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Related Experiment Videos

Propensities, probabilities, and the Boltzmann hypothesis.

David Shortle1

  • 1Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. dshort1@jhmi.edu

Protein Science : a Publication of the Protein Society
|May 23, 2003
PubMed
Summary

Statistical potentials estimate protein interaction strengths. Phi/psi probabilities fail for protein conformations, unlike propensities, suggesting Boltzmann hypothesis requires specified starting conformations for accurate free energy calculations.

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A consistent set of statistical potentials for quantifying local side-chain and backbone interactions.

Proteins·2005

Area of Science:

  • Structural biology
  • Computational biophysics

Background:

  • Statistical potentials, derived from protein structure databases, estimate interaction strengths in polypeptide chains.
  • Recent work models side-chain/backbone energetics using amino acid phi/psi propensities.

Purpose of the Study:

  • To evaluate the effectiveness of phi/psi probabilities versus propensities in calculating protein conformational free energies.
  • To investigate the applicability of the Boltzmann hypothesis in statistical potential calculations.

Main Methods:

  • Comparison of statistical potentials derived from phi/psi probabilities and phi/psi propensities.
  • Analysis of hypothetical reactions implied by different statistical measures.

Main Results:

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  • Commonly used phi/psi probabilities were found to inaccurately evaluate free energies, favoring all-helical structures.
  • Phi/psi propensities provide a more accurate model for side-chain/backbone interactions.

    • Conclusions:

    • The Boltzmann hypothesis may only be applicable for statistical potential calculations when the starting conformation is specified.
    • The success of the Boltzmann hypothesis in protein energetics likely stems from evolutionary time-scale equilibrium maintaining protein stability.