Ab initio method for predicting tertiary structures of globular proteins

We have developed an ab initio method for predicting the tertiary structures of globular proteins on the basis of the mechanisms of protein folding. This method is referred to as the `island model'. The term island implies a local structure yielded during folding such as secondary structure. Several islands pack into bigger ones step by step and then they reach a compact tertiary structure. The driving force of packing is hydrophobic interaction which brings hydrophobic residues closer through its long-range nature and the specificity of residue pairing after secondary-structure formation. The island model is applicable to any type of proteins irrespective of sequential homology, since the island model is simply based on physicochemical mechanisms of folding. The folding simulation based on the island model is reviewed by illustrating the results for representative globular proteins such as cytochrome b562, sea hare myoglobin and BPTI. These results indicate that the island model can elucidate the folding mechanism and predict the tertiary structures of proteins.