On the nature of the unfolded state: competing mechanisms in the unfolding of anhydrous protein ions

Protein ions undergo folding–unfolding transitions unaided by water. Experiment and simulations suggest a critical protonation state below which the native fold might be metastable. Here, we use molecular dynamics simulations of charged lysozyme to explore the underlying mechanism for the unfolding transition. Two processes are found to work simultaneously in vacuo: the unfolding bias associated with the repulsion between charged residues, and a bias induced by the unhindered rotation used in the simulation protocol. The latter emerges as a slow process that is always accessible to all lysozyme ions. The denatured state generated by centrifugal unfolding appears to be unique and independent of the total protein charge.