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Related Experiment Videos

A guest molecule-host cavity fitting algorithm to mine PDB for small molecule targets.

William C Byrem1, Stephen C Armstead, Shunji Kobayashi

  • 1Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Biochimica Et Biophysica Acta
|August 15, 2006
PubMed
Summary

A new algorithm screens protein cavities for inhaled anesthetic binding, identifying potential halothane targets. This method considers cavity shape, improving predictions for small molecule interactions within proteins.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Pharmacology

Background:

  • Inhaled anesthetic binding to proteins is influenced by molecular and cavity volumes.
  • Existing algorithms for protein cavity analysis do not account for molecular shape or flexibility.

Purpose of the Study:

  • To develop and apply a novel algorithm for screening protein cavities based on shape and volume.
  • To identify potential binding sites for halothane within protein structures.

Main Methods:

  • Developed an algorithm to determine spheroid dimensions matching protein cavity volume and surface area.
  • Applied the algorithm to 6,658 nonredundant protein structures from the Protein Data Bank (PDB).
  • Screened cavities for accommodation of halothane (radius 2.91 Å) and calculated packing coefficients.

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Main Results:

  • Identified 394,766 total cavities across all structures.
  • Found 58,681 cavities that fit halothane.
  • 11,902 cavities (20.3% of those fitting halothane) had suitable packing coefficients (0.46-0.64), present in 2,432 protein structures.

Conclusions:

  • The developed algorithm effectively incorporates shape dependence for screening guest-host relationships in protein cavities.
  • Proteins with numerous suitable cavities are more susceptible to functional alteration by halothane.
  • This approach enhances the prediction of small molecule occupancy in protein internal sites.