Fractal geometry study of DNA binding proteins.
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.
Xu
J
J
Department of Protein Engineering, Institute of Biophysics Academia Sinica, Beijing, P.R. China.
Chao
Y
Y
Chen
R
R
D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004926:Escherichia coli; D017709:Fractals; D008958:Models, Molecular; D017386:Sequence Homology, Amino Acid
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins