Disulfide Bonds Modulate Lysozyme Folding Pathways

Experiments on lysozyme folding [Dobson et al., 1994; Kiefhaber, 1995] show that it folds in parallel pathways: a slow kinetic pathway with well populated partially folded states and a faster pathway without any intermediates. We studied lysozyme folding using coarse-grained protein models and molecular dynamics simulations. The simulations do show that lysozyme has slower and faster folding pathways as predicted by the experiments. The folding timescale in the fast pathway is on the order of tens of milliseconds as expected for two-state folding globular proteins. In the slower pathway, the folding timescale is higher as the intermediate populated in this pathway is stable for hundreds of milliseconds. The intermediate populated is partially structured where the β domain is fully formed and the α domain is partially formed and there are no inter-domain contacts. These intermediates are kinetically trapped and require rearrangement in order to fold to its native state. The disulfide bonds play a major role in enhancing the lifetime of the intermediate as the conformational space available for the protein to rearrange is constrained due to the presence of the disulfide bonds. The kinetically trapped intermediates are not observed in the folding pathways when the disulfide bonds are absent