Team Leader
Kensaku Sakamoto Ph.D.

Laboratory for Nonnatural Amino Acid Technology

[Closed Mar. 2023]

E-mailkensaku.sakamoto[at]riken.jp

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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 Fri Mar 11 00:00:00 JST 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 Fri Nov 05 00:00:00 JST 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 Wed Apr 14 00:00:00 JST 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 Tue Jan 05 00:00:00 JST 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 Fri Apr 17 00:00:00 JST 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 Sun Dec 01 00:00:00 JST 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 Thu Jul 18 00:00:00 JST 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 Sat Dec 01 00:00:00 JST 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 Thu Nov 01 00:00:00 JST 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 Mon Oct 01 00:00:00 JST 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 Wed Sep 26 00:00:00 JST 2018 doi: 10.3390/molecules23102460

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