Molecular modeling studies are proposed to investigate DNA binding by two transcriptional regulatory proteins, the CI repressor from bacteriophage 434 and the Arc repressor from bacteriophage P22. The long-term objective of this work is to understand the relationship between the structure of these proteins and both the stability and specificity of their interactions with DNA. The proposed research will provide insight into structure-function relationships, molecular recognition, protein engineering, and drug discovery, that are particularly relevant to transcriptional regulation and oncogenesis. The specific goals of the proposed research are to calculate the contributions to stability and specificity of protein-phosphate contacts, base-specific contacts, and longer-range, non-contacting interactions. Continuum electrostatic and free energy calculations will be employed. The results will be carefully compared with experimentally determined crystal structures and measurements of thermodynamic stability. Interpretations from the molecular modeling studies will be used to construct an understanding of molecular recognition by Arc and 434 repressor. This understanding will be tested by proposing new mutations that will be studied experimentally and compared to theoretical results.
