A5024566042- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Chemical Synthesis and Analysis
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Peptidase Inhibition and Analysis
- Glycosylation and Glycoproteins Research
- Advanced biosensing and bioanalysis techniques
- Monoclonal and Polyclonal Antibodies Research
- Liver physiology and pathology
- Viral gastroenteritis research and epidemiology
- Ubiquitin and proteasome pathways
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- Carbohydrate Chemistry and Synthesis
- TGF-β signaling in diseases
- Lipid metabolism and biosynthesis
- Lipid Membrane Structure and Behavior
- Neuropeptides and Animal Physiology
- Microbial Natural Products and Biosynthesis
- Protein Degradation and Inhibitors
- Click Chemistry and Applications
- Machine Learning in Bioinformatics
Tokyo Institute of Technology
2023-2025
Life Science Institute
2023-2025
Institute of Science Tokyo
2025
The University of Tokyo
2013-2024
ETH Zurich
2017-2021
Board of the Swiss Federal Institutes of Technology
2018
Tokyo University of Science
2014-2015
Bunkyo University
2014
Revolution in an RNA-packaging capsid Artificial nucleocapsid proteins, which could be analogous to those used by viruses package their genomes, are a promising way protect and deliver RNAs. Using escalating challenge nucleases, Tetter et al. evolved protein that forms multimeric, spherical cages into highly efficient selectively packages its own encoding RNA. Cryo–electron microscopy of the final design intermediates revealed stepwise expansion size, enabled destabilizing amino acid...
Bioengineering of ribosomally synthesized and post-translationally modified peptides (RiPPs) is an emerging approach to explore the diversity pseudo-natural product structures for drug discovery purposes. However, despite initial advances in this area, bioactivity reprogramming multienzyme RiPP biosynthetic pathways remains a major challenge. Here, we report platform de novo functional thiopeptides based on reengineered biosynthesis lactazole A, natural assembled by five enzymes. The...
Abstract γ-Amino acids can play important roles in the biological activities of natural products; however, ribosomal incorporation γ-amino into peptides is challenging. Here we report how a selection campaign employing non-canonical peptide library containing cyclic γ 2,4 -amino resulted discovery very potent inhibitors SARS-CoV-2 main protease (M pro ). Two kinds acids, cis -3-aminocyclobutane carboxylic acid (γ 1 ) and (1 R ,3 S )-3-aminocyclopentane 2 ), were ribosomally introduced...
Significance Viruses consist of a protective proteinaceous shell that packages DNA or RNA genome. The critical step in the evolution primitive viruses was presumably emergence protein cages could load, protect, and transfer their own genetic information. Here, we show nonviral cage formed by Aquifex aeolicus lumazine synthase its encoding mRNA can be engineered evolved into virus-like nucleocapsids. optimized proteins specifically recognize designed motifs on cognate mRNAs, these tags also...
Abstract Due to their constrained conformations, cyclic β2,3-amino acids (cβAA) are key building blocks that can fold peptides into compact and rigid structures, improving peptidase resistance binding affinity target proteins, due conformations. Although the translation efficiency of cβAAs is generally low, our engineered tRNA, referred as tRNAPro1E2, enabled efficient incorporation peptide libraries using flexible in vitro (FIT) system. Here we report on design application a macrocyclic...
Macrocyclic peptides make up a unique class of modalities known for their high affinity, specificity, and ability to modulate protein–protein interactions, including receptor activation. Messenger RNA display, the Random Nonstandard Peptides Integrated Discovery (RaPID) system, stands out in identifying target-specific macrocyclic peptides, producing potent binders with low subnanomolar dissociation constants against diverse targets. It has often been discussed that this success is partly...
Abstract N-Terminal modification of peptides and proteins with long chain fatty acids (LCFAs) plays important roles in their cellular bioactivity localization. Such modifications are generally carried out by specific enzymes post-translation manners, thereby an alteration the N-terminal modifying groups requires either engineering or unusual intrinsic promiscuity. Here we report a versatile method using approach vitro ribosomal synthesis containing various at N-terminus. We charged Gly on...
Protein cages have recently emerged as an important platform for nanotechnology development. Of the naturally existing protein cages, viruses are among most efficient nanomachines, overcoming various barriers to achieve component replication and self-assembly in complex biological milieu. We designed artificial system that can carry out basic steps of viral particle assembly vivo. Our strategy is based on patchwork capsids formed from Aquifex aeolicus lumazine synthase a circularly permuted...
Glycosylation of proteins profoundly impacts their physical and biological properties. Yet our ability to engineer novel glycoprotein structures remains limited. Established bacterial glycoengineering platforms require secretion the acceptor protein periplasmic space preassembly oligosaccharide substrate as a lipid-linked precursor, limiting access glycan substrates respectively. Here, we circumvent these bottlenecks by developing facile platform that operates in cytoplasm. The Glycoli...
Aminoacylation of tRNA is an essential event in the translation system. Although modern system protein enzymes play sole role aminoacylation, primitive RNA molecules could have catalysed aminoacylation onto or tRNA-like molecules. Even though such so far are not identified from known organisms, vitro selection has generated catalysts a pool random sequences. Among them, set sequences, referred to as flexizymes (Fxs), discovered our laboratory able charge amino acids tRNAs. Significantly, Fxs...
Lasso-grafting (LG) technology is a method for generating de novo biologics (neobiologics) by genetically implanting macrocyclic peptide pharmacophores, which are selected in vitro against protein of interest, into loops arbitrary scaffolds. In this study, we have generated neo-capsid that potently binds the hepatocyte growth factor receptor MET LG anti-MET pharmacophores circularly permuted variant Aquifex aeolicus lumazine synthase (AaLS), self-assembling nanocapsule. By virtue displaying...
Receptor tyrosine kinases (RTKs) are generally activated through their dimerization and/or oligomerization induced by cognate ligands, and one such RTK hepatocyte growth factor (HGF) receptor, known as MET, plays an important role in tissue regeneration. Here we show the development of ubiquitin (Ub)-based protein ligand multimers, referred to U-bodies, which act surrogate agonists for MET derived from MET-binding macrocyclic peptides. Monomeric Ub constructs (U-body) were first generated...
Abstract Flexizymes are a family of aminoacylation ribozymes devised by in vitro selection our research group. They charge wide variety nonproteinogenic amino acids onto virtually any kind tRNAs, enabling us to reprogram the genetic code custom-made cell-free translation system. This reprogramming method was integrated with mRNA display method, which not only expresses nonstandard peptides such as macrocyclic but also selects ligands specifically binding target proteins. system is referred...
In the hypothetical RNA world, ribozymes could have acted as modern aminoacyl-tRNA synthetases (ARSs) to charge tRNAs, thus giving rise peptide synthesis along with evolution of a primitive translation apparatus. We previously reported T-boxzyme, Tx2.1, which selectively charges initiator tRNA N-biotinyl-phenylalanine (BioPhe) in situ Flexible In-vitro Translation (FIT) system produce BioPhe-initiating peptides. Here, we performed vitro selection elongation-capable T-boxzymes (elT-boxzymes),...
RNA aptamers are structured motifs that bind to specific molecules. A growing number of RNAs bearing aptamer elements, whose functions modulated by direct binding metabolites, have been found in living cells. Recent studies suggested more small metabolites likely exist and may be involved diverse cellular processes. However, conventional methods not necessarily suitable for the discovery such elements with lengths ranging from 50 200 nucleotides, due far abundant tRNAs this size range. Here,...
Fast and selective recognition of molecules at the nanometer scale without labeling is a much desired but still challenging goal to achieve. Here, we show use high-speed atomic force microscopy (HS-AFM) for real-time real-space unlabeled membrane receptors using tips conjugated with small synthetic macrocyclic peptides. The single-molecule method validated by experiments on human hepatocyte growth factor receptor (hMET), which selectively binds peptide aMD4. By testing comparing aMD4...
Abstract Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme lacking affinity nucleic acids into an artificial nucleocapsid efficiently packages and protects multiple copies its own encoding mRNA. Revealing remarkable convergence on molecular hallmarks natural viruses, accompanying changes reorganized protein...