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Related Experiment Videos

An improved hydrogen bond potential: impact on medium resolution protein structures.

Felcy Fabiola1, Richard Bertram, Andrei Korostelev

  • 1Kasha Laboratory of Biophysics, Florida State University, Tallahassee, Florida 32306-4380, USA.

Protein Science : a Publication of the Protein Society
|May 22, 2002
PubMed
Summary

A new force field improves protein structure refinement by accurately modeling directional hydrogen bonds. This method enhances macromolecular models, particularly when specific hydrogen bond criteria are applied.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Hydrogen bonds are crucial for protein structure and function.
  • Existing force fields often lack accurate directional descriptions of hydrogen bonds.
  • Carbonyl hydrogen bond acceptor angles exhibit a bimodal distribution, suggesting limitations in current models.

Purpose of the Study:

  • To develop and implement a new semi-empirical force field for describing directional hydrogen-bonding interactions.
  • To integrate this force field into macromolecular refinement packages.
  • To assess the impact of directional hydrogen bond restraints on protein structure refinement.

Main Methods:

  • Developed a new hydrogen bond potential with directional components and alternative target angles.

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  • Implemented the potential as a module for macromolecular refinement.
  • Optimized parameters using crystallographic data from multiple protein structures.
  • Performed stereochemically restrained refinement of medium-resolution protein structures.

    • Main Results:

    • Refinement using the new directional hydrogen bond potential improved protein structure quality.
    • A reduction in the free R-factor and over-fitting was observed.
    • Improvements were contingent upon the application of stringent hydrogen bond selection criteria.
    • The findings challenge common assumptions about hydrogen bonding in proteins.

    Conclusions:

    • The new directional hydrogen bond force field offers improved accuracy in macromolecular refinement.
    • Explicit hydrogen bonding terms in some force fields may be less effective than previously thought.
    • Careful selection of hydrogen bond restraints is critical for realizing computational benefits in structural biology.