Molecular Mechanics of Stutter Defects in Vimentin Intermediate Filaments

Abstract

Vimentin coiled-coil alpha-helical dimers are elementary protein building blocks of intermediate filaments, an important component of the cell’s cytoskeleton. All intermediate filament dimers feature a highly conserved ‘stutter’ region, a sequence of amino acids that interrupts the superhelical coiled-coil arrangement of the two alpha-helices, leading to a parallel arrangement of the alpha-helices in this region. Earlier studies have suggested that the stutter plays an important role in filament assembly. Here we show that the stutter also has a significant effect on the mechanical behavior of vimentin dimers. We develop an Extended Bell Model to provide a theoretical description of the unfolding behavior of coiled-coil structures, capable of capturing different molecular geometries and loading rates. The Extended Bell Model predicts that the stutter represents a molecular defect at which unfolding occurs at lower forces than in the rest of the protein. Our studies suggest that the presence of the stutter leads to a softer structure with more homogeneous plastic strain distribution under deformation. The predictions by the Extended Bell Model are confirmed by large-scale MD simulations of three model systems: Two parallel alpha-helices, a coiled-coil dimer, as well as a coiled-coil dimer with a stutter. The simulations prove that in agreement with the prediction based on our Extended Bell Model, the stutter represents the locations at which the protein structure has the least resistance to unfolding. We discuss the implications of this molecular architecture in terms of its biological function.