Kobayashi Y, Saito N
Department of Information Systems Science, Faculty of Engineering, Soka University, Tokyo, Japan.
J Protein Chem. 1997 Feb;16(2):83-98. doi: 10.1023/a:1026385816247.
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.
海兔肌红蛋白的折叠过程由岛屿模型激发，该模型不依赖序列同源性或来自已知结构数据库的统计推断。海兔肌红蛋白与抹香鲸肌红蛋白的序列同源性较低（28%），但结构相似性较高，而抹香鲸肌红蛋白已由岛屿模型模拟。它们的结构相似性从疏水残基对的分布在物理化学上得以体现，也就是说，这些是二级结构堆积的关键对。与序列同源性无关，二级结构可通过负责局部结构形成的氨基酸对之间的疏水相互作用堆积成三级结构。两种肌红蛋白的结果表明，与其他预测方法不同，岛屿模型适用于任何类型的蛋白质，除了疏水残基对的分布和二级结构的位置外无需额外信息。因此，目前的结果为岛屿模型在阐明蛋白质折叠机制和预测蛋白质结构方面的有效性提供了又一验证。
