Lecture GK-2

Secondary structure and modules

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.
• To introduce the ways in which the stereochemical quality of a protein structure can be assessed.

Objectives

After this lecture you will:

• be familiar with the criteria that are used in assessing the stereochemical quality of a protein;
• be able to recognise common protein secondary structure elements and understand how these can be recognised automatically.
• 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.

Supplementary Material

Some of the lecture slides are available on-line (PDF).

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.

The DSSP program is widely used to make secondary structure assignments in a standard way. The DSSP home page is maintained by Gert Vriend at the University of Nijmegen, and a scanned copy of the article describing the DSSP program is available on that site. Kabsch W. & Sander C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22:2577-2637.

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.