Class, Architecture, Topologies, and

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

Contains -18,000 domains organized according to then class, architecture, topology, and homologous supeifamilies. 

FIGURE 2 The class, architecture, topology, homology (CATH) classification of a protein. SOURCE Department of Biochemistry and Molecular Biology, University College, London. This figure can be viewed in color at . 

A comparison of the covalent connectivity associated with each of these architecture classes (Figure 1.7) reveals that the number of covalent bonds formed per step for linear and branched topology is a multiple (n = degree of polymerization) related to the monomer/initiator ratios. In contrast, ideal dendritic (Class IV) propagation involves the formation of an exponential number of covalent bonds per reaction step (also termed G = generation), as well as amplification of both mass (i.e. number of branch cells/G) and terminal groups, (Z) per generation (G). 

Class V of more ordered complexity. Examples of this new architecture have been synthesized and we have coined these new topologies megamers. 

The second virial coefficient is not a universal quantity but depends on the primary chemical structure and the resulting topology of their architecture. It also depends on the conformation of the macromolecules in solution. However, once these individual (i.e., non-universal) characteristics are known, the data can be used as scaling parameters for the description of semidilute solutions. Such scaling has been very successful in the past with flexible linear chains [4, 18]. It also leads for branched macromolecules to a number of universality classes which are related to the various topological classes [9-11,19]. These conclusions will be outlined in the section on semidilute solutions. 

Thus the architecture refers to the overall shape of the protein, whereas the topology or fold group describes the relative orientations of the secondary smictures in 3D and the order in which they are connected. The Class level is derived automatically, while the architecture is assigned manually. The assignments of structures to topology families and homologous superfamilies are made by sequence and structure comparisons. Four levels are added in the hierarchical matches. They are ... 

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