Mechanical Properties of Tubulin Molecules by Molecular Dynamics Simulations

The basic unit in microtubules is αβ-tubulin, a hetero-dimer consisting of an α- and a β-tubulin monomer. The mechanical characteristics of the dimer as well as of the individual monomers may be used to obtain new insight into the microtubule tensile properties. In the present work we evaluate the elastic constants of each of the monomers and the interaction force between them by means of molecular dynamics simulations. Molecular models of α-, β-, and αβ-tubulin were developed starting from the 1TUB.pdb structure from the RSCB database. Simulations were carried out in a solvated environment using explicit water molecules. In order to measure the monomers’ elastic constants, simulations were performed by mimicking experiments carried out with atomic force microscopy. A different approach was used to determine the interaction force between the α- and β-monomers using 8 different monomer configurations based on different inter-monomer distances. The obtained results show an elastic constant value for α-tubulin of 3.4–3.9 N/m, while for the β-tubulin the elastic constant was measured to be 1.8–2.4 N/m. The maximum interaction force between the monomers was estimated to be 11.2 nN. In perspective, these outcomes will allow exchanging atomic level description with key mechanical features enabling microtubule characterisation by continuum mechanics approach.