A5004774267- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Hemoglobin structure and function
- Biotin and Related Studies
- Microbial Metabolic Engineering and Bioproduction
- Cellular Mechanics and Interactions
- Glycosylation and Glycoproteins Research
- Computational Drug Discovery Methods
- vaccines and immunoinformatics approaches
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Biochemical and Molecular Research
- Advanced Proteomics Techniques and Applications
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Amino Acid Enzymes and Metabolism
- RNA modifications and cancer
- Metabolism and Genetic Disorders
- Metabolomics and Mass Spectrometry Studies
- Vibration Control and Rheological Fluids
- Porphyrin Metabolism and Disorders
Nagoya University
2016-2025
University of California, Berkeley
2022
Institute for Molecular Science
2022
Osaka University
2006-2022
Tokyo University of the Arts
2022
Kyoto University
2022
Nagahama Institute of Bio-Science and Technology
2020
Maebashi Institute of Technology
2011-2013
Japan Science and Technology Agency
2008-2011
SPring-8
2010
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number entries has almost tripled (120 to 340). In addition increase quantity, quality been significantly improved. The new incorporates interactions IDPs their binding partners more...
The differences between disulfide‐bonding cystine (Cys_SS) and free cysteine (Cys_SH) residues were examined by analyzing the statistical distribution of both types residue in proteins known structure. Surprisingly, Cys_SH display stronger hydrophobicity than Cys_SS residues. A detailed survey atoms which come into contact with sulfhydryl group (sulfur atom) revealed those are essentially same number variety as methyl isoleucine, but quite different to hydroxyl serine. Moreover,...
IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators regions, interaction regions to other molecules, post-translational modification sites, references structural domain assignments. In particular, explicitly describes protean segments that can be transformed from state an...
The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and filamentous F-form, which drive organelle transport cell motility. This mechanical work is driven by ATPase activity at catalytic site in F-form. For deeper understanding of cellular functions, reaction mechanism must be elucidated. Here, we show that a single molecule trapped F-form fragmin domain-1 binding present their crystal structures ATP analog-, ADP-Pi-, ADP-bound forms, 1.15-Å...
The actin capping protein (CP) tightly binds to the barbed end of filaments, thus playing a key role in actin-based lamellipodial dynamics. V-1 and CARMIL proteins directly bind CP inhibit filament activity CP. completely inhibits from interacting with end, whereas act on end-bound facilitate its dissociation (called uncapping activity). Previous studies have revealed striking functional differences between two regulators. However, molecular mechanisms describing how these remains poorly...
Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information understanding the related protein functions. We gathered 839 pairs of ligand-free ligand-bound states from monomeric or homo-dimeric proteins, constructed Structural Change DataBase (PSCDB). In database, we focused on whether...
A subset of the proteome is prone to aggregate formation, which prevented by chaperones in cell. To investigate whether basic principle underlying aggregation process common prokaryotes and eukaryotes, we conducted a large-scale analysis ~500 cytosolic budding yeast proteins using chaperone-free reconstituted translation system, compared obtained data with that ~3,000 Escherichia coli reported previously. Although physicochemical properties affecting propensity were generally similar E....
Protein-protein interactions are fundamental for all biological phenomena, and protein-protein interaction networks provide a global view of the interactions. The hub proteins, with many partners, play vital roles in networks. We investigated subcellular localizations proteins human network, found that ones localized multiple compartments, especially nucleus/cytoplasm (NCP), cytoplasm/cell membrane (CMP), nucleus/cytoplasm/cell (NCMP), tend to be hubs. Examinations keywords suggested among...
Cepharanthine (CEP) is a natural biscoclaurine alkaloid of plant origin and was recently demonstrated to have anti‐severe acute respiratory syndrome coronavirus 2 (anti‐SARS‐CoV‐2) activity. In this study, we evaluated whether analogues CEP may act as potential anti‐coronavirus disease 2019 drugs. A total 24 compounds resembling were extracted from the KNApSAcK database, their binding affinities target proteins, including spike protein main protease SARS‐CoV‐2, NPC1 TPC2 in humans, predicted...
A set of 16 kinds dinucleotide compositions was used to analyze the protein-encoding nucleotide sequences in nine complete genomes: Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Mycoplasma genitalium, pneumoniae, Synechocystis sp., Methanococcus jannaschii, Archaeoglobus fulgidus, and Saccharomyces cerevisiae. The composition significantly different between organisms. distribution genes from an organism clustered around its center space. closely related organisms such as...
To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) the miniprotein Trp-cage on computational grid. Within trajectories, 58 folding and 31 unfolding events were identified subjected to extensive comparison classification. Based an analogy with biological sequences, trajectories (arrays sequential snapshots structures) aligned by dynamic programming allowing gaps. A phylogenetic tree derived from alignments revealed four...
Histone H3 methylation at lysine 9 (H3K9) is a conserved epigenetic signal, mediating heterochromatin formation by trimethylation, and transcriptional silencing dimethylation. Defective GLP (Ehmt1) G9a (Ehmt2) histone methyltransferases, involved in mono dimethylation of H3K9, confer autistic phenotypes behavioral abnormalities animal models. Moreover, EHMT1 loss function results Kleefstra syndrome, characterized severe intellectual disability, developmental delays psychiatric disorders. We...
The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID-19) caused by novel SARS-CoV-2 a pandemic. There is, however, no confirmed anti-COVID-19 therapeutic currently. In order to assist structure-based discovery efforts for repurposing drugs against this disease, we constructed knowledge-based models of proteins and compared ligand molecules in template structures with approved/experimental components natural medicines. Our theoretical suggest several drugs,...
AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against DB and discovered an uncharacterized P-loop NTPase family. The the family was surprisingly novel, showing atypical topology for NTPases, noticeable twofold symmetry, two pairs independent putative active sites. Our findings show that structural is powerful approach to identifying undiscovered families.
Hamiltonian systems often reveal the chaotic phenomena with long time memory, and then average of a dynamical variable does not seem to converge toward certain constant monotonically. Even when looks like in limit under given initial condition, for many cases limiting value depends sensitively on data. Chaos system is usually discussed framework ergodic theory which guarantees weak law large number unique existence except measure zero set. However, hamiltonian chaos seems be difficult...
Transferases and hydrolases catalyze different chemical reactions express dynamic responses upon ligand binding. To insulate the molecule from surrounding water, transferases bury it inside protein by closing cleft, while undergo a small conformational change leave exposed to solvent. Despite these distinct ligand-binding modes, some are homologous. clarify how such catalytic modes possible with same scaffold, we examined solvent accessibility of molecules for 15 SCOP superfamilies, each...
Active-site residues are not often optimized for conformational stability (activity−stability trade-offs) in proteins from organisms that grow at moderate temperature. It is unknown if the activity−stability trade-offs can be applied to hyperthermophiles. Because enzymatic activity usually increases higher temperature and hyperthermophilic need high stability, they might sacrifice their activity. This study attempts clarify contribution of active-site a protein. We therefore examined...
Abstract The solute carrier 27A ( SLC27A ) gene family encodes fatty acid transport proteins (FATPs) and includes 6 members. During fetal postnatal periods of development, the growing brain requires a reliable supply acids. Because autism spectrum disorders (ASD) are now recognized as caused by impaired early it is possible that functional abnormalities genes may contribute to pathogenesis ASD. Here, we confirmed expression SLC27A3 SLC27A4 in human neural stem cells derived from induced...
Liquid-liquid phase separation (LLPS) within the cell can form biological condensates, which are increasingly recognized to play important roles in various processes. Most proteins involved LLPS known be intrinsically disordered containing regions (IDRs) with low complexity (LCRs). The driving were selected from databases of LLPS-related and then classified into three classes according components condensates. Through silico analyses, we found that homo class, those induce without partner...
In order to elucidate the mechanism of thermostability proteins from hyperthermophiles, X-ray crystalline structures pyrrolidone carboxyl peptidase a hyperthermophile, Pyrococcus furiosus (PfPCP), and its mutant protein with Ser substituted at Cys142 Cys188 were determined 2.2 2.7 A resolution, respectively. The obtained compared those previously reported for peptidases hyperthermophilie, Thermococcus litoralis (TlPCP), mesophile, Bacillus amyloliquefaciens (BaPCP). PfPCP structure is...