Aims

• To introduce the ways in which the stereochemical quality of a protein structure can be assessed.
• To look at arrangements of protein secondary structure elements and how proteins can be classified according to their structure.

Objectives

After this lecture you will:

• be familiar with the criteria that are used in assessing the stereochemical quality of a protein;
• be aware of some common secondary structure motifs and of alternative structural classification hierarchies, including CATH and SCOP.

Supplementary Material

Part I of Principles of Protein Structure, Comparative Protein Modelling and Visualisation contains a useful introduction to protein structure.

A validation suite that includes software for checking the stereochemical quality of a protein structure has been developed by a consortium with support from the EU. I recommend that you read the descriptions of the checks performed by PROCHECK, and that you look at some of the sample output produced by that program.

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.

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

A method for classifying protein topologies is presented in: Taylor, W.R. (2002) A 'periodic table' for protein structures. Nature, 416:657-60. (PubMed)