Packing energetics determine the folding routes of the RNase-H proteins

Abstract

Comparative studies of proteins from a family have been used to understand the factors that determine the folding routes of proteins. It has been conjectured that the folding mechanism of ribonuclease-H (RNase-H) proteins is determined by the topology of their fold. To test this hypothesis, we computationally studied the folding of four proteins from the RNase-H family, which have the overall RNase-H fold, but whose topologies differ in the region termed CORE in E. coli RNase-H. We simulated the folding of these proteins using molecular dynamics (MD) simulations of a coarse-grained structure-based model (SBM) which captures the effects of topology and found that the four proteins had similar folding routes. However, these simulated folding routes do not agree with the folding routes of those RNase-H proteins that have been experimentally characterized. We next simulated the proteins using an SBM which specifically accounts for packing energetics and found that these routes not only vary substantially across the simulated RNase-H proteins but also agree with experiments. Thus, the packing energetics determine the folding mechanism of the RNase-H proteins. By comparing the differing folding routes calculated from the two models, we isolated packing interactions that promote these differences. We find that the balance of packing energetics between CORE and the rest of the protein is different across the different RNase-Hs. This balance determines the folding route. Our studies suggest that proteins from the RNase-H family should be used for experimentally detecting structurally distinct folding routes.