Aims

• To place structural bioinformatics in a wider context.
• To introduce the basic principles of protein conformation.
• 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 basic features of protein conformation, and the abbreviations and symbols used in describing these;
• be aware of the twenty amino acid residues that are commonly found in proteins, and some of their properties;
• know about different levels of protein structure;
• be familiar with the criteria that are used in assessing the stereochemical quality of a protein;
• be aware of factors that affect protein stability;
• be able to recognise common protein secondary structure elements and understand how these can be recognised automatically.

Supplementary Material

The article Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains (Eur. J. Biochem., 1969, 17, 193-201) contains the Rules prepared by the IUPAC-IUB Commission on Biochemical Nomenclature. I encourage you to read through all six sections of this article, and the appendices.

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.

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.