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.
Kobayashi
Y
Y
Department of Information Systems Science, Faculty of Engineering, Soka University, Tokyo, Japan. koba@t.soka.ac.jp
Saito
N
N
D000595:Amino Acid Sequence; D000818:Animals; D001048:Aplysia / Q000737:chemistry*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017385:Sequence Homology; D013816:Thermodynamics; D014907:Whales
D009211:Myoglobin