Microtubules (MTs) are cytosolic filaments vital for multiple cellular processes such as cell division, cellular morphology and cellular trafficking. At the molecular level, the dynamic instability (random growth and shrinkage) of the MT is driven by the hydrolysis state of GTP in the β subunit of the tubulin dimers at the MT end. Here, we use large-scale molecular dynamics simulations and normal mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed by two neighboring protofilaments. We utilize recent high-resolution structures of dynamic MTs by Nogales et al. [Cell 157, 1117 (2014)] to simulate both a GDP octamer and an octamer with a single GTP cap layer. We analyze multiple replicas of long-time atomistic molecular dynamics (~2 μs simulation time) of both the GDP octamer and the octamer with a single GTP cap layer. Furthermore, using NMA, we calculate mechanical properties such as flexural rigidity (kf) persistence length (lp), bending modulus (Yf), stretching rigidity (ks) and stretching modulus (Ys) of both octamers, averaging over multiple replicas. Moreover, we next incorporate the negatively charged C-terminal tails, characterizing their effect on protofilament conformation and MT stability at varying salt concentrations. We propose that both the lateral and longitudinal contacts between PFs, as well as the phosphorylation state of the nucleotide, play cooperative roles in determining protofilament conformation and, therefore, the dynamic stability of the MT.

Effect of nucleotide state on the protofilament conformation of tubulin octamers

254th National Meeting (2017)

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