Atomistic Basis of Microtubule Dynamic Instability Assessed Via Multiscale Modeling

Abstract

Microtubule “dynamic instability,” the abrupt switching from assembly to disassembly caused by the hydrolysis of GTP to GDP within the β subunit of the αβ-tubulin heterodimer, is necessary for vital cellular processes such as mitosis and migration. Despite existing high-resolution structural data, the key mechanochemical differences between the GTP and GDP states that mediate dynamic instability behavior remain unclear. Starting with a published atomic-level structure as an input, we used multiscale modeling to find that GTP hydrolysis results in both longitudinal bond weakening (~ 4 kBT) and an outward bending preference (~ 1.5 kBT) to both drive dynamic instability and give rise to the microtubule tip structures previously observed by light and electron microscopy. More generally, our study provides an example where atomic level structural information is used as the sole input to predict cellular level dynamics without parameter adjustment.

Bending-torsional elasticity and energetics of the plus-end microtubule tip

“…Our conformational analysis shows that substantially more free energy is required to spontaneously form straight GDP-PFs than straight GTP-PFs at the MT tip (Fig. 2A), in good agreement with the re-cent experimental observation that subpopulations of straight GDP-oligomers occur extremely rarely [58] as well as with recent computational studies [31,32,33,35,36]. Moreover, not only does GTP hydrolysis appear to affect the confrontational rigidity of PFs, but its influence is also highly anisotropic, with GTP-PFs being more flexible with respect to both outward twist-bending and tangential swing and GDP-PFs being more rigid, but particularly rigid to motions in the tangential direction.…”

“…2C ). This finding correlates well with a recent MD study showing that GTP hydrolysis results in a ∼4 k B T longitudinal bond weakening [36] as well as with our previous finding that the longitudinal bonds in GDP-PFs are more fragile when subject to mechanical stretching [35]. We note, however, that the FDA provides only the enthalpic contribution to the longitudinal stability because the entropic penalty for eliminating solvent from tubulin's surface is not taken into account.…”

“…Relaxation dynamics and heterogeneity of MT plus-end tips At the MT tip, the elastic energy stored by straightened PFs is only insufficiently balanced by the total energy of lateral dimer-dimer interactions, which results in MT structures featuring irregularly splayed, curved PFs [25,26,27]. Recent atomistic MD simulation have predicted substantial differences in the bending rigidity of GTP-and GDP-bound free dimers, single PFs, and tubulin octamers [31,32,33,34,35,36]. Concomitantly, it has been proposed that the formation/breakage of lateral dimer-dimer contacts might also be nucleotide-dependent [37,38,39].…”

“…The complex bending-torsional coupling and the clockwise lattice twist of the individual PFs at the MT tip, particularly pronounced in GDP-MTs, suggests that the usually employed single angular variables describing the nucleotide-dependent radial bending angles between adjacent tubulins [45,46,47,27,36] may be insufficient to fully explain the conformational dynamics of PFs. We therefore asked, what are the essential collective variables that quantitatively describe bending-torsional PF fluctuations in our atomistic simulations and exactly how are these affected by the nucleotide state?…”

“…This draws attention to the lateral contacts, the exact role of which in the MT stability is still controversially debated [55]. With two notable exceptions [38,39], simulation studies have proposed that the stability of lateral PF-PF contacts is unaffected by the nucleotide state [32,35,33,34,36]. However, only in one of these studies [34], the lateral binding free energy was computed explicitly using enhanced sampling techniques, though with relatively moderate sampling times.…”