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Intramolecular cavities in globular proteins

S J Hubbard1, K H Gross, P Argos

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Protein Engineering
|May 1, 1994
PubMed
Summary

Internal protein cavities are common, especially in larger proteins, and are integral to tertiary structure. Their characteristics, morphology, and role in protein modeling and design were analyzed.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Internal cavities are a feature of protein structures.
  • Understanding these cavities is crucial for protein function and modeling.

Purpose of the Study:

  • To characterize the occurrence, morphology, and role of internal cavities in protein tertiary structure.
  • To determine the optimal probe size for cavity detection.
  • To compare empty and solvent-containing cavities.

Main Methods:

  • Analysis of internal cavities in 121 protein chains.
  • Investigation of cavity characteristics, including volume, location, and surface properties.
  • Comparison of empty versus solvent-containing cavities.
  • Assessment of residue mobility around cavities.

Main Results:

  • Cavities are non-artefactual and present in most proteins over 100 residues, primarily in the protein core.
  • Cavity volume correlates with protein size but constitutes a small fraction of total volume.
  • Solvent-containing cavities have a more polar surface and distinct amino acid/secondary structure preferences compared to empty cavities.
  • Residues enclosing cavities show no increased local mobility; water-filled cavities allow bulk solvent behavior and good hydrogen bonding.

Conclusions:

  • Internal cavities are inherent structural elements with specific properties.
  • These findings are valuable for protein modeling and rational protein design.
  • The study provides insights into the nature and implications of internal voids in proteins.

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