Protein-DNA complexes are extremely important in biology, controlling chromatin structure, DNA replication, and protein expression. In fact, mutations in transcriptional activators and repressors or in proteins involved in DNA replication are common causes of cancer. A greater understanding of the interactions that stabilize these complexes will improve our understanding of the disease states that result from mutations to DNA binding proteins. The goal of the project described in this proposal is to identify a set of general rules describing the role of electrostatics in the stability and binding affinity of protein- DNA complexes. A combination of theoretical and experimental approaches will be used to meet this goal. Continuum electrostatic calculations can suggest mutations that will improve the electrostatic complementarity in the Arc repressor- DNA complex, and the predicted mutations will be tested experimentally. In addition, mutations that improve Arc repressor-DNA binding will also be identified by combinatorial mutagenesis techniques, and calculations will be performed to analyze the changes in the electrostatic interactions in the complex.
