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Related Experiment Videos

Are predicted structures good enough to preserve functional sites?

L Wei1, E S Huang, R B Altman

  • 1Stanford Medical Informatics, Stanford University School of Medicine, CA 94305-5479, USA.

Structure (London, England : 1993)
|July 15, 1999
PubMed
Summary

Accurate protein structure prediction requires preserving functional sites. High-resolution models are essential for reliably identifying critical calcium-binding sites, not just overall structural similarity.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Elucidating protein function is a primary goal of structure prediction.
  • Assessed the preservation of functional site microenvironments in computed protein models.
  • Analyzed 653 ab initio models of a calcium-binding protein to evaluate calcium-binding site recognition.

Purpose of the Study:

  • To evaluate the reliability of computed protein models in preserving functional sites.
  • To determine the correlation between overall model quality and the preservation of specific binding sites.
  • To establish criteria for reliable modeling of calcium-binding sites.

Main Methods:

  • Generated 653 ab initio protein model structures.
  • Analyzed the microenvironment of calcium-binding sites within these models.

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  • Calculated root mean square deviation (rmsd) to assess structural similarity and binding site preservation.

    • Main Results:

    • Some models preserved calcium-binding sites, while many did not, irrespective of overall rmsd.
    • A weak correlation exists between overall structure rmsd and calcium-binding site preservation.
    • Reliable modeling of calcium-binding sites was achieved only with high-resolution models (rmsd < 2 Å within a 7 Å radius).

    Conclusions:

    • Protein structure prediction methods must be evaluated by their ability to preserve functional sites.
    • High-resolution structural models are crucial for accurately identifying functional binding sites, such as calcium-binding sites.