Positive Charge Cores in DNA-Binding Proteins

Abstract

There are many structural motifs of DNA-binding proteins, which play a central role in the regulation of gene expression. The structural motifs are, for example, helix-loop-helix (HLH), basic leucine zipper (bZIP), and Zinc finger. Because of the biological significance of DNA binding proteins, the structure of DNA-protein complexes have been extensively studied, and the information about the DNA-binding regions are already available for many DNA-binding proteins. Now, it is possible to identify the structural motifs by using the corresponding sequence motifs. However, the characteristics of DNA-binding proteins common to all structural motifs have hardly studied yet. Brendel and Kirlin (1989) pointed out that many DNA-binding proteins have multiclusters of electric charges as their common features according to the analysis of limited number of data [1]. The binding between negative charges of DNA and a positive charge cluster of a protein is physically sound, and if the charge clusters are really common features irrespective of the structural motifs, it will be very useful for the annotation of amino acid sequences from genome analysis. We analyzed, in this work, 955 DNA-binding proteins whose binding regions are known and found that there are dual clusters of positive charges at the distance of 20 to 30 residues for many DNA binding proteins of different structural motifs.