Predicting the Three Dimensional Structure of a Lattice Designed Model Protein from its Primary Structure

Through systematic studies of lattice Monte Carlo simulations of the folding of designed heteropolymers, we have identified a hierarchy of specific elementary phenomena which control the way single domain protein fold: a) formation of few, local elementary structures, b) creation of the (post-critical) folding nucleus through the assemblage together of the local elementary structures, c) relaxation of the remaining amino acids to the native conformation. These results, which are consistent with a two-state kinetics of the folding of small, single domain proteins, where the local elementary structures and the folding nucleus can be viewed as hidden intermediates along the reaction pathway, provide the basis for a strategy to read the tertiary structure of a protein from its amino acid sequence.