A5032503871- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced NMR Techniques and Applications
- Hemoglobin structure and function
- Ubiquitin and proteasome pathways
- Glycosylation and Glycoproteins Research
- RNA Research and Splicing
- Photoreceptor and optogenetics research
- Photosynthetic Processes and Mechanisms
- Mitochondrial Function and Pathology
- Spectroscopy and Quantum Chemical Studies
- Cancer, Hypoxia, and Metabolism
- Mass Spectrometry Techniques and Applications
- RNA and protein synthesis mechanisms
- Molecular spectroscopy and chirality
- Biochemical and Molecular Research
- Bacteriophages and microbial interactions
- DNA and Nucleic Acid Chemistry
- Amyotrophic Lateral Sclerosis Research
- RNA modifications and cancer
- Digital Media Forensic Detection
- ATP Synthase and ATPases Research
- Vector-borne infectious diseases
- Telecommunications and Broadcasting Technologies
- Crystallography and molecular interactions
Ritsumeikan University
2015-2024
Kyushu University
2024
Pharmaceutical Biotechnology (Czechia)
2016-2021
Kumamoto University
2021
Nagoya University
2016
Institute for Molecular Science
2016
Kyoto Prefectural University
2016
SPring-8
2006-2015
NTT (Japan)
2006-2011
The University of Tokyo
2007
Atomic detailed structural study of a transiently existing folding intermediate is severely limited because its short life. In ubiquitin, we found that pressure-stabilized equilibrium conformer shares common feature with the proline-trapped kinetic in pulse-labeling (1)H(2)H exchange NMR [Briggs, M. S. & Roder, H. (1992) Proc. Natl. Acad. Sci. USA 89, 2017-2021]. The locally unfolded entire segment from residues 33 to 42 and C-terminal 70-76. close identity an stabilized under pressure...
Although many proteins possess a distinct folded structure lying at minimum in funneled free energy landscape, thermal causes any protein to continuously access lowly populated excited states. The existence of states is an integral part biological function. transitions into the may lead misfolding and aggregation, little structural information currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species light. As acts...
Liquid–liquid phase separation (LLPS) of proteins and nucleic acids to form membraneless cellular compartments is considered be involved in various biological functions. The RNA-binding protein fused sarcoma (FUS) undergoes LLPS vivo vitro. Here, we investigated the effects pressure temperature on FUS by high-pressure microscopy UV/vis spectroscopy. phase-separated condensate was obliterated with increasing but observed again at a higher pressure. We generated pressure–temperature diagram...
Differentiating between devices of the same size is essential for ensuring their reliability. However, identifying subtle differences can be challenging, particularly when share similar characteristics, such as transistors on a wafer. To address this issue, we propose an indexing method current-voltage characteristics that assigns proximity numbers to devices. Specifically, demonstrate application locality-sensitive hashing (LSH) algorithm Coulomb blockade phenomena observed in PMOSFETs and...
A high-pressure 15N/1H two-dimensional NMR study has been carried out on folate-bound dihydrofolate reductase (DHFR) from Escherichia coli in the pressure range between 30 and 2000 bar. Several cross-peaks HSQC spectrum are split into two with increasing pressure, showing presence of a second conformer equilibrium first. Thermodynamic analysis temperature dependencies indicates that is characterized by smaller partial molar volume (ΔV = −25 mL/mol at 15 °C) enthalpy entropy values,...
We examined the effects of trimethylamine N-oxide (TMAO) and urea (known osmolytes) on liquid-liquid phase separation (LLPS) fused in sarcoma (FUS) three FUS-LLPS states: LLPS states at atmospheric pressure with low- high-salt concentrations a re-entrant state above 2 kbar. Temperature- pressure-scan turbidity measurements revealed that TMAO contributed to stabilizing destabilizing LLPS, respectively. These results can be attributed excluded volume effect (preferential hydration)...
High-pressure 15N/1H two-dimensional NMR spectroscopy has been utilized to study conformational fluctuation of a 76-residue protein ubiquitin at pH 4.5 20 degrees C. The on-line variable pressure cell technique is used in conjunction with high-field spectrometer operating 750 MHz for 1H the range between 30 and 3500 bar. Large, continuous reversible pressure-induced 15N chemical shifts were observed 68 backbone amide groups, including 7.52 ppm shift Val70 bar, indicating large-scale change...
Cold-induced conformational transition of ubiquitin was studied at pH 4.5 under a constant pressure 2 kbar using variable one-dimensional 1H and two-dimensional 15N/1H NMR spectroscopy as well IR spectroscopy. Although tendency for preferential stabilization peculiar locally disordered partially hydrated conformer I, identical with that previously found variable-pressure 0 degrees C, is recognized, the folded N to unfolded U occurs largely cooperatively decreasing temperature, reaching near...
Abstract Intracellular aggregation of fused in sarcoma (FUS) is associated with the pathogenesis familial amyotrophic lateral sclerosis (ALS). Under stress, FUS forms liquid droplets via liquid–liquid phase separation (LLPS). Two types wild-type LLPS exist equilibrium: low-pressure (LP-LLPS) and high-pressure (HP-LLPS); former dominates below 2 kbar latter over kbar. Although several disease-type variants have been identified, molecular mechanism underlying accelerated cytoplasmic granule...
Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) a well-studied model for ligand binding, L99A mutant T4 lysozyme. On increasing O2 concentration 8.9 mM, changes (1)H, (15)N, (13)C chemical shifts signal broadening were observed specifically backbone amide side chain methyl groups located around two hydrophobic protein. O2-induced longitudinal relaxation...
The ionization of internal groups in proteins can trigger conformational change. Despite this being the structural basis most biological energy transduction, these processes are poorly understood. Small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy experiments at ambient high hydrostatic pressure were used to examine how presence Lys-66, buried hydrophobic core a stabilized variant staphylococcal nuclease, affect conformation dynamics. NMR atmospheric showed...
It is becoming increasingly clear that proteins transiently populate high-energy excited states as a necessary requirement for function. Here, we demonstrate rational mutation based on the characteristics of structure and dynamics obtained from pressure experiments new strategy amplifying particular fluctuations in proteins. We have previously shown ubiquitin populates conformer, N2, at high pressures. show Q41N favors N2: high-pressure nuclear magnetic resonance (NMR) shows N2 ∼70%...
The RNA-binding protein fused in sarcoma (FUS) undergoes liquid–liquid phase separation (LLPS) both vivo and vitro. Self-assembled liquid droplets of FUS transform into reversible hydrogels more irreversible toxic aggregates. Although LLPS can be a precursor aggregates, generic method to study kinetics the formation has not been developed. Here, we demonstrated pressure-jump transition between 1-phase state FUS-LLPS states observed at low pressure (<2 kbar, LP-LLPS) high (>2 HP-LLPS) using...