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Protein dynamics and structural waters in bromodomains.

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Area of Science:

  • Epigenetics
  • Structural biology
  • Computational chemistry

Background:

  • Bromodomains are epigenetic readers that bind acetylated lysines on histone tails.
  • Human genomes contain 61 bromodomains, which are structurally conserved but recognize diverse motifs.
  • Recognition selectivity is hypothesized to depend on dynamic factors rather than static structures.

Purpose of the Study:

  • To investigate the role of dynamics in bromodomain recognition selectivity.
  • To explore the behavior of binding site dynamics and structural water molecules in four distinct bromodomains.
  • To elucidate the contribution of dynamic factors to the specific binding of bromodomains.

Main Methods:

  • Utilized 1 μs molecular dynamics (MD) simulations.
  • Employed the RSFF2 force field for simulations.
  • Studied four representative bromodomains: ATAD2, BAZ2B, BRD2(1), and CREBBP.

Main Results:

  • Observed distinct dynamic patterns in the ZA-loops and BC-loops across the four bromodomains.
  • Demonstrated varied binding pocket opening and closing dynamics.
  • Characterized unique structural and energetic properties of water molecules within the binding pockets.

Conclusions:

  • Bromodomain binding pocket dynamics, particularly loop flexibility, dictate recognition selectivity.
  • Structural water molecules play a crucial role in both recognition and selectivity.
  • Dynamic factors, including water molecule behavior, are key to understanding bromodomain specificity.