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Analysis of Complex Networks by Frank Emmert-Streib, Matthias Dehmer

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9.5 Identification of Macromolecular Assemblies in Crystal Packing

The biochemical functions of many proteins are dependent on their ability to form complexes. The way in which protein chains assemble in a complex represents the protein quaternary structure (PQS). Experimental identification of PQS is a complicated procedure that normally involves use of several complementing techniques, such as mobility and mass measurements [86, 87], light scattering [86], neutron and X-ray scattering [88, 89], nuclear magnetic resonance [90], electron microscopy [91], and others. However, most protein structure data (80% of the PDB) come from experiments on X-ray diffraction on macromolecular crystals [92]. It is reasonable to expect that stable protein complexes do not change during crystallization, and therefore they should be identifiable in crystal packing.

The inference of PQS from crystallographic data is not a straightforward procedure. A complex may be represented as a graph, where vertices are protein chains and edges are interchain interfaces that bind chains together. The binding force of interfaces comes from hydrophobic interactions [93, 94] and weak bonds, such as hydrogen bonds, salt bridges, and disulphide bonds [94–96]. There is no obvious way, in general, to discriminate between inter- and intracomplex interfaces. Numerous attempts to find a set of discriminating parameters have had limited success [97–99].

Chemically, a complex represents a stable structure if its free Gibbs ...

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