Studies on protein-DNA interactions using the resonant recognition model. Application to repressors and transforming proteins.

The structural features of protein-DNA interactions have been evaluated using a new information theory algorithm for the analysis of protein structure/function dependence: the so-called resonant recognition model. The physicochemical basis of this analysis was firstly validated with the trp-repressor-operator interaction as a well-defined example. The amino acid and structural features predicted by these procedures to be crucial for repressor-operator interaction were found to be clustered around the known three-dimensional structure of the active site of the trp repressor. Similar methods of analysis have been extended to the less-well-defined example of the Ha-ras p21 protein family. The results of this analysis have indicated two distinct interactive regions in p21, one associated with the guanine-nucleotide-binding site, whilst the second is proposed to be associated with a binding site for an activator protein. These studies indicate that the p21 protein, besides the ability to function as a plasma-membrane-associated guanine-nucleotide-binding regulatory protein and bind free guanine nucleotides in the cytoplasm, has the structural ability to bind guanine incorporated in DNA. Thus, p21-related proteins may have the potential to function as an DNA-binding and regulating protein with the mode of upstream DNA binding closely related to their oncogenic function.