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Structure-based analysis of HU-DNA binding.

Kerren K Swinger1, Phoebe A Rice

  • 1Department of Biochemistry and Molecular Biology, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA.

Journal of Molecular Biology
|November 14, 2006
PubMed
Summary
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Prokaryotic proteins HU and IHF bend DNA for compaction and regulation. This study quantizes their binding affinities, revealing how DNA distortion enhances protein interaction and aids in understanding DNA-protein mechanics.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • HU and IHF are abundant prokaryotic nucleoid proteins crucial for DNA compaction and regulation.
  • These proteins are key models for studying DNA bending and sequence-specific interactions.
  • While IHF is sequence-specific, HU preferentially binds distorted or damaged DNA.

Purpose of the Study:

  • To quantify the binding affinities of Anabaena HU (AHU) to DNA structures from recent cocrystal structures.
  • To investigate how DNA structural distortions influence IHF binding affinity.
  • To estimate conformational strain relieved by DNA nicks mediated by IHF.

Main Methods:

  • Determination of binding affinities for AHU-DNA complexes using biophysical techniques.
  • Analysis of cocrystal structures to correlate DNA conformation with protein binding.

Related Experiment Videos

  • Estimation of conformational strain energy based on binding and structural data.

    • Main Results:

    • AHU-DNA complex formation yielded binding free energies from 10-14.5 kcal/mol (nanomolar to low picomolar K(d) values).
    • DNA structural distortions significantly enhanced IHF binding affinity.
    • AHU exhibits sequence preference for A+T-rich regions with narrow minor grooves, similar to eukaryotic nucleosomes.

    Conclusions:

    • DNA structural distortions play a critical role in modulating the binding affinity of HU and IHF.
    • The findings provide insights into the mechanics of DNA bending and protein-mediated DNA conformational changes.
    • AHU's sequence preference suggests conserved mechanisms in DNA organization across prokaryotes and eukaryotes.