Kinjo Akira R, Nishikawa Ken
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan.
Bioinformatics. 2005 May 15;21(10):2167-70. doi: 10.1093/bioinformatics/bti330. Epub 2005 Feb 18.
One-dimensional (1D) structures of proteins such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it is still not clear whether a given set of 1D structures contains sufficient information for recovering the underlying 3D structure. Here we show that the 3D structure of a protein can be recovered from a set of three types of 1D structures, namely, secondary structure, contact number and residue-wise contact order which is introduced here for the first time. Using simulated annealing molecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of sizes ranging from 56 to 146 residues. By selecting the structures best satisfying the restraints, all the proteins showed a coordinate RMS deviation of <4 A from the native structure, and, for most of them, the deviation was even <2 A. The present result opens a new possibility to protein structure prediction and our understanding of the sequence-structure relationship.
蛋白质的一维（1D）结构，如二级结构和接触数，为理解蛋白质的天然三维（3D）结构如何在氨基酸序列中编码提供了直观的图像。然而，尚不清楚给定的一组一维结构是否包含恢复潜在三维结构的足够信息。在这里，我们表明蛋白质的三维结构可以从一组三种类型的一维结构中恢复，即二级结构、接触数和首次在此引入的残基接触序。使用模拟退火分子动力学模拟，针对各种结构类别且大小范围从56至146个残基的16种蛋白质，寻找满足给定天然一维结构限制的结构。通过选择最符合限制的结构，所有蛋白质与天然结构的坐标均方根偏差<4 Å，并且对于大多数蛋白质，偏差甚至<2 Å。目前的结果为蛋白质结构预测以及我们对序列 - 结构关系的理解开辟了新的可能性。
