Structure Prediction and Nanomechanical Properties of Human Vimentin Intermediate Filament Dimers

Abstract

Intermediate filaments (IFs), in addition to microtubules (MTs) and microfilaments (MFs), are one of the three major components of the cytoskeleton in eukaryotic cells. As the basic building block of IFs, the properties of the IF dimmer re crucial to fully understand the molecular basis for the properties of the IF network in cells. However, the structure of IF dimers remains unknown, which has thus far prevented the elucidation of its nanomechanical properties, in particular molecular-level mechanisms of deformation. Here we present the development of a full atomistic molecular model of the vimentin dimmer, a coiled-coil structure consisting of four alpha-helixes (AHs). The structure is found to be stable in molecular dynamics simulation after an extensive equilibration process. After careful structure prediction, the behavior of the IF dimer under mechanical stress is investigated; including studies of changing the pulling velocity and a detailed analysis of the associated deformation and rupture mechanisms. Most notably, we observe a transition of AHs to beta-sheets (BSs) under mechanical deformation, as has been observed indirectly in earlier experimental studies. Our result helps to better understand the structure and fracture mechanism of this important protein filament.