Determination of the Nuclear Magnetic Resonance Solution Structure of an Antennapedia Homeodomain-DNA Complex

Billeter, Martin; Qian, Yan Qiu; Otting, Gottfried; Müller, Martin; Gehring, Walter; Wüthrich, Kurt

doi:10.1006/jmbi.1993.1661

Cited by 272 publications

(244 citation statements)

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“…However, major differences observed between specific and non-specific complexes might be a tight complex versus a loose complex. Although some other changes such as bending could be induced in the conformation of either DNA or the protein, the structural analyses of the complexes of the homeodomain and the specific DNA did not indicate such conformational changes [15][16][17][18][19]. Therefore, the reasons why the enthalpy term contributed more than the entropy term to the association of the homeodomain with the specific DNA could be that many contacts such as hydrogen bonds and van der Waals' contacts formed at the boundary should contribute favorably to such binding.…”

Section: Dlnka/d(1/t) = -Ah/rmentioning

confidence: 92%

“…The interactions between homeodomains and DNA have been extensively analyzed by foot-printing methods and gel shift assays [6][7][8][9][10][11][12][13][14]. Direct structural analysis of the complexes has also been performed with NMR and X-ray [15][16][17][18][19]. The results indicated that a homeodomain binds to a specific sequence of less than 10 bp.…”

Section: Introductionmentioning

confidence: 99%

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Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Seimiya¹,

Kurosawa²

1996

FEBS Letters

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The kinetics of binding of the Antp homeodomain to three kinds of DNA fragment were analyzed by measurements of surface plasmon resonance at various temperatures. Non-specific and specific binding of the homeodomain to DNA was examined. In the case of non-specific binding, the association rate constant (kass) was estimated to be 1.41-2.62X 105 M -1 s -1 and the dissociation rate constant (kdiss) was 1.36-3.10 X 10 -2 s -1, thus, the dissociation constant (KI)) was 0.847-1.72 × 10 7 M. The association seemed to be driven by entropy. In the case of specific binding, by contrast, the enthalpy term seemed to contribute more to the binding than did the entropy term. The kass was 2.04-2.59X105 M -1 s -1 and the kdiss was 0.759-1.16X10 -3 s -1, thus, the /to was 2.93-5.69X 10 -9 M. These values were measured under the condition of 150 mM NaCl. Both interactions were strongly dependent on the concentration of NaC1. The /to at 50 mM NaCI became several tens of times smaller than those at 150 mM. Possible reasons for the differences between non-specific and specific interactions are discussed.

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Section: Dlnka/d(1/t) = -Ah/rmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Seimiya¹,

Kurosawa²

1996

FEBS Letters

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“…Homeodomains are small proteins that bind to DNA and regulate gene expression. Here we show the complex of the antennapedia homeodomain of drosophila melanogaster (fruit fly) and its DNA binding site [13], using three different types of visualization. The structure of this complex was determined by X-ray crystallography [13]; the coordinates are taken from the PDB file 1AHD.…”

Section: Biomoleculesmentioning

confidence: 99%

Visual Analysis of Biomolecular Surfaces

Natarajan

Koehl

Wang

et al. 2008

Mathematics and Visualization

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Summary. Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

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“…For each conformer, 1,500 steps of conjugate gradient minimization were performed, after which a small total gradient was attained. The analysis of the structures in terms of RMSD values (McLachlan, 1979), atom displacements (Billeter et ai., 1989), identification of hydrogen bonds (Levitt, 1983), and solvent-accessible surface (Richmond, 1984;Billeter et al, 1990a) were performed with the program MOLMOL (Koradi et al, 1996), which was also used to prepare the stereo drawings of the Er-l l structure.…”

Section: P Luginbiihl Et Almentioning

confidence: 99%

The NMR solution structure of the pheromone Er‐11 from the ciliated protozoan Euplotes raikovi

Luginbühl¹,

Wu²,

Zerbe³

et al. 1996

Protein Science

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The NMR solution structure of the pheromone Er-11, a 39-residue protein from the ciliated protozoan Euplotes ruikovi, was calculated with the distance geometry program DIANA from 449 NOE upper distance constraints and 97 dihedral angle constraints, and the program OPAL was employed for structure refinement by molecular mechanics energy minimization in a water bath. For a group of 20 conformers used to characterize the solution structure, the average of the pairwise RMS deviations from the mean structure calculated for the backbone heavy atoms N, C a , and C' of residues 2-38 was 0.30 A. The molecular architecture is dominated by an up-down-up bundle of three short helices with residues 2-9, 12-19, and 22-32, which is closely similar to the previously determined structures of the homologous pheromones Er-1, Er-2, and Er-10. This finding provides structural evidence for the capability shown by these pheromones to compete with each other in binding reactions to their cell-surface receptors.

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Determination of the Nuclear Magnetic Resonance Solution Structure of an Antennapedia Homeodomain-DNA Complex

Cited by 272 publications

References 0 publications

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Visual Analysis of Biomolecular Surfaces

The NMR solution structure of the pheromone Er‐11 from the ciliated protozoan Euplotes raikovi

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