Ab initio structure predictions using a hierarchic approach applied to 434 CRO and Drosophila homeodomain

A discrete-state ab initio protein structure prediction procedure is presented, based on the assumption that some protein fold in an hierarchical way, where the early folding of independent units precedes and helps complete structure formation. It involves a first step predicting, by means of threading algorithms and local structure prediction methods, the location of autonomous protein subunits presenting favorable local and tertiary interactions. The second step consists of predicting the structure of these units by Monte Carlo simulated annealing using several database-derived potentials. In a last step, these predicted structures are used as starting conformations of additional simulations, keeping these structures frozen and including the complete protein sequence. This procedure is applied to two small DNA-binding proteins, 434 cro and the Drosophila melanogaster homeodomain that contain 65 and 47 residues, respectively, and is compared to the nonhierarchical procedure where the whole protein is predicted in a single run. The best predicted structures were found to present root-mean-square deviation relative to the native conformation of 2.7 A in the case of the homeodomain and of 3.9 A for 434 cro; these structures thus represent low-resolution models of the native structures. Strikingly, not only the helices were correctly predicted but also intervening turn motifs.