Modeling the effects of lattice defects on microtubule breaking and healing

Abstract

Microtubule reorganization often results from the loss of polymer induced through breakage or active destruction by energy-using enzymes. Pre-existing defects in the microtubule lattice likely lower structural integrity and aid filament destruction. Using large-scale molecular simulations, we model diverse microtubule fragments under forces generated at specific positions to locally crush the filament. We show that lattices with 2% defects are crushed and severed by forces three times smaller than defect-free ones. We validate our results with direct comparisons of microtubule kinking angles during severing. We find a high statistical correlation between the angle distributions from experiments and simulations indicating that they sample the same population of structures. Our simulations also indicate that the mechanical environment of the filament affects breaking: local mechanical support inhibits healing after severing, especially in the case of filaments with defects. These results recall reports of microtubule healing after flow-induced bending and corroborate prior experimental studies that show severing is more likely at locations where microtubules crossover in networks. Our results shed new light on mechanisms underlying the ability of microtubules to be destroyed and healed in the cell, either by external forces or by severing enzymes wedging dimers apart. © 2016 Wiley Periodicals, Inc.

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots

“…In particular, molecular dynamics simulations can apply pulling or pushing forces at particular locations along the microtubule lattice to determine the work required to destroy the lattice. 61–64 In these works, it is clear that the intramolecular bonds between dimers are the weak points in the lattice, and they come apart before dimers are unraveled. 64 These studies are complimented by several experimental studies of the structure of filaments during and after forced destruction by depolymerizing enzymes or severing enzymes.…”

“…61–64 In these works, it is clear that the intramolecular bonds between dimers are the weak points in the lattice, and they come apart before dimers are unraveled. 64 These studies are complimented by several experimental studies of the structure of filaments during and after forced destruction by depolymerizing enzymes or severing enzymes. 65–67 Other studies have used atomic force microscopy (AFM) techniques to specifically push on microtubules.…”

Katanin catalyzes microtubule depolymerization independently of tubulin C‐terminal tails

“…In addition to these structural studies, molecular dynamics simulations have suggested that it would be easier to remove a dimer by pushing into the lattice, rather than pulling to unravel a dimer (Barsegov et al, ; Jiang, Bailey, et al, ; Theisen, Desai, Volski, & Dima, ). Such computational results are additional evidence that the unfoldase mechanism is less likely than a wedging or pushing mechanism.…”

“…Several groups, including our own, have noted that katanin has the ability to depolymerize microtubules in addition to severing them (Díaz‐Valencia et al, ; McNally & Vale, ; Zhang et al, ). This activity is important when regulating microtubule length, particularly at the cortex in interphase cells and kinetochore fibers in mitosis (Jiang, Bailey, Burke, Ross, & Dima, ; Jiang, Rezabkova, et al, ; McNally, Audhya, Oegema, & McNally, ; Zhang et al, ; Zhang, Rogers, Buster, & Sharp, ). We have shown that katanin can depolymerize taxol‐stabilized microtubules in an ATP‐dependent manner (Díaz‐Valencia et al, ; Zhang et al, ).…”

Molecular Investigations into the Unfoldase Action of Severing Enzymes on Microtubules

“…the Regular (REG) model, which represents the GDP type lattice, and the All Homogenous model (AHM), which mimics the GMPCPP type lattice [Kononova et al, 2014, Jiang et al, 2017, Szatkowski et al, 2019, as described in the Methods section. Here we examined the unfoldase mechanism where the MT severing enzyme removes dimers through pulling on the CTT(s) of the tubulin dimer.…”