Effect of a Variable Nonbonded Attractive Pair Interaction on the Relaxation Dynamics of in Vacuo Unfolded Lysozyme

Starting from a partly unfolded conformer of in vacuo lysozyme, we study the configurational transitions and molecular shape changes that accompany the relaxation (and eventual refolding) of the protein. In particular, we explore the effect of a variable monomer-monomer interaction on the folding dynamics within an ensemble of relaxation trajectories. We find that a strong attractive potential does not necessarily produce configurational "freezing," but instead can be consistent with nativelike refolding. In contrast, a reduction in attraction below a critical value suppresses polymer collapse and eventually leads to complete unfolding. Our results suggest that, qualitatively, folding behavior may not be strongly dependent on the details of the model force field, but rather a feature associated with a range of potential energy functions.