Electronic properties of DNA binding site in transcription OmpR family: semiempirical molecular orbital calculations

To elucidate a common feature of OmpR family enhancing the transcription ability of RNA polymerase, we investigated structures and electronic properties of DNA binding sites of OmpR family by semiempirical molecular orbital (MO) calculations. The results clarify that the highest occupied MO is localized on the 2nd aspartic-acid existing near the DNA backbones for almost all members of OmpR family. Therefore, the 2nd aspartic-acid of DNA binding site is expected to be essential for the nonspecific interaction between OmpR and DNA backbones. The effect of amino-acid mutation on the structures and electronic properties of OmpR family was also investigated.