BDR researchers coming from diverse research fields are working together to achieve higher goals.

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Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

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Careers & Study

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About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

坂本 健作チームリーダーの写真

Team Leader
Kensaku Sakamoto Ph.D.

Laboratory for Nonnatural Amino Acid Technology

[Closed Mar. 2023]


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Engineered genetic codesunleashes the potential of biosystems.

What is Synthetic biology?
Proteins useful for life-science studies and medical applications can be synthesized in living cells programmed with the blueprint for the proteins. The cells engineered to utilize novel amino acids in proteins will facilitate the addition of artificial marks onto proteins, and also the synthesis of proteins linked to pharmaceuticals. These cells will help to realize new structures and functions of proteins. We also exploit this platform technology to provide unique, technical supports for drug discovery.

Synthetic biology for creating novel molecular diversity

Collaborations with Structural Biology
Synthetic Biology should work together with Structural Biology, to develop novel proteins and enzymes based on structural knowledge. Not only for engineering, has such collaboration proved useful for elucidating structural basis for the functions of proteins, receptors, and enzymes.

tertiary structure of a stabilized enzyme and the local structure around a bromotyrosine

Novel protein stabilization mechanism: Proteins can structurally be stabilized by incorporating non-natural amino acids (bromotyrosines in this case) into them. The left panel shows the tertiary structure of a stabilized enzyme, which was revealed by X-ray crystallography. The right panel shows the local structure around a bromotyrosine included in the whole structure at the left. This amino acids is snugly located between two lysine residues, thereby contributing to the enhanced stability of the enzyme. The other incorporated bromotyrosines also contribute to the stability in similar manners.

Research Theme

  • Engineering the genetic code in living cells
  • Developing novel proteins with non-natural amino acids
  • Technology development to engineer antibodies useful as biologics

Selected Publications

Wada A, Umeki Y, Annoura T, Saito-Nakano Y.
In Vitro and In Vivo Antiamebic Activity of Iron-Targeting Polypyridine Compounds against Enteric Protozoan Parasite Entamoeba histolytica.
ACS Infectious Diseases 8(3), 457-462 (2022) doi: 10.1021/acsinfecdis.1c00418

Padhi AK, Kumar A, Haruna KI, et al.
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes.
Briefings in Bioinformatics 22(6), bbab338 (2021) doi: 10.1093/bib/bbab338

Terasawa K, Kato Y, Ikami Y, et al.
Direct homophilic interaction of LAMP2A with the two-domain architecture revealed by site-directed photo-crosslinks and steric hindrances in mammalian cells.
Autophagy (2021) doi: 10.1080/15548627.2021.1911017

Hayashi A, Haruna KI, Sato H, et al.
Incorporation of Halogenated Amino Acids into Antibody Fragments at Multiple Specific Sites Enhances Antigen Binding.
Chembiochem 22(1), 120-123 (2021) doi: 10.1002/cbic.202000429

Seki E, Yanagisawa T, Kuratani M, et al.
Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase.
Acs Synthetic Biology 9(4), 718-732 (2020) doi: 10.1021/acssynbio.9b00288

Sakamoto K, Hayashi A.
Synthetic tyrosine tRNA molecules with noncanonical secondary structures.
International Journal of Molecular Sciences 20(1), 92 (2019) doi: 10.3390/ijms20010092

Yanagisawa T, Kuratani M, Seki E, et al.
Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
Cell chemical biology 26(7), 936-949 (2019) doi: 10.1016/j.chembiol.2019.03.008

Teramoto H, Amano Y, Iraha F, et al.
Genetic code expansion of the silkworm Bombyx mori to functionalize silk fiber.
ACS Synthetic Biology 7, 801-806 (2018) doi: 10.1021/acssynbio.7b00437

Ohtake K, Mukai T, Iraha F, et al.
Engineering an automaturing transglutaminase with enhanced thermostability by genetic code expansion with two codon reassignments.
ACS Synthetic Biology 7, 2170-2176 (2018) doi: 10.1021/acssynbio.8b00157

Handoko L, Kaczkowski B, Hon C-C, et al.
JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics 13, 410-431 (2018) doi: 10.1080/15592294.2018.1469891

Yamaguchi A, Iraha F, Ohtake K, Sakamoto K.
Pyrrolysyl-tRNA Synthetase with a Unique Architecture Enhances the Availability of Lysine Derivatives in Synthetic Genetic Codes.
Molecules (Basel, Switzerland) 23(10), E2460 (2018) doi: 10.3390/molecules23102460


Photo of team leader, Kensaku Sakamoto

Team LeaderKensaku Sakamoto

  • kensaku.sakamoto[at]riken.jp
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Deputy Team LeaderMotoaki Wakiyama

  • motoaki.wakiyama@riken.jp

Senior Research ScientistAkira Wada

  • awada[at]riken.jp

Senior Technical ScientistAkiko Matsumoto (Hayash)

  • akiko.matsumoto[at]riken.jp

Research ScientistKazumasa Ohtake

  • kazumasa.ohtake[at]riken.jp

Technical ScientistMihoko Takahashi

  • mihoko.takahashi[at]riken.jp

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