Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF

Area of Science:

• Structural biology
• Biophysics
• Molecular biology

Background:

• Integration host factor (IHF) is known to bend linear DNA.
• The effect of IHF on torsionally constrained DNA, common in vivo, is not well understood.

Purpose of the Study:

• To investigate the reciprocal relationship between DNA supercoiling and the DNA-bending protein IHF.
• To elucidate the role of IHF in the context of topologically constrained DNA.

Main Methods:

• Atomistic molecular dynamics simulations.
• Utilized DNA minicircles to model torsionally constrained DNA.

Main Results:

• Supercoiled DNA's increased curvature enhances IHF wrapping, creating a topologically dependent complex.
• IHF acts as a 'supercoiling relief' factor, compacting DNA and specifically positioning plectonemes.
• IHF functions as a 'supercoiling buffer,' restraining DNA under- or overtwisting.
• DNA bridging by IHF was observed, dividing DNA into independent topological domains.

Conclusions:

• A reciprocal influence between IHF and DNA supercoiling exists, impacting DNA topology.
• The findings suggest that interactions between DNA-binding proteins and supercoiling may be a general mechanism for other DNA-protein complexes.