Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule
Journal article, 2021

Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end.

Equilibrium dynamics

Molecular dynamics

Protofilament

Diabetes

Alzheimer’s disease

Microtubules

Small drugs

Author

Alexandr Nasedkin

Chalmers, Physics, Biological Physics

Inna Ermilova

Chalmers, Physics, Nano and Biophysics

Jan Swenson

Chalmers, Physics, Nano and Biophysics

European Biophysics Journal

0175-7571 (ISSN) 1432-1017 (eISSN)

Vol. In Press

Subject Categories

Physical Chemistry

Biophysics

Theoretical Chemistry

DOI

10.1007/s00249-021-01553-1

PubMed

34215900

More information

Latest update

7/15/2021