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Non-specific DNA-driven quinary interactions promote structural transitions in proteins.

Soundhararajan Gopi1, Athi N Naganathan1

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Charged residues on protein surfaces are crucial for ligand interactions, particularly for DNA-binding domains (DBDs).
  • DBDs typically exhibit an anisotropic distribution of positive charges to interact with the negatively charged DNA polymer.
  • Some DBDs exist in a disordered state in solution without DNA.

Purpose of the Study:

  • To investigate the thermodynamic behavior of nine different DBDs from three families (LacR, engrailed, Brk).
  • To determine how non-specific electrostatic interactions with DNA influence protein structural transitions.
  • To understand the impact of DNA proximity and orientation on protein folding landscapes.

Main Methods:

  • Detailed electrostatic calculations were performed.
  • Statistical mechanical modeling of folding landscapes was employed.
  • Analyses were conducted at varying distances and relative orientations to DNA.

Main Results:

  • Non-specific electrostatic interactions between proteins and DNA can induce significant structural transitions in DBDs.
  • Observed behaviors include folding of intrinsically disordered domains and partial unfolding of ordered proteins.
  • The study revealed (de-)population of intermediate states in protein folding pathways due to DNA interactions.

Conclusions:

  • The folding landscape of DBDs is tunable by their distance and orientation relative to DNA.
  • Quinary interactions, agnostic to DNA sequence, significantly impact protein structure and dynamics.
  • These findings offer insights into the complex kinetic-thermodynamic behaviors observed in DBDs, even in the absence of DNA.