Assessment of hydrophobicity scales for protein stability and folding using energy and RMSD criteria

Abstract

De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role in such simulations as they define the energetic interactions between protein residues, thus determining the energetically favorable conformation. While many HSs have been developed over the years using various methods, it is surprising that the scales show very weak consensus in their assignment of hydrophobicity indexes to the various residues. In this work, several HSs are systematically assessed via atomistic Monte Carlo simulation of folding of small proteins, by converting the HSs of interest into residue-residue contact energy matrices. HSs that poorly preserve native structures of proteins were tuned by applying a linear transformation. Subsequently, folding simulations were used to examine the ability of the HSs to correctly fold the proteins from a random initial conformation. Root mean square deviation (RMSD) and energy of the proteins during folding were sampled and used to define an ER-score, as the correlation between the 2-dimensional energy-RMSD (ER) histogram with 50% lowest energy conformations and the ER histogram with 50% lowest RMSD conformations. Thus, we were able to compare the ability of the different HSs to predict de novo protein folding quantitatively.