Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments

TL;DR

This study combines coarse-grained simulations and experiments to directly observe and quantify the fragmentation and depolymerization of protein filaments, revealing the energy-dependent relationship between these processes.

Contribution

It provides the first direct simulation and experimental evidence of filament breakup and depolymerization, establishing a quantitative law linking rates to bond energies.

Findings

Depolymerization rate is significantly higher than fragmentation rate.

The ratio of rates follows an exponential law based on bond energies.

Experimental measurements support the simulation predictions.

Abstract

While a significant body of investigations have been focused on the process of protein self-assembly, much less is understood about the reverse process of a filament breaking due to thermal motion into smaller fragments, or depolymerization of subunits from the filament ends. Indirect evidence for actin and amyloid filament fragmentation has been reported, although the phenomenon has never been directly observed either experimentally or in simulations. Here we report the direct observation of filament depolymerization and breakup in a minimal, calibrated model of coarse-grained molecular simulation. We quantify the orders of magnitude by which the depolymerization rate from the filament ends $k_\mathrm{off}$ is larger than fragmentation rate $k_{-}$ and establish the law $k_\mathrm{off}/k_- = \exp [( \varepsilon_\| - \varepsilon_\bot) / k_\mathrm{B}T ] = \exp [0.5 \varepsilon / k_\mathrm{B}T ]$, which accounts for the topology and energy of bonds holding the filament together. This mechanism and the order-of-magnitude predictions are well supported by direct experimental measurements of depolymerization of insulin amyloid filaments.