Prediction of Mutational Effect in the Protein-DNA Recognition with the Aid of Computer Graphics

抄録

We have developed a simple method to predict the effect of mutations of bases and amino acid residues on the binding affinity between protein and DNA, automated the procedure and visualized the results on computer graphics system. This method evaluates mostly local effects such as steric hindrances, H-bonds, and van der Waals interactions, which reflect a rough measure of surface complementarity in the interface of interacting molecules. We discuss its application to the interaction between λ repressor and DNA. Despite its simplicity, the results of the computer simulation have shown a high correlation with experimental results. Therefore, the method can be effectively used for investigating the mechanism of protein-DNA recognition, and serves as a useful guide for designing mutagenesis experiments.