A5051946629- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Mitochondrial Function and Pathology
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Amoebic Infections and Treatments
- ATP Synthase and ATPases Research
- Antibiotic Resistance in Bacteria
- Nuclear Structure and Function
- Pediatric Hepatobiliary Diseases and Treatments
- Hemoglobin structure and function
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Metabolism and Genetic Disorders
- Cell death mechanisms and regulation
- Autophagy in Disease and Therapy
- Parasitic Infections and Diagnostics
- Craniofacial Disorders and Treatments
- Cleft Lip and Palate Research
- Trace Elements in Health
- Fish Biology and Ecology Studies
- Endoplasmic Reticulum Stress and Disease
- Advanced Proteomics Techniques and Applications
- Lipid Membrane Structure and Behavior
National Institute of Advanced Industrial Science and Technology
2015-2024
Shizuoka Cancer Center
2021
Center For Reconstructive Urethral Surgery
2019
Osaka City General Hospital
2019
Keio University
2019
Creative Commons
2019
Kyoto first Red Cross hospital
2017
Italian Association for Cancer Research
2016
Japan Society for the Promotion of Science
2010-2012
Nagoya University
2003-2008
Mitochondria provide numerous essential functions for cells and their dysfunction leads to a variety of diseases. Thus, obtaining complete mitochondrial proteome should be crucial step toward understanding the roles mitochondria. Many proteins have been identified experimentally but list is not yet available. To fill this gap, methods computationally predict from amino acid sequence developed are widely used, unfortunately, accuracy far perfect. Here we describe MitoFates, an improved...
Mitochondria fulfill central functions in cellular energetics, metabolism, and signaling. The outer membrane translocator complex (the TOM complex) imports most mitochondrial proteins, but its architecture is unknown. Using a cross-linking approach, we mapped the active down to single amino acid residues, revealing different transport paths for preproteins through Tom40 channel. An N-terminal segment of passes from cytosol channel recruit chaperones intermembrane space that guide transfer...
We present the results for CAPRI Round 30, first joint CASP-CAPRI experiment, which brought together experts from protein structure prediction and protein-protein docking communities. The comprised 25 targets amongst those submitted CASP11 experiment of 2014. included mostly homodimers, a few homotetramers, two heterodimers, chains that could readily be modeled using templates Protein Data Bank. On average 24 groups 7 CASP predictions each target, 12 per target participated in scoring...
Vast numbers of proteins are transported into and out the nuclei by approximately 20 species importin-β family nucleocytoplasmic transport receptors. However, significance multiple parallel pathways that receptors constitute is poorly understood because only limited cargo have been reported. Here, we identified specific to 12 human import with a high-throughput method employs stable isotope labeling amino acids in cell culture, an vitro reconstituted system, quantitative mass spectrometry....
A predictive software system, SOSUI-GramN, was developed for assessing the subcellular localization of proteins in Gramnegative bacteria.The system does not require sequence homology data any known sequences; instead, it uses only physicochemical parameters N-and C-terminal signal sequences, and total sequence.The precision prediction to extracellular, outer membrane, periplasm, inner membrane cytoplasmic medium 92.3%, 89.4%, 86.4%, 97.5% 93.5%, respectively, 000with corresponding recall...
Breaking signals of secondary structure put strong limitations on the tertiary structures proteins. In addition to proline and glycine clusters, which are well-known breakers, clusters amphiphilic residues were found be a novel type breaker. These breakers depend specific environmental factors. Such conditions included average hydrophobicity, helical periodicity, density serine threonine residues, presence tryptophan tyrosine clusters. Principal component analysis factors was conducted in...
The classical nuclear export signal (NES), also known as the leucine-rich NES, is a protein localization often involved in important processes such transduction and cell cycle regulation. Although 15 years has passed since its discovery, limited structural information high sequence diversity have hampered understanding of NES. Several consensus sequences been proposed to describe it, but they suffer from poor predictive power. On other hand, NetNES server provides only computational method...
Apoptotic cell death is a defining and ubiquitous characteristic of metazoans, but its evolutionary origins are unclear. Although Caenorhabditis Drosophila played key roles in establishing the molecular bases apoptosis, it now clear that pathways these animals do not reflect ancestral characteristics. Conversely, recent work suggests apoptotic networks cnidarians may be complex vertebrate-like, hence characterization complement representatives basal cnidarian class Anthozoa will help us to...
Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses formulated explain this diversity. To resolve any contradiction, estimating primitive state and clarifying changes from that necessary. Here, we present more likely models of translocases, specifically translocase outer membrane (TOM)...
Abstract Gibberellin (GA) is a major hormone for plant growth and development. GA response derived from the degradation of DELLA repressor proteins after GA-dependent complex formation GID1 receptor with DELLA. Genistein known tyrosine (Tyr) kinase inhibitor inhibits degradation. However, biological role Tyr phosphorylation on remains unclear. Here, we demonstrate that GARU (GA RING E3 ubiquitin ligase) mediates ubiquitin-dependent GID1, TAGK2 Tyr-kinase target genistein GARU–GID1A...
The human importin-β family consists of 21 nucleocytoplasmic transport carrier proteins that carry and RNAs across the nuclear envelope through pores in specific directions. These carriers are responsible for thousands proteins, but cargo allocation each carrier, which is necessary information if one wishes to understand physiological context transport, poorly characterized. To address this issue, we developed a high-throughput method identify cargoes by applying stable isotope labeling...
Abstract Background The outer membranes of mitochondria are thought to be homologous the Gram negative bacteria, which contain 100's distinct families β -barrel membrane proteins (BOMPs) often forming channels for transport nutrients or drugs. However, only four mitochondrial BOMPs (MBOMPs) have been confirmed date. Although estimates as high 100 made in past, number yet undiscovered MBOMPs is an open question. Fortunately, recent discovery a integration signal (the -signal) gave us...
Abstract Abscisic acid (ABA) is the main phytohormone involved in abiotic stress response and its adaptation, a candidate agrichemical. Consequently, several agonists of ABA have been developed using yeast two-hybrid system. Here, we describe novel cell-free-based drug screening approach for development validation receptor agonists. Biochemical this between 14 receptors (PYR/PYL/RCARs) 7 type 2C-A protein phosphatases (PP2CAs) revealed same interactions as those previous proteome data,...
The caspases, a family of cysteine proteases, play multiple roles in apoptosis, inflammation, and cellular differentiation. Caspase-8 (Casp8), which was first identified humans, functions as an initiator caspase the apoptotic signaling mediated by cell-surface death receptors. To understand evolution function Casp8 protein family, casp8 orthologs were from comprehensive range vertebrates invertebrates, including sponges cnidarians, characterized at both gene levels. Some introns have been...
Outer membrane proteins (OMPs) are essential components of the outer Gram-negative bacteria. In terms protein targeting and assembly, current dogma holds that a 'β-signal' imprinted in final β-strand OMP engages β-barrel assembly machinery (BAM) complex to initiate insertion into membrane. Here, we revealed an additional rule signals equivalent β-signal repeated other, internal β-strands within bacterial OMPs, by peptidomimetic mutational analysis. The signal is needed promote efficiency...