Linked Life Data

7903398

Source:http://linkedlifedata.com/resource/pubmed/id/7903398

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
1994-1-24
pubmed:abstractText
The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance constraints in the homeodomain, 151 upper distance constraints within the DNA duplex, and 39 intermolecular protein-DNA upper distance constraints. These data were used as the input for the structure calculation with simulated annealing followed by molecular dynamics in a water bath and energy refinement. A group of 16 conformers was thus generated which represent the solution structure of the Antp(C39S) homeodomain-DNA complex. The new structure determination confirms the salient features reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove with the turn of the helix-turn-helix motif outside the contact area with the DNA, and the N-terminal arm of the homeodomain contacting the minor groove of the DNA. In addition, distinct amino acid side-chain-DNA contacts could be identified, and evidence was found that the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium between two or several different DNA contact sites. The molecular dynamics calculations in a water bath yielded structures with hydration water molecules in the protein-DNA interface, which coincides with direct NMR observations of hydration waters. In the Appendix the experimental data obtained with the Antp(C39S) homeodomain-DNA complex and the techniques used for the structure calculation are evaluated using a simulated input data set derived from the X-ray crystal structure of a DNA complex with a homologous homeodomain. This study indicates that a nearly complete set of NOE upper distance constraints for the Antp(C39S) homeodomain and the protein-DNA interface was presently obtained. It further shows that the structure calculation used here yields a precise reproduction of the crystal structure from the simulated input data, and also results in hydration of the protein-DNA interface in the recalculated complex.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
20
pubmed:volume
234
pubmed:geneSymbol
Antp
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1084-93
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed-meshheading:7903398-Animals, pubmed-meshheading:7903398-Antennapedia Homeodomain Protein, pubmed-meshheading:7903398-DNA-Binding Proteins, pubmed-meshheading:7903398-Deoxyribonucleoproteins, pubmed-meshheading:7903398-Drosophila Proteins, pubmed-meshheading:7903398-Drosophila melanogaster, pubmed-meshheading:7903398-Genes, Homeobox, pubmed-meshheading:7903398-Homeodomain Proteins, pubmed-meshheading:7903398-Hydrogen Bonding, pubmed-meshheading:7903398-Macromolecular Substances, pubmed-meshheading:7903398-Magnetic Resonance Spectroscopy, pubmed-meshheading:7903398-Models, Molecular, pubmed-meshheading:7903398-Nuclear Proteins, pubmed-meshheading:7903398-Nucleic Acid Conformation, pubmed-meshheading:7903398-Protein Structure, Secondary, pubmed-meshheading:7903398-Solutions, pubmed-meshheading:7903398-Transcription Factors
pubmed:year
1993
pubmed:articleTitle
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.
pubmed:affiliation
Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't