Non-covalent interactions between ATP and RecA DNA-repairing proteins: DFT and semiempirical calculations

The role of Bacterial RecA in the structural maintenance of genomes and the genetic information they carry has been established. In particular, the RecA \quad DNA-repairing protein from \textit{D. Radiodurans}, a radiation-resistant bacteria, is crucial for \quad the repair of double strand breaks (DSBs). We have performed semi-empirical free-energy calculations and QM/MM calculations to study their non-covalent interactions with ATP and ADP. Such studies provide insight into the mechanisms of ATP/ADP $\to $ RecA energy transfer and, therefore, about specific functional uses of incoming energy for DNA repairing mechanisms. We present a detailed analysis of the non-covalent interactions which minimize the interaction Gibbs free energies leading to the most stable non-covalent binding sites. Van der Waal, hydrogen bonding and electrostatic interactions has been quantified which provides a detailed insight into the mechanisms of ATP-RecA interaction. Further, possible chemical interactions and functional roles of RecA proteins are explored based on the previously mentioned studies. \textit{Acknowledgements}: Funded, in part, by DTRA award 106339 (JHR). Dr. Mark C. Palenik and Mrs. Lora Beard are gratefully acknowledged