Inference of Macromolecular Assemblies From Crystalline State

J Mol Biol. 2007 Sep 21;372(3):774-97. doi: 10.1016/j.jmb.2007.05.022. Epub 2007 May 13.

Abstract

We discuss basic physical-chemical principles underlying the formation of stable macromolecular complexes, which in many cases are likely to be the biological units performing a certain physiological function. We also consider available theoretical approaches to the calculation of macromolecular affinity and entropy of complexation. The latter is shown to play an important role and make a major effect on complex size and symmetry. We develop a new method, based on chemical thermodynamics, for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments. As found, biological units may be recovered at 80-90% success rate, which makes X-ray crystallography an important source of experimental data on macromolecular complexes and protein-protein interactions. The method is implemented as a public WWW service.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Calibration
  • Crystallization
  • Crystallography, X-Ray
  • DNA / chemistry
  • Dimerization
  • Entropy
  • Ligands
  • Macromolecular Substances / chemistry*
  • Models, Molecular
  • Protein Structure, Secondary
  • Proteins / chemistry
  • Solutions

Substances

  • Ligands
  • Macromolecular Substances
  • Proteins
  • Solutions
  • DNA