Lecture: Structural Bioinformatics 1

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 lecture handout, featuring some of the lecture slides, is available on-line.
Download PDF

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 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.

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