Prediction of the tertiary structure of parathyroid-hormone-related protein (residues 1-34) by the island model

Statistical mechanics of protein structural transitions: Insights from the island model

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô’s views on the hierarchic structure of science.

Refolding of myoglobins of nonhomologous sequences by the island model

The folding process of sea hare myoglobin was stimulated by the island model, which does not rely on sequence homologies or statistical inference from database of known structure. Sea hare myoglobin has low sequence homology (28%), but high structural similarity, with sperm whale myoglobin, which was already simulated by the island model. Their structural similarity is shown physiochemically from the distribution of hydrophobic-residue pairs, that is, the key pairs for packing of the secondary structures. Irrelevant to the sequence homology, the secondary structures can be packed into the tertiary structure through the hydrophobic interactions among the amino acid pairs responsible for the local structure formation. The results on the two species of myoglobins indicate that, in contrast to other prediction methods, the island model is applicable to any type of protein without extra information other than the distribution of hydrophobic-residue pairs and the positions of the secondary structures. Consequently the present results provide another verification of the validity of the island model for elucidating the mechanisms of protein folding and predicting protein structures.

A simplified amino acid potential for use in structure predictions of proteins

A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site-site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed phi and psi angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the introduction of an effective potential. The model is tested on two small proteins, avian pancreatic polypeptide and a parathyroid hormone-related protein, by simulating folding from an initially extended state using Monte Carlo methods. The reduced amino acid description is able to satisfactorily reproduce the experimentally determined native structures.

Refolding of cytochrome b562 and its structural stabilization by introducing a disulfide bond

The packing mechanism of the secondary structures (4-alpha-helices and 3(10)-helix) of cytochrome b562 is simulated by the "island model," where the formation of protein structure is accomplished by the growth-type mechanism with the driving force of packing of the long-range and specific hydrophobic interactions. Packing proceeds through the formation of the structure at the nonhelical part, where a lot of hydrophobic pairs are distributed. Consequently, conformation, nearly similar to the native one, is successfully obtained. With the help of this result, the theoretical prediction of the possibility of forming this disulfide mutant (N22C/G82C) of b562 can be performed prior to the experiments by our geometrical criterion ("lampshade"). This criterion is expected to be a significant principle for introducing possible disulfide bonds into a protein to be engineered.