Lecture GK-1

Introduction; protein conformation

Aims

• To place structural bioinformatics in a wider context.
• To introduce the basic principles of protein conformation.

Objectives

After this lecture you will:

• be aware that knowing the three-dimensional structures of macromolecules can give new insights into biological function, enabling scientists to formulate new hypotheses and design new experiments;
• 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;
• understand how distances and angles can be calculated.

Supplementary Material

Some of the lecture slides are available on-line (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 source code for the geometry routines mentioned in the lecture is available online (local access only).