The unfolding mechanism of monomeric mutant SOD1 by simulated force spectroscopy

Mechanical unfolding of mutated apo, disulfide-reduced, monomeric superoxide dismutase 1 protein (SOD1) has been simulated via force spectroscopy techniques, using both an all-atom (AA), explicit solvent model and a coarse-grained heavy-atom G (o) over bar (HA-G (o) over bar) model. The HA-G (o) over bar model was implemented at two different pulling speeds for comparison. The most-common sequence of unfolding in the AA model agrees well with the most common unfolding sequence of the HA-G (o) over bar model, when the same normalized pulling rate was used. Clustering of partially-native structures as the protein unfolds shows that the AA and HA-G (o) over bar models both exhibit a dominant pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches after the protein is about half-unfolded. The force-extension curve exhibits multiple force drops, which are concomitant with jumps in the local interaction potential energy between specific beta-strands in the protein. These sudden jumps in the potential energy coincide with the dissociation of specific pairs of beta-strands, and thus intermediate unfolding events. The most common sequence of beta-strand dissociation in the unfolding pathway of the AA model is beta-strands 5, 4, 8, 7, 1, 2, then finally beta-strands 3 and 6. The observation that beta-strand 5 is among the first to unfold here, but the last to unfold in simulations of loop-truncated SOD1, could imply the existence of an evolutionary compensation mechanism, which would stabilize beta-strands flanking long loops against their entropic penalty by strengthening intramolecular interactions. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.