Yusuke Azuma

ORCID: 0000-0003-3543-3159
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About
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Research Areas
  • Bacteriophages and microbial interactions
  • Monoclonal and Polyclonal Antibodies Research
  • Glycosylation and Glycoproteins Research
  • RNA and protein synthesis mechanisms
  • Biochemical and Structural Characterization
  • Advanced biosensing and bioanalysis techniques
  • Atomic and Subatomic Physics Research
  • RNA Interference and Gene Delivery
  • Peptidase Inhibition and Analysis
  • Lipid Membrane Structure and Behavior
  • X-ray Diffraction in Crystallography
  • Advanced NMR Techniques and Applications
  • Enzyme Structure and Function
  • Biochemical and Molecular Research
  • Antimicrobial Peptides and Activities
  • Ubiquitin and proteasome pathways
  • Magnetic and transport properties of perovskites and related materials
  • Advanced Polymer Synthesis and Characterization
  • Advanced Electron Microscopy Techniques and Applications
  • Solid-state spectroscopy and crystallography
  • Advanced MRI Techniques and Applications
  • Ferroelectric and Piezoelectric Materials
  • Magnetic Field Sensors Techniques
  • Plant tissue culture and regeneration
  • Inorganic Chemistry and Materials

Jagiellonian University
2020-2025

ETH Zurich
2015-2023

Kyoto Bunkyo University
2009-2018

Kyoto University
2009-2018

Board of the Swiss Federal Institutes of Technology
2018

Kyoto University Institute for Chemical Research
2009-2018

Suzuka University of Medical Science
2010

Chiba University
2010

Gunma University
2010

Health Sciences University of Hokkaido
2010

Abstract Genetic fusion of cargo proteins to a positively supercharged variant green fluorescent protein enables their quantitative encapsulation by engineered lumazine synthase capsids possessing negatively charged lumenal surface. This simple tagging system provides robust and versatile means creating hierarchically ordered assemblies for use as nanoreactors. The generality the strategy its effect on enzyme function were investigated with eight structurally mechanistically distinct catalysts.

10.1002/anie.201508414 article EN Angewandte Chemie International Edition 2015-12-23

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...

10.1073/pnas.1800527115 article EN Proceedings of the National Academy of Sciences 2018-05-07

Iron-bearing self-folding polymers were created with amphiphilic random copolymers as active, versatile, and recyclable polymer-supported catalysts for living radical polymerization (LRP). The key is to build bis(imino)pyridine ligand cavities iron complexes linking units within polymers. Self-folding polymer ligands are synthesized by the intramolecular imine cross-linking of self-folded bearing hydrophilic poly(ethylene glycol) (PEG), hydrophobic dodecyl, urea/aniline pendants...

10.1021/acsmacrolett.7b00498 article EN ACS Macro Letters 2017-07-20

Compartmentalization of proteases enables spatially and temporally controlled protein degradation in cells. Here we show that an engineered lumazine synthase cage, which possesses a negatively supercharged lumen, can exploit electrostatic effects to sort substrates for encapsulated protease. This proteasome-like nanoreactor preferentially cleaves positively charged polypeptides over both anionic zwitterionic substrates, inverting the inherent substrate specificity guest enzyme approximately...

10.1021/jacs.7b11210 article EN publisher-specific-oa Journal of the American Chemical Society 2017-12-26

Abstract We present our results of a radio frequency (RF) imaging method in which microwave pulse errors the field view do not directly result deterioration quantitative accuracy amplitude detected RF by utilizing multifrequency resonance. The is transferred to diamond nitrogen-vacancy (NV) center electron spin states, are read out as light emission from NV centers using wide-field microscope at high throughput an image with pixel size (1.65 μm) 2 . Importantly, simplifies setup required for...

10.35848/1347-4065/adaecb article EN Japanese Journal of Applied Physics 2025-01-27

Degradation during production and delivery is a significant bottleneck in developing biomolecular therapies. Here, we show that encapsulation protein cages formed by engineered variants of cage-forming lumazine synthase establishes an effective route for microbial isolation otherwise difficult-to-express, degradation-prone polypeptides. In this system, genetic fusion to cage component protomer ensures efficient guest packaging while being produced host bacterial cells. Meanwhile, the...

10.1101/2025.02.04.636450 preprint EN cc-by-nd bioRxiv (Cold Spring Harbor Laboratory) 2025-02-08

Hollow proteinaceous particles are useful nanometric containers for delivery and catalysis. Understanding the molecular mechanisms geometrical theory behind polymorphic protein assemblies provides a basis designing ones with desired morphology. As such, we found that circularly permuted variant of cage-forming enzyme, Aquifex aeolicus lumazine synthase, cpAaLS, assembles into variety hollow spherical cylindrical structures in response to changes ionic strength. Cryogenic electron microscopy...

10.1021/acsnano.4c16192 article EN cc-by ACS Nano 2025-02-24

Self-assembling protein cages are useful as nanoscale molecular containers for diverse applications in biotechnology and medicine. To expand the utility of such systems, there is considerable interest customizing structures natural cage-forming proteins designing new ones. Here we report that a circularly permuted variant lumazine synthase, enzyme from Aquifex aeolicus (AaLS) affords versatile building blocks construction nanocompartments can be easily produced, tailored, diversified. The...

10.1021/jacs.7b10513 article EN Journal of the American Chemical Society 2017-12-19

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...

10.1021/jacs.7b10798 article EN Journal of the American Chemical Society 2017-12-26

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...

10.1038/s41467-019-13283-2 article EN cc-by Nature Communications 2019-11-27

Abstract Endocytosis is an important route for the intracellular delivery of biomacromolecules, wherein their inefficient endosomal escape into cytosol remains a major barrier. Based on understanding that membranes are negatively charged, we focused potential cationic lytic peptides developing endosomolysis agents to release such entrapped molecules. As such, venom peptide, Mastoparan X, was employed and redesigned serve as tool. Appending tri‐glutamate unit N‐terminus attenuates...

10.1002/anie.201807534 article EN Angewandte Chemie International Edition 2018-08-13

Protein cages that readily encapsulate active enzymes of interest present useful nanotools for delivery and catalysis, wherein those with programmable disassembly characteristics serve as particularly attractive platforms. Here, a general guest packaging system based on an artificial protein cage, TRAP-cage, the which can be induced by addition reducing agents, is established. In this system, TRAP-cage SpyCatcher moieties in lumen prepared using genetic modification building block assembled...

10.1002/smll.202312286 article EN cc-by-nc Small 2024-05-13

The temperature-dependent Nb K-edge absorption spectra of several mixed-ion Pb-containing perovskite compounds were analysed to determine the displacement and trace its changes through phase transitions. Both extended x-ray fine structure (EXAFS) pre-edge region involved in analysis. results show that, studied, occupies an off-centre position with symmetry lower than that implied by macroscopic symmetry. magnitude direction do not display any noticeable temperature change are affected Nb–O...

10.1088/0953-8984/15/14/317 article EN Journal of Physics Condensed Matter 2003-03-31

Imine-functionalized reversible microgel star polymers were synthesized by dynamic covalent cross-linking of hydrogen-bonding block copolymer micelles in organic media. This approach allows the precision and wide range control molecular weight (Mw = 100–10 000 K; Mw/Mn ∼1.1) via preforming copolymers. For this, a urea aniline-functionalized methacrylate (ApUMA) was newly designed as key monomer. The methyl (MMA) ApUMA, prepared ruthenium-catalyzed living radical polymerization, efficiently...

10.1021/acs.macromol.6b02403 article EN Macromolecules 2017-01-04

Two pairs to win: of iminodiacetic acid (Ida) moieties were incorporated in the leucine zipper segment GCN4-bZIP protein such a way that Ida each pair i and i+2 positions. Complex formation groups with CoII led destabilization helical structure thus enabled reversible switching binding target AP-1 site (see picture).

10.1002/anie.200902888 article EN Angewandte Chemie International Edition 2009-08-04

Abstract Proteine, die genetisch mit einer super‐positiv geladenen Variante des grün fluoreszierenden Proteins verbunden wurden, können quantitativ in ein Lumazin‐Synthase‐Kapsid geladen werden, das negativ Innenfläche ausgestattet ist. Dieses einfache System ist eine ebenso robuste wie vielseitige Methode, um hierarchisch geordnete Proteinkomplexe herzustellen, dann als Nanoreaktoren verwendet werden können. Die allgemeine Anwendbarkeit dieser Beladungsstrategie und ihre Auswirkung auf...

10.1002/ange.201508414 article DE Angewandte Chemie 2015-12-23

10.1007/978-1-4939-7893-9_4 article EN Methods in molecular biology 2018-01-01

Hand in Hand: Zwei Paare von Iminodiessigsäure(Ida)-Einheiten wurden das Leucin-Zippersegment des GCN4-bZIP-Proteins so eingebaut, dass sich die Ida-Einheiten eines jeden Paars an den Positionen i und i+2 befanden. Komplexbildung zwischen Ida-Gruppen CoII bewirkte eine Destabilisierung der helicalen Struktur, was ein reversibles Schalten Bindung Proteins Zielposition AP-1 ermöglichte (siehe Bild). Detailed facts of importance to specialist readers are published as ”Supporting Information”....

10.1002/ange.200902888 article EN Angewandte Chemie 2009-08-04

Local structure of ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{TiO}}_{3}$ with $x=0--0.75$ has been studied using x-ray-absorption fine-structure spectra, measured at the Ba K edge room temperature. The dependence mean-square relative displacements and third cumulant Ba-O Ba-Ti distribution functions on Sr concentration have analyzed. results show that off-center displacement vanishes abruptly $x=0.3,$ which is boundary point between tetragonal cubic phases, whereas Ti...

10.1103/physrevb.62.2969 article EN Physical review. B, Condensed matter 2000-08-01

Temperature dependence of the Nb displacement relative to center oxygen octahedron in NaNbO3 has been studied by polarized K XAFS. Spectra were measured at two orientations a single crystalline sample. Room temperature EXAFS data are good agreement with earlier X-ray diffraction data: antiferroelectric displacements found be orthogonal b axis. Analysis dependent didn't reveal any abrupt changes Nb-O distances phase transition points. In all high-temperature paraelectric phases appeared...

10.1107/s0909049500018069 article EN Journal of Synchrotron Radiation 2001-03-01
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