Aims

• To introduce the basic principles of protein conformation.

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;
• understand how distances and angles can be calculated;
• 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.

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 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.

The source code for geometry routines mentioned in the lecture is available online (local access only).