Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins

Abstract

Most proteins must fold to a well-defined structure with a minimal stability to perform their function. Here we use a simple, molecular dynamics-based, energy decomposition approach to map the principal energetic interactions in a set of proteins representative of different folds. This work involves the all-atom simulation and analysis of the native structures and mutants of five different proteins representative of an all-alpha (yACPB, Protein A), all-beta (SH3), and a mixed alpha/beta fold (Proteins G and L). Given a certain structure, a native sequence and a set of mutants, we show that our model discriminates the ability of a mutation to yield a more or less stable protein, in agreement with experimental data, catching the principal energetic determinants of protein stabilization. Our approach identifies the interaction determinants responsible to define a fold and shows that mutations can either modulate the strength of pair-wise coupling between residues important for folding, or modify the profile of the principal interactions. Furthermore, we address the question of how to evaluate the fitness of a sequence to a given structure by comparing the information contained in the energy map, which recapitulates the chemistry of the sequence, to that contained in the contact map, which recapitulates the fold topology. The results show that the better fit between the energetic properties of the sequence and the fold topology corresponds to a higher stabilization of the protein. We discuss the relevance of these observations to the analysis of protein designability and to the rational evolution of new sequences.