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Cavities and packing at protein interfaces

S J Hubbard1, P Argos

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Protein Science : a Publication of the Protein Society
|December 1, 1994
PubMed
Summary
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Internal protein cavities, though small, increase with protein size and differ based on location. Water-filled cavities are larger and more polar, impacting protein structure and function.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Protein internal cavities (voids) are crucial for structure and function.
  • Understanding cavity characteristics aids in protein design and modeling.

Purpose of the Study:

  • To analyze and classify internal protein cavities.
  • To identify distinct features of different cavity types (intradomain, interdomain, intersubunit).
  • To investigate the role of water in cavities and their impact on protein properties.

Main Methods:

  • Analysis of protein structures to identify and quantify internal cavities.
  • Classification of cavities into three types: within domains, between domains, and between subunits.
  • Characterization of cavity properties such as volume, surface polarity, and water content.

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Main Results:

  • Cavity volume is a small fraction of total protein volume but increases with protein size.
  • Water-filled cavities have more polar surfaces and are larger, with water satisfying hydrogen bonding potential.
  • Intersubunit and interdomain cavities are larger, more surface-occupying, and more frequently water-filled than intradomain cavities.
  • Cavity-surrounding atoms exhibit reduced flexibility.

Conclusions:

  • Protein cavities exhibit diverse characteristics based on their location and water content.
  • Cavity properties influence protein shape complementarity, docking, and oligomeric protein function.
  • Findings offer guidelines for protein modeling and design, particularly concerning cavity characteristics.