38 results match your criteria: "Riken Quantitative Biology Center (QBiC)[Affiliation]"

Structured water near surfaces is important in nonclassical crystallization, biomineralization, and restructuring of cellular membranes. In addition to equilibrium structures, studied by atomic force microscopy (AFM), high-speed AFM (H-S AFM) can now detect piconewton forces in microseconds. With increasing speeds and decreasing tip diameters, there is a danger that continuum water models will not hold, and molecular dynamic (MD) simulations would be needed for accurate predictions.

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DiRect: Site-directed mutagenesis method for protein engineering by rational design.

Biochem Biophys Res Commun

April 2021

Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center (QBiC), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. Electronic address:

Site-directed mutagenesis (SDM), an indispensable method in molecular biology and protein engineering, is rather time-consuming and laborious. Protein engineering, especially that of enzymes, nowadays increasingly relies on rational design approaches in which both SDM and protein expression are the bottlenecks because they are generally based on the recombinant DNA technology. Here, we developed a new PCR-based mutagenesis method, DiRect, that achieves high performance in product quality (≥99% substitution) without recombinant DNA technology.

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Adult T-cell leukemia/lymphoma (ATL) is an aggressive T-cell neoplasm caused by human T-cell leukemia virus type I (HTLV-I). Therapeutic interventions have not been associated with satisfactory outcomes. We showed that the porphyrin metabolic pathway preferentially accumulates the endogenous photosensitive metabolite, protoporphyrin IX (PpIX) in ATL, after a short-term culture with 5-aminolevulinic acid (ALA).

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High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis.

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Comparison of the 3-D patterns of the parasympathetic nervous system in the lung at late developmental stages between mouse and chicken.

Dev Biol

December 2018

Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan; AMED Core Research for Evolutional Science and Technology (AMED-CREST), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo 100-0004, Japan. Electronic address:

Although the basic schema of the body plan is similar among different species of amniotes (mammals, birds, and reptiles), the lung is an exception. Here, anatomy and physiology are considerably different, particularly between mammals and birds. In mammals, inhaled and exhaled airs mix in the airways, whereas in birds the inspired air flows unidirectionally without mixing with the expired air.

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Theoretical study on photo-induced processes of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium halide species: an application of constrained density functional theory.

Phys Chem Chem Phys

February 2018

Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC), QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan.

1-Methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium (MNEI) has potential as a versatile sensor that can measure the electronegativity of anions based on the fluorescence intensity upon irradiation. To clarify the factors that determine the fluorescence intensity, constrained density functional theory (CDFT) was applied to explore the electron transfer (ET) states of MNEI halide species (MNEI-X; X = F, Cl, Br, I). According to the CDFT potential energy surface, intra-molecular ET (S) states on MNEI are responsible for the intensity of absorption and fluorescence spectra.

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Article Synopsis
  • Feedback control plays a crucial role in cellular responses, and this study reveals a new way that the PHLDA1 protein negatively affects ErbB receptor signaling by preventing receptor oligomerization.
  • The research shows that the ligand heregulin increases PHLDA1 expression in MCF-7 cells, which binds to ErbB3 and reduces the interaction between ErbB3 and ErbB2 when PHLDA1 levels are decreased.
  • A mathematical model was developed to show that PHLDA1 inhibits the formation of dimers and tetramers in ErbB receptors, and this model's predictions were confirmed through single-molecule imaging experiments.
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Filopodia protrude from the leading edge of cells and play important roles in cell motility. Here we report the mechanism of myosin X (encoded by Myo10)-induced multi-cycle filopodia extension. We found that actin, Arp2/3, vinculin and integrin-β first accumulated at the cell's leading edge.

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Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g.

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Porhyromonas gingivalis, a causative bacterium of periodontitis, is implicated in the etiology of rheumatoid arthritis (RA), mainly because of expressing peptidyl arginine deiminase (PAD) that generates RA-related autoantigens. However, compared with other periodontopathic bacteria, the precise role of P. gingivalis in RA is largely unknown.

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In vivo analysis of protein crowding within the nuclear pore complex in interphase and mitosis.

Sci Rep

July 2017

Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.

The central channel of the nuclear pore complex (NPC) is occupied by non-structured polypeptides with a high content of Phe-Gly (FG) motifs. This protein-rich environment functions as an entropic barrier that prevents the passage of molecules, as well as the binding sites for karyopherins, to regulate macromolecular traffic between the nucleoplasm and the cytoplasm. In this study, we expressed individual Nups fused with a crowding-sensitive probe (GimRET) to determine the spatial distribution of protein-rich domains within the central channel in vivo, and characterize the properties of the entropic barrier.

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Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status.

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One-step micromolding of complex 3D microchambers for single-cell analysis.

Lab Chip

February 2017

Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.

Herein we examined the extent of replicability of the PDMS microchamber device transferred from the master mold with complex 3D structures fabricated via micro stereolithography. Due to the elastomeric properties of PDMS, the reversely tapered micromold, with the diameter ratio of ∼5 from the largest to the narrowest part, was precisely transferred without breaking. We obtained the mathematical model to estimate the stress exerted on the mold during the demolding process.

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Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved.

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The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data.

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Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems.

J Comput Chem

June 2017

Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo Kobe, 640-0047, Japan.

Parallelization of molecular dynamics (MD) simulation is essential for investigating conformational dynamics of large biological systems, such as ribosomes, viruses, and multiple proteins in cellular environments. To improve efficiency in the parallel computation, we have to reduce the amount of data transfer between processors by introducing domain decomposition schemes. Also, it is important to optimize the computational balance between real-space non-bonded interactions and reciprocal-space interactions for long-range electrostatic interactions.

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CRK and CRKL adapter proteins play essential roles in development and cancer through their SRC homology 2 and 3 (SH2 and SH3) domains. To gain insight into the origin of their shared functions, we have investigated their evolutionary history. We propose a term, crk/crkl ancestral (crka), for orthologs in invertebrates before the divergence of CRK and CRKL in the vertebrate ancestor.

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Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.

J Chem Theory Comput

October 2016

RIKEN Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

The graphics processing unit (GPU) has become a popular computational platform for molecular dynamics (MD) simulations of biomolecules. A significant speedup in the simulations of small- or medium-size systems using only a few computer nodes with a single or multiple GPUs has been reported. Because of GPU memory limitation and slow communication between GPUs on different computer nodes, it is not straightforward to accelerate MD simulations of large biological systems that contain a few million or more atoms on massively parallel supercomputers with GPUs.

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Intermolecular electron transfer states of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium iodide obtained by constrained density functional theory.

Phys Chem Chem Phys

July 2016

Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC), QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan.

Electron transfer (ET) states of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium iodide are responsible for its photophysics. Investigation of an ET state based on constrained density functional theory (CDFT) revealed that nonradiative decay from the ET excited state is mediated by the interaction of the iodine atom with the 1,8-naphthalimide or the imidazolium group.

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In current plant biotechnology, the introduction of exogenous DNA encoding desired traits is the most common approach used to modify plants. However, general plant transformation methods can cause random integration of exogenous DNA into the plant genome. To avoid these events, alternative methods, such as a direct protein delivery system, are needed to modify the plant.

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Fluorescent proteins have been widely used in biology because of their compatibility and varied applications in living specimens. Fluorescent proteins are often undesirably sensitive to intracellular conditions such as pH and ion concentration, generating considerable issues at times. However, harnessing these intrinsic sensitivities can help develop functional probes.

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Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.

Cell Chem Biol

January 2016

Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), 1-3, Yamadaoka, Suita, Osaka 565-0874, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), 1-7-1, Ohte-machi, Chiyoda-ku, Tokyo, 100-0004, Japan. Electronic address:

Organism-level systems biology aims to identify, analyze, control and design cellular circuits in organisms. Many experimental and computational approaches have been developed over the years to allow us to conduct these studies. Some of the most powerful methods are based on using optical imaging in combination with fluorescent labeling, and for those one of the long-standing stumbling blocks has been tissue opacity.

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Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.

Biophys J

February 2016

Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas. Electronic address:

The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations.

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Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1-14 d, with the exact time required dependent on the sample type and the experimental purposes.

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Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.

J Comput Chem

November 2015

Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC), 1-6-5 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo, 650-0047, Japan.

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations.

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