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Related Experiment Videos

Conformational attractors on the Ramachandran map.

D Walther1, F E Cohen

  • 1Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143-0450, USA.

Acta Crystallographica. Section D, Biological Crystallography
|March 25, 1999
PubMed
Summary

Differential Ramachandran maps reveal how protein backbone angles converge to specific conformations as crystallographic resolution improves. This analysis aids in assessing protein structure quality and identifying conformational attractors.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein backbone dihedral angles (phi and psi) are fundamental to protein structure.
  • Ramachandran maps are standard tools for analyzing these angles.
  • Conventional maps have limitations in sensitivity and detail.

Purpose of the Study:

  • To systematically analyze the correlation between protein dihedral angle distributions and crystallographic parameters.
  • To develop novel differential Ramachandran maps for enhanced sensitivity.
  • To assess the suitability of R factor and free R factor for structure quality evaluation.

Main Methods:

  • Analysis of frequency distributions of protein backbone dihedral angles (phi and psi).
  • Generation of novel differential Ramachandran maps.

Related Experiment Videos

  • Correlation with crystallographic parameters: resolution, R factor, and free R factor.
  • Comparison of different crystallographic refinement packages.

    • Main Results:

    • Differential Ramachandran maps reveal conformational 'attractors' as resolution improves.
    • Alpha-helical conformations show significant consolidation at higher resolutions.
    • Convergence to attractors observed for all secondary structures and random coils.
    • Free R factor is more suitable for structure quality assessment than R factor.
    • No significant artificial biases found in tested refinement programs.

    Conclusions:

    • Differential Ramachandran maps offer improved sensitivity for analyzing protein backbone conformations.
    • Resolution is a key factor influencing phi/psi distributions and conformational convergence.
    • The free R factor is a reliable indicator of protein structure quality.
    • The resolution-based differential Ramachandran map is a valuable reference tool.