Coarse-Grained Simulation of Persistence Length and Twisting Dynamics of Micrometer-Scale Microtubules

Microtubules (MTs) are hollow cytoskeletal polymers with
exceptional
mechanical rigidity and dynamic instability, distinguishing them from
conventional helical polymers. Their unique biophysical properties
pose significant challenges for computational modeling, particularly
on biologically relevant length scales. In this study, we developed
a helix-based ultra-coarse-grained (HB-UCG) model for MT dynamic simulation,
based on the electron microscopy density data of helical MTs. Using
this model, we constructed MTs of up to 35 μm in length and
investigated the relationship between the persistence length and contour
length. Validation against experimental data confirmed the HB-UCG
model’s ability to simulate MT mechanical properties accurately.
Additionally, we performed coarse-grained molecular dynamics (CGMD)
simulations approaching the millisecond scale, capturing the formation
of kinks through MT twisting and quantifying the associated shear
strains. We also simulated the helicity of a single MT and compared
it with the experimental values of MT bundles, suggesting that inter-MT
interactions have an important influence on the helicity of the MT
bundles. Our work provides a valuable CG model for studying micrometer-scale
MT dynamics in cellular environments.