Conformational changes of the BS2 operator DNA upon complex formation withthe Antennapedia homeodomain studied by NMR with C-13/N-15-labeled DNA

The NMR structures have been determined for a C-13/N-15 doubly labeled 14 b ase-pair DNA duplex comprising the BS2 operator sequence both free in solut ion and in the complex with the Antennapedia homeodomain. The impact of the DNA labeling is assessed from comparison with a previous structure of the same complex that was determined using isotope labeling only for the protei n. Differences between the two structure determinations are nearly complete ly limited to the DNA, which retains the global B-conformation of the free DNA also in the complex. Local protein-induced conformational changes are a narrowing of the minor groove due to the interaction with the N-terminal a rm of the homeodomain, and changes of the sugar puckers of the deoxyriboses G5 and C6, which are apparently induced by van der Waals interactions with Tyr25, and with Gln50 and Arg53, respectively. The high conservation of th ese amino acid residues in homeodomains suggests that protein-induced shift s in some sugar puckers contribute to the affinity of homeodomains to their cognate DNA. The data obtained here with the Antennapedin homeodomain-DNA complex clearly show that nucleic acid isotope-labeling can support detaile d conformational characterization of DNA in complexes with proteins, which will be indispensable for structure determinations of complexes containing globally distorted DNA conformations. (C) 1999 Academic Press.