Lecture 3

Protein conformation

Aims

• To introduce concepts related to protein conformation.

Objectives

After this lecture you will be able to:

• describe the polypeptide backbone and the 20 common side chain types;
• describe protein secondary structure elements, and the main chain hydrogen bond patterns associated with these;
• discuss factors that affect protein stability;
• implement code to compute distances and angles;
• describe how protein secondary structure elements can be recognised automatically.

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 article Nomenclature and Symbolism for Amino Acids and Peptides (Biochem. J., 1984, 219, 345-373) describes the three-letter and one-letter systems for naming amino acid residues.

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

The DSSP program is widely used to make secondary structure assignments in a standard way. The DSSP home page is maintained by Gert Vriend. Kabsch W. & Sander C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22:2577-2637 (doi:10.1002/bip.360221211).

Data files for experiemntally determined macromolecular structures can be downloaded from the Worldwide Protein Data Bank (wwPDB). Documentation on that site includes a description of PDB File Format.