Molecular dynamics (MD) study of the structural and dynamical properties of an intrinsically disordered protein (IDP)

Mechanical gradients in the hard tissues of biological materials are essential for dissipation of stress and large forces that lead to damage. Despite the lack of mineralization, the Nereis virens worm jaw has mechanical properties comparable to human dentin and superior to synthetically engineered polymers. These remarkable properties arise from an extensive coordination of Zn²⁺ with a histidine rich IDP, Nvjp-1, imparting the jaw with mechanical and chemical gradients that greatly enhance its functionality. In a recent study [1], we used all atom MD simulations to investigate how Zn²⁺ binding to Nvjp-1 mediates sclerotization of the Nereis virens jaw. It was shown that zinc capture occurs at low pH mainly by polar residues with at most two residues interacting with a given zinc ion. A pH shift to alkaline conditions leads to additional zinc-residue coordination resulting in a reduction of the radius of gyration that correlates with sclerotization. Here we present results on structure factor, intermediate scattering function, and backbone N-H vector correlations for pristine and metal-bound Nvjp -1. These results may be combined with small angle x-ray scattering (SAXS) and nuclear magnetic resonance (NMR) data to understand the role of metal centers on the structural and dynamical properties of biological materials.

1. J. Phys. Chem. B 2022, 126, 6614.