title: Fractal geometry study of DNA binding proteins.
abstract: 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.
authors.affiliation: Department of Protein Engineering, Institute of Biophysics Academia Sinica, Beijing, P.R. China.
authors.forename: J
authors.initials: J
authors.lastname: Xu
authors.forename: Y
authors.initials: Y
authors.lastname: Chao
authors.forename: R
authors.initials: R
authors.lastname: Chen
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins