title: Conformational changes of the BS2 operator DNA upon complex formation with the Antennapedia homeodomain studied by NMR with 13C/15N-labeled DNA.
abstract: The NMR structures have been determined for a 13C/15N doubly labeled 14 base-pair DNA duplex comprising the BS2 operator sequence both free in solution 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 protein. Differences between the two structure determinations are nearly completely 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 arm 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 these amino acid residues in homeodomains suggests that protein-induced shifts in some sugar puckers contribute to the affinity of homeodomains to their cognate DNA. The data obtained here with the Antennapedia homeodomain-DNA complex clearly show that nucleic acid isotope-labeling can support detailed conformational characterization of DNA in complexes with proteins, which will be indispensable for structure determinations of complexes containing globally distorted DNA conformations.
authors.affiliation: Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, Zürich, CH-8093, Switzerland.
authors.forename: C
authors.initials: C
authors.lastname: Fernández
authors.forename: T
authors.initials: T
authors.lastname: Szyperski
authors.forename: M
authors.initials: M
authors.lastname: Billeter
authors.forename: A
authors.initials: A
authors.lastname: Ono
authors.forename: H
authors.initials: H
authors.lastname: Iwai
authors.forename: M
authors.initials: M
authors.lastname: Kainosho
authors.forename: K
authors.initials: K
authors.lastname: Wüthrich
mesh_terms: D051943:Antennapedia Homeodomain Protein; D002247:Carbon Isotopes; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D018398:Homeodomain Proteins / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009587:Nitrogen Isotopes; D009687:Nuclear Proteins; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D017433:Protein Structure, Secondary; D014157:Transcription Factors
chemical_list: D051943:Antennapedia Homeodomain Protein; D002247:Carbon Isotopes; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009587:Nitrogen Isotopes; D009687:Nuclear Proteins; D009838:Oligodeoxyribonucleotides; D014157:Transcription Factors; D004247:DNA