Relaxation dynamics of biopolymers seeded with unfolded lysozyme transients in acuo. The role of primary sequence in protein folding

Abstract

The availability of experimental data on biomolecular ions diffusing in a low-pressure gas has raised a number of important questions about the folding behaviour of anhydrous proteins in acuo. In this work, we explore an important aspect of the folding mechanism for anhydrous proteins, namely, its sensitivity to changes in primary sequence. To this end, we study the computer-simulated relaxation dynamics of protein conformers that share the same initial unfolded backbone geometry, but that differ in the primary sequences. The initial unfolded (transient) conformers are derived from an in acuo unfolding run of lysozyme. The relaxation behaviour of unfolded disulfide-intact lysozyme is compared with that of four other different sequences threaded to the same unfolded backbone geometry: disulfide-reduced lysozyme, cytochrome c′, polyglycine and polyalanine. Using a large ensemble of molecular dynamics trajectories, we monitor configurational transitions in a two-dimensional space of order parameters that convey changes in compactness and chain entanglement. Our results indicate that both disulfide-intact and disulfide-reduced lysozyme relax to structures with quasi-native compactness and entanglement. However, fast refolding appears to be more efficient in the presence of the disulfide bridges, since noncompact intermediates persist longer in disulfide-reduced lysozyme. The cytochrome c′ sequence threaded onto the lysozyme transient shows similar relaxation behaviour to that of disulfide-intact lysozyme. Yet, the cytochrome c′ sequence gives rise to several long-lived intermediates, one of which displays global molecular shape features similar to those of native cytochrome c′. In contrast, the relaxation of the polyglycine transient exhibits no initial large-scale collapse, but rather resembles the “pearling” transition of homopolymers (i.e., the initial formation of small locally compact blobs of chain). Polyalanine displays an intermediate behaviour, characterized by instances of both successful and frustrated global collapse. These findings shed light on how primary sequence affects specifically the formation of initial, persistent folding intermediates in acuo.