S. Takada

Theoretical insights into rotary mechanism of MotAB in the bacterial flagellar motor

This study uses computational modeling and molecular dynamics simulations to elucidate the proton-transfer coupled rotation mechanism of MotAB in bacterial flagellar motors.

Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

This paper introduces Hi-C metainference, a Bayesian method to model chromatin organization, revealing that gene loci in mouse embryonic stem cells are dynamically condensed and organized as crumpled globules.

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study

This study uses molecular simulations to show that Nanog forms micelle-like clusters in condensates via hydrophobic interactions, with surface domains mediating condensate bridging and DNA recruitment.

Postsynaptic protein assembly in three- and two-dimensions studied by mesoscopic simulations

This study compares phase separation in 3D and 2D systems using mesoscopic simulations of PSD proteins, showing distinct behaviors in membrane-bound versus cytosolic environments.

Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response

This study identifies ULK1 as the kinase responsible for phosphorylating p62, which activates NRF2 in a redox-independent manner through retention of KEAP1 in p62 bodies.

End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images

This paper introduces an end-to-end differentiable method for blind tip reconstruction in AFM images, showing robustness to noise and accurate surface geometry reconstruction.

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

This paper introduces a new potential, the stoichiometric interaction potential, to improve mesoscopic simulations of liquid-liquid phase separation in multidomain proteins, achieving quantitative agreement with experimental data.

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

The paper implements residue-level coarse-grained models in GENESIS to enable large-scale molecular dynamics simulations of biomolecules, improving computational efficiency and handling heterogeneous systems.

Key residue on cytoplasmic dynein for asymmetric unbinding and unidirectional movement along microtubule

This study identifies a key residue in cytoplasmic dynein responsible for asymmetric unbinding and unidirectional movement along microtubules through computational simulations and in vitro experiments.

Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells

The paper investigates how the balance of membrane binding and dissociation of MinD determines wave mode selection in Min waves reconstituted in artificial cells.

F0-F1 coupling and symmetry mismatch in ATP synthase resolved in every F0 rotation step

The paper uses molecular dynamics simulations and cryo-EM structures to analyze symmetry mismatch in ATP synthase during each rotation step, revealing mechanical couplings and structural adaptations.

Heterodimers of functionally divergent ARF-GEF paralogues prevented by self-interacting dimerisation domain

The paper shows that GNOM and GNL1 ARF-GEFs form homodimers but not heterodimers due to self-interacting dimerisation domains, preventing potentially harmful interactions.

modeling DNA opening in the eukaryotic transcription initiation complexes

This study uses molecular dynamics simulations to model DNA opening in eukaryotic transcription initiation complexes, identifying an intermediate state and key interactions involved in the process.

Fine-tuning of β-catenin in thymic epithelial cells is required for postnatal T cell development

This study investigates the role of β-catenin in thymic epithelial cells during postnatal T cell development, showing that its expression must be finely tuned to support proper thymus function.

Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

The paper investigates cooperation among c-subunits in FoF1-ATP synthase by analyzing ATP synthesis and proton pump activities with mutated cE56D subunits, showing decreased activity with increasing mutation separation.

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

This study uses molecular dynamics simulations guided by atomic force microscopy to model how the condensin hinge domain binds dsDNA, showing different binding surfaces in open and closed conformations.

Rigid-Body Fitting to Atomic Force Microscopy Images for Inferring Probe Shape and Biomolecular Structure

This paper develops a method to infer AFM probe shape and molecular structure from images by rigid-body fitting, showing that similarity scores vary depending on the target molecule.

DNA translocase repositions a nucleosome by the lane-switch mechanism

The paper identifies a lane-shift mechanism for downstream nucleosome repositioning by DNA translocases using simulations and experimental validation.

The Kinetic Landscape of Nucleosome Assembly: A Coarse-Grained Molecular Dynamics Study

This study uses molecular dynamics simulations to analyze the kinetic landscape of nucleosome assembly, revealing transition networks and the role of DNA bending and histone association in positioning sequences.

Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

This paper develops a Kalman smoother method to resolve data asynchronicity in HS-AFM movies, improving the accuracy of structural dynamics capture.

The Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurement with Biomolecular Simulations

The paper develops a particle filter method to integrate HS-AFM data with coarse-grained MD simulations, showing that more particles improve likelihood and enabling inference of true conditions from AFM movies.

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

This paper introduces a method to flexibly fit biomolecular structures to AFM images using biased molecular simulations, demonstrating its effectiveness with synthetic and real data.

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

The paper uses molecular dynamics simulations to study proton-transfer coupled rotations in yeast mitochondrial ATP synthase FO motor, finding 36-degree steps per proton transfer and high efficiency.

Diverse stepping motions of cytoplasmic dynein revealed by kinetic modeling

The paper develops a kinetic model of cytoplasmic dynein's bipedal stepping motions, showing how different stepping patterns arise from ATP hydrolysis and conformational changes.

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

This study uses molecular dynamics simulations to show how ATP-dependent chromatin remodelers induce DNA sliding through twist defect formation during inchworm motion.

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

The paper introduces a model that integrates protein binding assays and structural data to simulate protein-DNA interactions and reproduce specificity.

Reconstruction of atomistic structures from coarse-grained models for protein-DNA complexes

This study develops a method to reconstruct all-atom structures from coarse-grained protein-DNA complex models, improving accuracy at the interface and validating through multiple metrics.

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

This study uses molecular simulations to show that nucleosome sliding depends on DNA sequence, with strong positioning sequences sliding in large jumps and uniform sequences sliding in a rotation-coupled manner.

Fetal therapy model of myelomeningocele with three-dimensional skin using amniotic fluid cell-derived induced pluripotent stem cells

This study uses iPSC-derived artificial skin to treat a rat model of myelomeningocele during pregnancy, showing potential for antenatal therapy.