N. Kodera

Atom filtering algorithm and GPU-accelerated calculation of simulation atomic force microscopy images

The paper introduces a GPU-accelerated atom filtering algorithm to improve the efficiency of simulated atomic force microscopy (AFM) image calculations for biomolecular structures.

S100A11 promotes focal adhesion disassembly via myosin II-driven contractility and Piezo1-mediated Ca2+ entry

This study identifies S100A11's role in promoting focal adhesion disassembly through myosin II-driven contractility and Piezo1-mediated Ca2+ entry.

Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions

The paper predicts biomolecular placement on AFM substrates using electrostatic interactions and applies it to HS-AFM observations of specific proteins.

Structural dynamics of E6AP E3 ligase HECT domain and involvement of flexible hinge loop in ubiquitin chain synthesis mechanism

This study uses high-speed atomic force microscopy to demonstrate the structural dynamics of the E6AP HECT domain and shows how hinge loop flexibility affects Ub chain formation.

Actin binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II

The paper shows that the Rng2CHD domain inhibits actin filament motility on myosin II at low binding ratios, suggesting it modulates actin-myosin interactions through structural changes.

Chained structure of dimeric F1-like ATPase in Mycoplasma mobile gliding machinery

This study determines the structure of a dimeric F1-like ATPase in Mycoplasma mobile gliding machinery, showing it resembles F1-ATPase and supports an evolutionary link.

Unraveling the host-selective toxic interaction of cassiicolin with lipid membranes and its cytotoxicity

This study investigates how cassiicolin toxins interact with plant lipid membranes, showing that their cytotoxicity depends on lipid composition and that specific rubber clones resist the toxins.

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.

Movements of Mycoplasma mobile gliding machinery detected by high-speed atomic force microscopy

This study uses high-speed atomic force microscopy to visualize and analyze the real-time movements of the internal gliding machinery in Mycoplasma mobile.

Native cyclase-associated protein and actin from Xenopus laevis oocytes form a 4:4 complex with a tripartite structure

The paper isolates and characterizes a 4:4 XCAP1-actin complex from Xenopus oocytes, revealing a tripartite structure with potential functional implications.

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.

Direct visualization of translational GTPase factor-pool formed around the archaeal ribosomal P-stalk by high-speed atomic force microscopy

This study uses HS-AFM to visualize the dynamic structure of the archaeal ribosomal P-stalk and shows how it facilitates the assembly of GTPase factors for translation elongation.