Zhang Yan-ping, Sheng Ya-jun, Zheng Wei, He Ping-an, Ruan Ji-shuo
Department of Mathematics, School of Science, Hebei University of Engineering, Handan 056038, China.
Graduate School at ShenZhen, Tsinghua University, Guangdong 518055, China.
Biomed Res Int. 2015;2015:909567. doi: 10.1155/2015/909567. Epub 2015 Feb 2.
The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.
氨基酸的疏水性和亲水性在蛋白质折叠、其与环境及其他分子的相互作用以及催化机制中起着非常重要的作用。基于这两个物理化学指标，引入了蛋白质序列的二维图形表示；同时，提出了一种新的数值特征来计算不同序列的距离，以便在此图形表示的基础上分析序列的相似性/不相似性。此外，我们将新的距离应用于九个物种的ND5蛋白的相似性/不相似性分析，并基于包含639个结构域的数据集预测四个主要类别。结果表明该方法简单有效。
