Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling

Abstract

We report molecular dynamics (MD) simulation and atomistically informed continuum modeling of the nanomechanics of the β-helix protein motif, a key building block of amyloids associated with Alzheimer’s, Huntington’s and prion diseases, forming a nanotube-like protein structure. We find that the β-helix structure is extremely extensible and can sustain tensile deformation up to 800% engineering strain without rupture of the covalently bonded protein backbone. Our atomistic simulation results reveal that the instantaneous strength of the tube is proportional to the rate of H-bond rupture, providing a link between the dynamics of hydrogen bond rupture and the mechanical signature of the protein structure. This finding proves that concurrent as opposed to sequential breaking of bonds leads to higher mechanical resistance, corroborating earlier results found in studies of β-sheet protein domains. Inspired by the beta-helical domain of the needle-like cell puncture device of bacteriophage T4, we carry out compressive loading simulations of the β-helix, and show that this protein motif can withstand extremely large compressive loads, far exceeding the tensile strength. Different mechanical deformation modes under compressive loading are summarized in a deformation map. Our findings illustrate the potential of the β-helix protein motif as an inspiration for nano-scale materials applications, ranging from stiff nanotubes to self-assembling peptide based fibers inspired by amyloids.