Computer Simulations of Post-Translationally Modified Microtubules

Microtubules are large, multimeric, hollow tubes made of tubulin found in all eukaryotic cells. They are integral to DNA segregation, organelle localisation and intracellular cargo transport. Microtubules are rich in post-translational modifications (PTMs), particularly along tubulin C-terminal tails, which modulate dynamics, protein recruitment and motor protein processivity. These modifications make up the Tubulin Code, which encodes a set of signals that result in specific and consistent changes in factors such as microtubule stability and levels of protein recruitment. The current understanding of each modifications effect is limited, due to limitations in both in vitro and in silico methods. Atomistic molecular dynamics (MD) simulations of microtubules have only been possible for the last 10 years, meaning aspects such as the effect of PTMs on microtubule dynamics are yet to be fully explored. This project presents a method for building and parameterising post-translationally modified microtubules for atomistic MD simulations. This was used to generate 100 ns simulations of a 7-protofilament model (PF Sheet) with either 10 residue poly(glycine) or poly(glutamate) chains. These were compared against an unmodified 13-protofilament microtubule simulation. These simulations showed the ends of both models curve away from the centre, caused by the plus end GDP-cap. Negatively charged poly(glutamate) chains positioned between protofilaments were found to interfere with inter-protofilament salt bridges, causing model to break apart. The smaller model flattened out during each simulation, which was not observed in the Short MT simulation, adding to existing evidence that microtubule fragment models do not accurately represent complete microtubules in atomistic simulations.