Kenichi Umeda

Characterization of the trimeric TOM complex by HS-AFM single-molecule analysis

This study uses HS-AFM to show yeast TOM complexes predominantly form trimers that dynamically dissociate into dimers and monomers, revealing structural and dynamic features of the TOM complex.

Dual role of the RIG-I 2CARD as a signaling module and a brake on dsRNA translocation

This study shows the RIG-I 2CARD acts as both a signaling module and a brake on dsRNA translocation using high-speed atomic force microscopy.

Submolecular video-imaging of the Smc5/6 complex topologically bound to DNA

This study uses high-speed atomic force microscopy to visualize the dynamics of the Smc5/6 complex interacting with DNA at submolecular resolution, revealing its DNA binding mechanisms.

HS-AFM Reveals Hierarchical RNA Folding Driving Condensate Assembly and Material States

This study uses HS-AFM to show how RNA folding leads to condensate assembly and distinct material states at the nanoscale.

Maturation-dependent structural dynamics and nanomechanical properties of dengue virus revealed by high-speed AFM and 3D force mapping

This study uses high-speed AFM and 3D force mapping to analyze the structural dynamics and nanomechanical properties of dengue virus particles across maturation states.

Actin monomers influence the interaction between Xenopus cyclase-associated protein 1 and actin filaments

This study investigates how actin monomers affect XCAP1's interaction with actin filaments using high-speed atomic force microscopy, revealing differences in binding dynamics and preferences.

CaMKIIα holoenzymes self-organize into worm-like mesoscale clusters

This study shows that CaMKII holoenzymes form worm-like mesoscale clusters under spatial confinement, with activation leading to cluster expansion and a mutant variant forming clusters even without activation.

Submolecular-scale Hairpin DNA Folding Dynamics Studied by High-Speed AFM with Optical Tweezers

This study combines optical tweezers with high-speed AFM to visualize DNA folding dynamics, revealing reversible structural changes and metastable intermediates.

Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM

The paper uses high-speed AFM to show that CaMKII/{beta} heterododecamers form stable structures with adjacent CaMKII{beta} subunits, revealing their structural role.

Mycobacterial DNA-binding protein 1 (MDP1) induces RNA condensation as revealed by high-speed AFM

This study shows that MDP1 from Mtb induces RNA condensation through its IDR and PTMs, forming globular structures, while E. coli-expressed MDP1 forms chain-like condensates.

High-speed AFM reveals fluctuations and dimer splitting of the N-terminal domain of GluA2-γ2

This study uses HS-AFM to visualize NTD dynamics of GluA2-γ2, showing dimer splitting and its role in synaptic clustering.

Deciphering the actin structure-dependent preferential cooperative binding of cofilin

The paper investigates how cofilin binds preferentially to actin filaments by analyzing structural differences and their impact on binding and cluster formation.

Evolutionarily acquired activity-dependent transformation of the CaMKII holoenzyme

The paper uses high-speed atomic force microscopy to study activity-dependent structural dynamics of CaMKII in rat, hydra, and C. elegans, revealing species-specific structural changes and phosphatase tolerance in rat CaMKII.

Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

This study elucidates the mechanism of CRISPR-Cas3-mediated DNA degradation in E. coli, showing how EcoCas3 cleaves ssDNA and degrades dsDNA through specific and non-specific interactions with EcoCascade.