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Quantifying allosteric effects in proteins.

Dengming Ming1, Michael E Wall

  • 1Computer and Computational Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.

Proteins
|April 12, 2005
PubMed
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This study introduces theoretical tools, allosteric potential (Dx) and rate divergence (Dk), to quantify how protein-ligand interactions affect protein function. Effective allosteric regulation arises from interactions that significantly alter protein conformational distributions.

Area of Science:

  • Biophysics
  • Computational Biology
  • Biochemistry

Background:

  • Allosteric regulation is crucial for controlling protein activity through ligand binding, but the structural basis for effective regulation remains unclear.
  • Understanding the relationship between protein structure and allosteric effects is essential for designing novel regulatory mechanisms.

Purpose of the Study:

  • To develop theoretical tools for quantifying the impact of protein-ligand interactions on protein conformational and reaction rate distributions.
  • To investigate the structural determinants of effective allosteric regulation.

Main Methods:

  • Defined allosteric potential (Dx) and rate divergence (Dk) using Kullback-Leibler divergence.
  • Derived Dx in the harmonic approximation, identifying contributions from eigenvalue spectrum changes (D[stackxomega]), mean conformation changes (D[stackxDeltax]), and eigenvector changes (Dxv).

Related Experiment Videos

  • Applied normal modes analysis to calculate these terms for lysozyme-ligand interactions and simulated random interactions.

    • Main Results:

    • Calculations for lysozyme and tri-N-acetyl-D-glucosamine revealed that known binding-site interactions are associated with large Dxv values.
    • Simulated random interactions showed smaller Dxv values compared to natural binding sites.

    Conclusions:

    • Allosteric potential calculations can aid in predicting functional protein binding sites.
    • Effective ligand interactions in nature likely occur at intrinsic control points that induce substantial changes in protein conformation.