Xu J, Chao Y, Chen R
Department of Protein Engineering, Institute of Biophysics Academia Sinica, Beijing, P.R. China.
J Theor Biol. 1994 Dec 7;171(3):239-49. doi: 10.1006/jtbi.1994.1228.
The main aim of this paper is to search for three-dimensional structure homology between DNA-binding proteins. The run of a protein's main chain is depicted by a sequence, which is constituted by the fractal indices, where each index describes how twisted or extended a partial protein segment is. Two proteins are compared by constructing a dot matrix between two such sequences, and the matrix is searched for dot-concentrated rectangles which is an indication of tertiary homology. This new method is applied to DNA-binding proteins which are selected from Brookhaven Protein Data Bank, among which most contain a helix-turn-helix motif. The dot-matrix shows that there is tertiary homology between two motifs. Other interesting results are also presented in this paper.
本文的主要目的是寻找DNA结合蛋白之间的三维结构同源性。蛋白质主链的走势由一个序列描绘，该序列由分形指数构成，其中每个指数描述了蛋白质部分片段的扭曲或伸展程度。通过在两个这样的序列之间构建点矩阵来比较两种蛋白质，并在矩阵中搜索点密集的矩形，这表明存在三级同源性。这种新方法应用于从布鲁克海文蛋白质数据库中选取的DNA结合蛋白，其中大多数含有螺旋-转角-螺旋基序。点矩阵显示两个基序之间存在三级同源性。本文还给出了其他有趣的结果。
