Variations in chain compactness and topological complexity uncover folding processes in the relaxation dynamics of unfolded in vacuo lysozyme

Abstract

Chain collapse and the formation of a near-native tertiary structure are believed to be two key features controlling the progress of a protein folding transition. In this work, we study the interrelation between these two properties along computer-simulated relaxation trajectories of unfolded in vacuo lysozyme. Large-scale molecular shape transitions are monitored within a space defined by two discriminating descriptors of chain compactness and entanglement (or “topological”) complexity. For the system studied here, results indicate that successful refolding into native-like conformers requires a balance between polymer collapse and a topologically “correct” organization of chain loops. Although no single factor dominates the relaxation paths, compactization appears to be a necessary condition for near-native refolding. Whenever initial collapse is limited or absent, we find a “derailed” folding path with high configurational frustration. We also show that disulfide-reduced lysozyme unfolds differently, yet relaxes to the pattern of molecular shapes characteristic of the folded states of disulfide-intact lysozyme.