Chemomechanical simulation of microtubule dynamics with explicit lateral bond dynamics

TL;DR

This paper presents a detailed chemomechanical model of microtubule dynamics that simulates catastrophe and rescue events, providing insights into microscopic structural features and force feedback effects.

Contribution

The model integrates lateral bond dynamics, hydrolysis, and mechanical stretching at the dimer level, enabling realistic long-term simulations of microtubule behavior.

Findings

Simulation reproduces catastrophe and rescue rates consistent with experiments.

Insights into GTP-tubulin cap structure and catastrophe triggers.

Force feedback influences hydrolysis and stability of microtubules.

Abstract

We introduce and parameterize a chemomechanical model of microtubule dynamics on the dimer level, which is based on the allosteric tubulin model and includes attachment, detachment and hydrolysis of tubulin dimers as well as stretching of lateral bonds, bending at longitudinal junctions, and the possibility of lateral bond rupture and formation. The model is computationally efficient such that we reach sufficiently long simulation times to observe repeated catastrophe and rescue events at realistic tubulin concentrations and hydrolysis rates, which allows us to deduce catastrophe and rescue rates. The chemomechanical model also allows us to gain insight into microscopic features of the GTP-tubulin cap structure and microscopic structural features triggering microtubule catastrophes and rescues. Dilution simulations show qualitative agreement with experiments. We also explore the consequences of a possible feedback of mechanical forces onto the hydrolysis process and the GTP-tubulin cap structure.