Abstract
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.
