Jump to main content
Jump to site search

Issue 23, 2009
Previous Article Next Article

Structural analysis of the DNA target site and its interaction with Mbp1

Author affiliations

Abstract

The solution structure of a 14 base-pair non-self complementary DNA duplex containing the consensus-binding site of the yeast transcription factor Mbp1 has been determined by NMR using a combination of scalar coupling analysis, time-dependent NOEs, residual dipolar couplings and 13C-edited NMR spectroscopy of a duplex prepared with one strand uniformly labeled with 13C-nucleotides. As expected, the free DNA duplex is within the B-family of structures, and within experimental limits is straight. However, there are clear local structural variations associated with the consensus CGCG element in the binding sequence that are important for sequence recognition. In the complex, the DNA bends around the protein, which also undergoes some conformational rearrangement in the C-terminal region. Structural constraints derived from paramagnetic perturbation experiments with spin-labeled DNA, chemical shift perturbation experiments of the DNA, previous cross-saturation, chemical shift perturbation experiments on the protein, information from mutational analysis, and electrostatics calculations have been used to produce a detailed docked structure using the known solution conformation of the free protein and other spectroscopic information about the Mbp1:DNA complex. A Monte Carlo-based docking procedure with restrained MD in a fully solvated system subjected to available experimental constraints produced models that account for the available structural data, and can rationalize the extensive thermodynamic data about the Mbp1:DNA complex. The protein:DNA interface is closely packed and is associated with a small number of specific contacts. The structure shows an extensive positively charged surface that accounts for the high polyelectrolyte contribution to binding.

Graphical abstract: Structural analysis of the DNA target site and its interaction with Mbp1

Back to tab navigation

Supplementary files

Publication details

The article was received on 24 Jun 2009, accepted on 17 Sep 2009 and first published on 07 Oct 2009


Article type: Paper
DOI: 10.1039/B912309A
Citation: Org. Biomol. Chem., 2009,7, 4981-4991
  •   Request permissions

    Structural analysis of the DNA target site and its interaction with Mbp1

    A. V. Chernatynskaya, L. Deleeuw, J. O. Trent, T. Brown and A. N. Lane, Org. Biomol. Chem., 2009, 7, 4981
    DOI: 10.1039/B912309A

Search articles by author

Spotlight

Advertisements