A5076215084- Geometric and Algebraic Topology
- Protein Structure and Dynamics
- Homotopy and Cohomology in Algebraic Topology
- Mathematical Dynamics and Fractals
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Geometric Analysis and Curvature Flows
- Advanced Differential Equations and Dynamical Systems
- Lung Cancer Treatments and Mutations
- RNA modifications and cancer
- Cancer Immunotherapy and Biomarkers
- Molecular Junctions and Nanostructures
- Monoclonal and Polyclonal Antibodies Research
- Advanced Physical and Chemical Molecular Interactions
- Carbon Nanotubes in Composites
- Material Dynamics and Properties
- Computational Drug Discovery Methods
- Algebraic Geometry and Number Theory
- Analytical Chemistry and Chromatography
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Cancer, Hypoxia, and Metabolism
- Scientific Research and Discoveries
Kyoto Sangyo University
2004-2024
Sanyo-Onoda City University
2023
National Institute of Advanced Industrial Science and Technology
2012-2022
Waseda University
2022
National Institute for Japanese Language and Linguistics
2020
Indian Institute of Technology Madras
2013
Osaka University
2009
The University of Tokyo
2006-2008
Kobe University
2000-2007
Cyber Laser (Japan)
2006
Abstract Accumulating evidence indicates that CD8+ T cells in the tumor microenvironment and systemic CD4+ T-cell immunity play an important role mediating durable antitumor responses. We longitudinally examined peripheral blood of patients with non–small lung cancer found responders had significantly (P < 0.0001) higher percentages effector, CD62Llow prior to PD-1 blockade. Conversely, percentage CD25+FOXP3+ was = 0.034) nonresponders. developed a formula, which demonstrated 85.7%...
The protein cysteine residue is one of the amino acids most susceptible to oxidative modifications, frequently caused by stress. Several applications have enabled cysteine-targeted proteomics analysis with simultaneous detection and quantitation. In this study, we employed a quantitative approach using set iodoacetyl-based reactive isobaric tags (iodoTMT) evaluated transient cellular oxidation ratio free reversibly modified thiols under DTT hydrogen peroxide (H2O2) treatments. treatment (1...
Abstract EGFR-mutated lung cancer accounts for a significant proportion of cases worldwide. For these cases, osimertinib, third-generation EGFR tyrosine kinase inhibitor, is extensively used as first-line or second-line treatment. However, cells acquire resistance to osimertinib in 1 2 years. Thus, thorough clarification mechanisms highly anticipated. Recent next-generation sequencing (NGS) samples identified several genetically defined such C797S MET amplification. nongenetically are not...
In this paper we study boundedness of conjugation invariant norms on diffeomorphism groups manifold pairs. For the group ${\mathcal D} \equiv {\rm Diff}(M,N)_0$ a closed pair $(M, N)$ with $\dim N \geq 1$, first clarify relation among fragmentation norm, generated commutator length $cl$ and support in balls $clb$ show that D}$ is weakly simple relative to union some normal subgroups D}$. these norms, focuses case where $N$ $m$ circles. case, rotation angle induces quasimorphism $\nu :...
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, scores are not sufficiently precise to represent protein-ligand binding affinity. Here, we developed an efficient computational method calculating affinity, which based on mechanics generalized Born/surface area (MM-GBSA) calculations and Jarzynski identity. identity exact relation between free energy differences work done through non-equilibrium process, MM-GBSA...
Protein–protein interactions play an essential role in the regulation of various cellular processes. Understanding recognition mechanism protein–protein complexes is a challenging task molecular and computational biology. In this work, we have developed energy based approach for identifying binding sites important residues complexes. The new different from traditional distance contacts which repulsive are treated as well within specific cutoff been same way. We found that residue-pairs with...
Abstract To detect drug candidates for dengue haemorrhagic fever (DHF), we employed a computational repositioning method to perform an integrated multiple omics analysis based on transcriptomic, proteomic, and interactomic data. We identified 3,892 significant genes, 389 proteins, 221 human proteins by transcriptomic analysis, proteomic human–dengue virus protein–protein interactions, respectively. The were selected using gene expression profiles inverse drug–disease relationships compared...
The configuration isomers α,α-, α,β-, and β,β-trehalose are distinguishable by a relative ion abundance analysis using collision-induced dissociation MS/MS measurements in electrospray ionization quadrupole-time-of-flight mass spectrometry. of the Y-type fragment α,α-trehalose is highest that lowest, indicating α-glycosyl bonds cleave more easily than β-glycosyl bonds. depends on both α- linkage type number reaction path glycosyl bond cleavage calculated computationally molecular orbital...
Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting binding sites in complexes long standing goals molecular computational biology.We have developed an energy based approach identifying site residues complexes. The been analyzed with sequence structure parameters such as propensity, neighboring vicinity sites, conservation score conformational switching.We observed that propensities amino acid...
The emergence of bacterial multidrug resistance is an increasing problem in treatment infectious diseases. An important cause for the bacteria expression efflux transporters. and toxic compound extrusion (MATE) transporters are most recently recognized as unique system antimicrobials therapeutic drugs due to energy stored either Na+ or H+ electrochemical gradient. In present study, high throughput virtual screening natural collections against NorM - a MATE transporter from Neisseria...
The efficacy and safety of lenvatinib (LEN) as a second/third-line treatment for unresectable hepatocellular carcinoma (HCC) after sorafenib (SOR) therapy remains unknown. We evaluated the outcomes LEN treatment, investigated sensitivity SOR-resistant HCC cell line (PLC/PRF5-R2) to LEN, assessed their signal transduction pathways by protein array analysis. retrospectively enrolled 57 patients with HCC. Fifty-three radiologically comprised 34 molecular-targeted agent (MTA)-naive (first-line),...
We have developed the database TMFunction, which is a collection of more than 2900 experimentally observed functional residues in membrane proteins. Each entry includes numerical values for parameters IC50 (measure effectiveness compound inhibiting biological function), V(max) (maximal velocity transport), relative activity mutants with respect to wild-type protein, binding affinity, dissociation constant, etc., are important understanding sequence-structure-function relationship In...
Mechanisms of fragmentation glycosyl bond linkages in various saccharides were investigated by using computational calculations to find general rules sodiated oligosaccharides mass spectrometry. The revealed that alpha-Glc, alpha-Gal, beta-Man, alpha-Fuc, beta-GlcNAc, and beta-GalNAc cleaved more easily than beta-Glc, beta-Gal, alpha-Man because the transition states former stabilized anomeric effect. 1-6 linkage was stable others, since with flexible energy other sodium cation. sialyl most...
Abstract Metabolic reprogramming, including the Warburg effect, is a hallmark of cancer. Indeed, diversity cancer metabolism leads to heterogeneity, but accurate assessment metabolic properties in tumors has not yet been undertaken. Here, we performed absolute quantification expression levels 113 proteins related carbohydrate and antioxidant pathways, stage III colorectal surgical specimens from 70 patients. The effect appeared protein between tumor normal mucosa demonstrated. Notably,...
We describe a new method for probing phase separation of polymer-blend systems in spherical microparticles generated from microdroplets dilute polymer solution. Two-dimensional optical diffractiona technique sensitive to material inhomogeneity on length scale ≈30 nmis used probe phase-separation behavior bulk-immiscible polymers attoliter and femtoliter volumes. Under conditions rapid solvent evaporation (≈2−10 ms) relatively low mobility, homogeneous composite particles can be formed using...
We show that homogeneous polymer blend microparticles can be prepared in situ from droplets of dilute solution codissolved polymers. Provided the droplet is small enough (<10 mum), solvent evaporation rapid to inhibit phase separation. Thus polymers are being mixed need not miscible, which greatly enhances applicability technique. From analysis two-dimensional Fraunhofer diffraction (angular scattering) patterns, we both real and imaginary parts refractive index tuned by adjustment relative...
We studied the interactions between SH2 domain of growth factor receptor binding protein 2 (Grb2) and ErbB receptor-derived phosphotyrosyl peptides using molecular dynamics, free energy calculations, surface plasmon resonance (SPR) analysis. Binding energies for nine were calculated MM-PBSA continuum solvent method, excellent qualitative agreement with SPR experimental data, a correlation coefficient 0.92, was obtained. Consistent previous findings, consensus sequence pYXNX showed favorable...
Protein−DNA recognition plays an essential role in the regulation of gene expression. Understanding mechanism protein−DNA complexes is a challenging task molecular and computational biology. In this work, scoring function based approach has been developed for identifying binding sites delineating important residues complexes. This considers both repulsive interactions effect distance between atoms protein DNA. The results showed that positively charged, polar, aromatic are binding. These...
G-Protein Coupled Receptors (GPCRs) are one of the most important pharmaceutical targets. Recent studies have revealed that many GPCRs form homo- and/or hetero-oligomers. The molecular mechanisms oligomerization not fully understood yet, due to lack structural data for GPCR complexes. Therefore, accurate interface prediction would accelerate investigations and signaling via GPCRs. However, is difficult, because various subtypes often use different regions as their interfaces, even when...
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at active site of to enhance towards sialylglycans, molecular dynamics simulations 20 ns carried out wild type mutated WGAs (WGA1, WGA2, WGA3) in complex sialylgalactose examine change specificity. MD reveal bound conformational flexibility sialylgalactose. The polar...
Efflux proteins are membrane proteins, which involved in the transportation of multidrugs. The annotation efflux genomic sequences would aid to understand function. Although percentage genomes is estimated be 25-30%, there no information about content proteins. For annotating such class it necessary develop a reliable method identify from amino acid sequence information. In this work, we have developed based on radial basis function networks using position specific scoring matrices (PSSM)...