Inference of macromolecular assemblies from crystalline state.
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.
Krissinel
Evgeny
E
European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Henrick
Kim
K
D002138:Calibration; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D019281:Dimerization; D019277:Entropy; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012996:Solutions
D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins; D012996:Solutions; D004247:DNA