Aims

• To emphasise the modular structure of many proteins.
• To look at arrangements of protein secondary structure elements and how proteins can be classified according to their structure.
• To describe how domains can be assigned automatically.

Objectives

After this lecture you will:

• know that proteins often consist of structural domains;
• be aware of some common secondary structure motifs and of alternative structural classification hierarchies, including CATH and SCOP;
• know how to interpret distance maps;
• understand, in outline, how domain assignment can be performed.

Supplementary Material

Peer Bork has collected some cartoons of modular extracellular proteins.

SCOP is a hierarchical structural classification of proteins. I recommend that you read the detailed description of SCOP.

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H). I recommend that you read the detailed description of CATH.

Several distance maps are shown on The Protein Kinase Resource web site.

The algorithm used by DOMAK to identify structural domains is described in:

Siddiqui, A.S. and Barton G.J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Science, 4, 872-884. (Pubmed)

The algorithm used by STRUDL to identify structural domains is described in:

Wernisch, L., Hunting, M. and Wodak, S.J. (1999) Identification of structural domains in proteins by a graph heuristic. Proteins: Structure, Function and Genetics, 35, 338-352. (Pubmed)