S. Kubo

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.

Investigating EMT-mediated resistance to EGFR tyrosine kinase inhibitors in NSCLC using innovative organoid models

This study investigates EMT-mediated resistance to EGFR TKIs in NSCLC using organoid models, finding links between EMT markers and resistance, and suggesting potential therapeutic strategies.

Effect of alpha-tubulin acetylation on the doublet microtubule structure

This study examines how alpha-tubulin acetylation affects doublet microtubule structure in Tetrahymena cilia using cryo-EM, MD, and mass spectrometry, finding small-scale structural changes and a link to phosphorylation.

Inference of Selective Force on House Mouse Genomes during Secondary Contact in East Asia

The paper analyzes 163 house mouse genomes to study selective forces during secondary contact in East Asia, finding genomic admixture and sex chromosome conflict.

Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by molecular dynamic simulation

This study uses molecular dynamics to show that poly-glutamylation inhibits dynein-2 motility and targets retrograde transport to the A-tubule.

Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins

The paper uses cryo-EM to analyze native doublet microtubules in Tetrahymena thermophila, identifying MIPs and showing their role in cilia function through CFAP77 knockout.

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.

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.

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.

Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-electron microscopy

This study uses cryo-electron microscopy to reveal the structure of outer dynein arms attached to microtubules and proposes a model for their remodeling and activation through molecular dynamics simulations.

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 inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

The paper identifies new inner junction proteins in cilia and shows they form an interaction hub involving tubulin post-translational modifications.

Structural basis for two-way communication between dynein and microtubules

This study investigates the structural basis of two-way communication between dynein and microtubules using NMR and cryo-EM, revealing conformational changes in the MTBD and their implications for dynein movement.

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.