Lecture: Protein Structure 2

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 protein domains 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;
• be aware of factors that affect protein stability;
• be aware of modular proteins that contain combinations of domains in different structural contexts;
• be aware of alternative structural classification hierarchies, including SCOP and CATH;
• be aware of comparative modelling, fold recognition and secondary structure prediction.

Supplementary Material

The lecture handout contains some of the lecture slides.

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

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.

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.

Rob Russell has written A Guide to Structure Prediction that includes practical advice and links to useful software.