Biology subjects

Mayumi, K.

Publications and source records attributed to Mayumi, K..

3 recordsLinked to original sources

bioRxiv2026

Kinetic hierarchy of Kai protein complex formation governs the cyanobacterial circadian oscillator

Cyanobacterial circadian oscillations arise from a phosphorylation cycle of KaiC that is coupled to reversible complex formation with KaiA and KaiB. Although representative assemblies such as A2C6, B6C6, and A12B6C6 have been structurally characterized, quantitative understanding of their stoichiometry, affinity, and formation kinetics during the oscillation cycle remains limited. Here, we systematically quantified AC, BC and ABC complex formation using phosphorylation-mimetic KaiC and controlled protein mixing ratios by integrating analytical ultracentrifugation with small-angle X-ray/neutron scattering. A2C6 formation exhibits graded dependence on the phosphorylation state of KaiC and occurs rapidly in solution. In contrast, B6C6 formation behaves in a switch-like manner, showing strong selectivity for the hyperphosphorylation mimic and proceeding on a slow timescale ([~] 6 h). Upon B6C6 formation, KaiA rapidly associates with the complex to generate AnB6C6, with KaiA occupancy n determined by the mixing ratio through fast redistribution among coexisting complexes. This behavior enables dynamic allocation of KaiA among clock complexes. Together, these quantitative insights delineate a hierarchy of assembly dynamics--fast, graded AC exchange; slow, state-selective BC formation; and rapid KaiA redistribution--revealing a mechanistic basis for the dynamic regulation of the Kai oscillator.

biophysics↗

bioRxiv2025

Membrane-enhanced repulsive interactions regulate protein diffusion in cell-size space

Intracellular molecular organization is often explained by attractive interactions driving clustering and phase separation. Although consideration of repulsive forces is essential in physics, their roles remain unclear in cellular contexts. Here, we demonstrated the fundamental role of repulsion in regulating protein diffusion within cell-size space. By analyzing negatively charged protein diffusion in bulk solutions and in cell-size spaces with membranes, we revealed that membrane-enhanced repulsion inhibited protein diffusion in cell-size spaces. This was due to the amplified electrostatic interactions among proteins because of the large membrane area-to-volume ratio. Notably, ATP, a cellular central energy source, further inhibited protein diffusion in cell-size spaces, whereas protein wave propagation on the membrane counteracted this inhibition. These findings suggest an active regulatory mechanism restoring molecular mobility by dynamically adjusting membrane-enhanced repulsive forces. Our study challenges the traditional emphasis on attractive interactions, highlighting repulsion as a critical tunable factor governing molecular transport and spatial organization in cells. TeaserProtein diffusion within crowded cell-size spaces is tuned by membrane-enhanced repulsion and its active regulation.

biophysics↗

bioRxiv2020

A neuromechanical model and kinematic analyses for Drosophila larval crawling based on physical measurements

Animal locomotion requires dynamic interactions between neural circuits, muscles, and surrounding environments. In contrast to intensive studies on neural circuits, the neuromechanical basis for animal behaviour remains unclear due to the lack of information on the physical properties of animals. Here, we proposed an integrated neuromechanical model based on physical measurements by taking Drosophila larvae as a model of soft- bodied animals. The biomechanical parameters of fly larvae were measured by the stress- relaxation test. By optimizing parameters in the neural circuit, our neuromechanical model succeeded in quantitatively reproducing the kinematics of larval locomotion that were obtained experimentally. This model could reproduce the observation of optogenetic studies reported previously. The model predicted that peristaltic locomotion could be exhibited in a low friction condition. Analysis of floating larvae provided results consistent with this prediction. Furthermore, the model predicted a significant contribution of intersegmental connections in the central nervous system, which contrasts with a previous study. This hypothesis allowed us to make a testable prediction for the variability in intersegmental connection in sister species of the genus Drosophila. Our model based on physical measurement provides a new foundation to study locomotion in soft-bodied animals and soft robot engineering.

neuroscience↗