A simulation protocol to study proteins in vacuo. Controlled re-folding and re-unfolding transitions

Computed simulations suggest that denatured anhydrous proteins can re-fold into quasi-native structures unaided by water, in agreement with experimental evidence. Using a novel protocol for dynamics simulations, we report on in vacuo relaxation studies of a partly unfolded intermediate of apo-cytochrome c′. We find a range of accessible paths that include direct native-like re-folding, reversible re-unfolding, and full unfolding. The timescale for these processes can be regulated by modifying the coupling to the simulated thermal bath. The simulation strategy and the tools developed to follow molecular shape changes provide a robust approach to study intrinsic properties of protein folds.