation of 3-Iodo-L-tyrosine into Proteins and Single-wavelength Anomalous Dispersion Phasing with Soft X-ray in Protein Crystallography

K. Sakamoto, K. Murayama, 2009 .

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

Gota Kawai, Satoru Watanabe, Shigeyuki Yokoyama, 2002, RNA.

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

Masami Hagiya, Masanori Arita, Kensaku Sakamoto, 1997, DNA Based Computers.

An expanded genetic code facilitates antibody chemical conjugation involving the lambda light chain.

S. Yokoyama, K. Sakamoto, Akifumi Kato, 2021, Biochemical and biophysical research communications.

Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids

S. Yokoyama, K. Sakamoto, Y. Fujii, 2023, International journal of molecular sciences.

Engineering of Escherichia coli β-lactamase TEM-1 variants showing higher activity under acidic conditions than at the neutral pH.

K. Sakamoto, Mihoko Takahashi, 2018, Biochemical and biophysical research communications.

Regioselective Carbon–Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry

T. Kigawa, S. Yokoyama, K. Sakamoto, 2006, Chembiochem : a European journal of chemical biology.

Molecular computation by DNA hairpin formation.

K Sakamoto, H Gouzu, K Komiya, 2000, Science.

Regioselective Carbon–Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry

T. Kigawa, S. Yokoyama, K. Sakamoto, 2006, Chembiochem : a European journal of chemical biology.

Cell-Free Protein Synthesis Using S30 Extracts from Escherichia coli RFzero Strains for Efficient Incorporation of Non-Natural Amino Acids into Proteins

S. Yokoyama, K. Sakamoto, T. Terada, 2019, International journal of molecular sciences.

Genetic Code Expansion: Another Solution to Codon Assignments

K. Sakamoto, 2022, International journal of molecular sciences.

Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes.

S. Yokoyama, K. Sakamoto, Akifumi Kato, 2017, Bioconjugate chemistry.

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

Takayoshi Watanabe, Shigeyuki Yokoyama, Yoshihisa Fujiwara, 2016, Bioconjugate chemistry.

Variants of the industrially relevant protease KP-43 with suppressed activity under alkaline conditions developed using expanded genetic codes

A. Yamaguchi, K. Sakamoto, Tatsuya Osamura, 2018, Biochemistry and biophysics reports.

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

O. Nureki, S. Yokoyama, K. Sakamoto, 1996, Journal of molecular biology.

Genetic Code Expansion of the Silkworm Bombyx mori to Functionalize Silk Fiber.

K. Sakamoto, Takuhiro Ito, Hidetoshi Teramoto, 2018, ACS synthetic biology.

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

S. Yokoyama, K. Sakamoto, T. Mukai, 2010, Protein science : a publication of the Protein Society.

Complexity analysis of the SAT engine: DNA algorithms as probabilistic algorithms

Masami Hagiya, John A. Rose, Kensaku Sakamoto, 2002, Theor. Comput. Sci..

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

Masahito Yamamoto, Azuma Ohuchi, Masami Hagiya, 2005, Natural Computing.

Conformational Addressing Using the Hairpin Structure of Single-Strand DNA

Masahito Yamamoto, Azuma Ohuchi, Masami Hagiya, 2003, DNA.

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

S. Yokoyama, K. Sakamoto, R. Fukunaga, 2008, Journal of molecular biology.

Crystal structure of eukaryotic translation initiation factor 2B

T. Umehara, S. Yokoyama, K. Sakamoto, 2016, Nature.

Synthetic Tyrosine tRNA Molecules with Noncanonical Secondary Structures

K. Sakamoto, Akiko Hayashi, 2018, International journal of molecular sciences.

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

S. Yokoyama, K. Sakamoto, Nobumasa Hino, 2012, Methods in molecular biology.