Intermolecular contacts between the lambda-Cro repressor and the operator DNA characterized by nuclear magnetic resonance spectroscopy

The specific interaction between lambda phage Cro repressor and the DNA fra gment bearing the consensus sequence of operators has been studied using nu clear magnetic resonance (NMR). Using both N-15- and C-13/N-15- labeled lam bda-Cro in complex with unlabeled DNA, chemical shift assignments of the la mbda-Cro-DNA complex were obtained using heteronuclear NMR experiments. Int er-molecular contacts between the protein and DNA were identified using het eronuclear filtered NOESY experiments. The inter-molecular contacts were su pplemented with intra-protein and intra-DNA NOE constraints to dock lambda- Cro to the bent B-form DNA using restrained molecular dynamics. The structu re of one of the subunits of lambda-Cro in the complex is essentially the s ame as that of the unbound form. In the complex, inter-molecular NOEs were observed between the "helix-turn-helix" region comprising the alpha 2 and a lpha 3 helices of the lambda-Cro protein and the major groove of the DNA. T he methyl group of Thr17 forms a hydrophobic contact with the methyl group of the thymine at base pair 1 in the DNA, and Val25 and Ala29 make hydropho bic contacts with the methyl group of the thymine at base pair 5. The prese nce and the absence of these contacts can explain the difference in the aff inity of lambda-Cro to several variants of the operator sequence.