Robert B. Best

Laboratory of Chemical Physics

NIDDK, National Institutes of Health

How important are non-native interactions for protein folding? Insights from

all-atom simulations

The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures the transition states for all the proteins with a folding free energy barrier remarkably well. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein alpha3D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms.