Thermal Folding and Mechanical Unfolding Pathways of Protein Secondary Structures

Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfolding. Opposite cross-correlations are found for an $\alpha$-helix and a $\beta$-hairpin structure. In a tandem of two $\alpha$-helices, the two constituent helices unravel nearly simultaneously. A simple condition for simultaneous vs. sequential unraveling of repeat units is presented.