A5103110430- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Protein Structure and Dynamics
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- Enzyme Structure and Function
- Photoreceptor and optogenetics research
- Metalloenzymes and iron-sulfur proteins
- Mass Spectrometry Techniques and Applications
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Spectroscopy and Quantum Chemical Studies
- Gene Regulatory Network Analysis
- Machine Learning in Bioinformatics
- Enzyme Catalysis and Immobilization
- Bacterial Genetics and Biotechnology
- Metabolism and Genetic Disorders
- Microbial Metabolic Engineering and Bioproduction
- ATP Synthase and ATPases Research
- Plant Molecular Biology Research
- Cancer therapeutics and mechanisms
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
Japan Tobacco (Japan)
2023
University of Hyogo
2011-2021
Hyogo University
2012-2019
University of Tsukuba
2005-2017
Japan Science and Technology Agency
2007-2013
Institute of Molecular Biology and Biophysics
2013
Applied Science Private University
2012
The University of Tokyo
1995-2010
Naval Research Laboratory Information Technology Division
2010
Gunma Industrial Technology Center
2008
High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure an enzyme with editing activity translation is presented here at 2.5 angstroms resolution. enzyme, isoleucyl–transfer RNA synthetase, activates not only cognate substrate l -isoleucine but also minimally distinct -valine first, aminoacylation step. Then, second, “editing” step, synthetase itself rapidly hydrolyzes valylated products. For this two-step...
The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses higher plants as well variety plant-specific reactions. They share DNA binding domain, designated the which contains an invariant WRKYGQK sequence CX4-5CX22-23HXH zinc motif. Herein, we report NMR solution structure C-terminal domain Arabidopsis thaliana WRKY4 protein. consists four-stranded beta-sheet, with pocket formed by conserved Cys/His residues located at one...
Abstract Mitochondrial cytochrome c oxidase (C O) transfers electrons from (Cyt. ) to O 2 generate H O, a process coupled proton pumping. To elucidate the mechanism of electron transfer, we determined structure mammalian Cyt. –C complex at 2.0‐Å resolution and identified an transfer pathway C O. The specific interaction between is stabilized by few electrostatic interactions side chains within small contact surface area. Between two proteins are three water layers with long inter‐molecular...
Abstract The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid–regulated transcription. Herein, we report the NMR solution structure of Arabidopsis thaliana cold-responsive factor RAV1. consists a seven-stranded open β-barrel two α-helices located at ends barrel significantly similar to noncatalytic restriction enzyme EcoRII. An titration experiment revealed recognition interface that enabled...
The peptide group connecting Tyr440 and Ser441 of the bovine cytochrome c oxidase is involved in a recently proposed proton-transfer path (H-path) where, at variance with other pathways (D- K-paths), usual hydrogen-bond network interrupted, thus making this proton propagation rather unconventional. Our density-functional based molecular dynamics simulations show that, despite anomaly provided that can reach nearby water, multistep pathway become viable for such reaction: A initially...
Aminoacyl-tRNA synthetases (aaRSs) are critical for the translational process, catalyzing attachment of specific amino acids to their cognate tRNAs. To ensure formation correct aminoacyl-tRNA, and thereby enhance reliability translation, several aaRSs have an editing capability that hinders misaminoacylated We investigated theoretically mechanism reaction a class I enzyme, leucyl-tRNA synthetase (LeuRS), complexed with tRNALeu, employing ab initio hybrid quantum mechanical/molecular...
By using finite temperature first principles molecular dynamics, the mechanism of enzymatic reaction ribozyme was investigated for both anionic and radical charge states modeled RNA fragment. In case system, a pseudorotation subsequent 3' → 2' migration occur in vacuum, rather than self-cleavage phosphodiester. On other hand, when either divalent metal ion (Mg2+) catalyst or continuous hydrogen bond network solvent is present, path species changes dramatically, going toward...
The role of metal cations (Mg2+) in the cleavage reaction fully hydrated RNA enzymes is investigated via Car−Parrinello calculations. We find that action two catalysts most efficient way to promote, on one hand, proton abstraction from O2'−H triggers nucleophilic attack and, other weakening and subsequent P−O5' bond. elimination shown lead an increase activation energy. Furthermore, we also OH- included coordination shell Mg2+ close O2' promotes initial prevents its transfer ribozyme both...
The production of useful quantities G protein-coupled receptors is a major problem not only for screening various drug compounds but also in performing structural biology studies. To solve this problem, we investigated the possibility using transgenic silkworms these receptors. Using human μ-opioid receptor gene, constructed three silkworm strains that produced expressed significant amounts fat body and silk gland. product was evaluated saturation ligand-binding assay. exhibited ligand...
Interactions between metal ions and π systems (metal-π interactions) are known to confer significant stabilization energy. However, in biological systems, few structures with metal-π coordination have been determined; thus, its roles must still be elucidated. The cation-π interactions not correctly described by current molecular mechanics even when using a polarizable force field, thus they require quantum mechanical calculations for accurate estimation. the huge computational costs of...
We have developed an innovative system, AI QM Docking Net (AQDnet), which utilizes the three-dimensional structure of protein-ligand complexes to predict binding affinity. This system is novel in two respects: first, it significantly expands training dataset by generating thousands diverse ligand configurations for each complex and subsequently determining energy configuration through quantum computation. Second, we devised a method that incorporates atom-centered symmetry function (ACSF),...
SATB1 is a transcriptional regulator controlling the gene expression that essential in maturation of immune T-cell. binds to nuclear matrix attachment regions DNA, where it recruits histone deacetylase and represses transcription through local chromatin remodeling. Here we determined solution structure region-binding domain, possessing similarity CUT DNA-binding human by NMR spectroscopy. The consists five α-helices, which N-terminal four are arranged similarly four-helix domain hepatocyte...
Electron-DNA anion collisions were studied using an electrostatic storage ring with a merging electron-beam technique. The rate of neutral particles emitted in started to increase from definite threshold energies, which increased regularly ion charges steps about 10 eV. These energies almost independent the length and sequence DNA, but depended strongly on charges. Neutral came breaks DNAs, rather than electron detachment. step energy approximately agreed plasmon excitation energy. It is...
DNA has recently attracted much attention in view of its possible applications to nano-devices. Despite extensive efforts, however, the experimental results electrical conductivity dry are still rather controversial. In this report, we indicate that a key issue interpret could be role counter metal cations, which expected alter electronic properties pure DNA. particular, although metallic cations passivated by hydration, some divalent anhydrous ones originating drying processes may exist and...
An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and molecular (MM) AMBER, has been developed for QM/MM hybrid calculations. A protein–DNA complex is used as test system to investigate the following two types of schemes. In 'subtractive' scheme, electrostatic interactions between regions are truncated in QM calculations; an 'additive' long-range within cut-off distance from introduced into one-electron integration terms Hamiltonian. these calculations, 338...