A simple method for assessing the mutational effect on the protein-DNA interaction: application to amino acid...

We have developed a simple method to assess the effect of mutations on the binding affinity change in the protein-DNA interaction. In this method, we evaluate the contribution of the local geometric effect in protein-DNA recognition by calculating the change in interaction energy caused by mutations, and assess the binding activity by introducing the binding affinity index. We applied this method to the interaction between lambda repressor and DNA. In spite of the simplicity of the present method, the calculated results qualitatively agree with experimental results for a limited number of mutants of lambda repressor. The mutational effects are mostly attributed to the complementary interactions in the protein-DNA complex. Although the method is still preliminary and should be the subject of further experimental verification, it may be used effectively at the planning stage of mutagenesis experiments to narrow down the selection of mutation by excluding unreasonable mutations.