Aims

• To revise the basic principles of protein conformation.
• To explain the steps involved in comparative protein modelling.
• To introduce the ways in which the stereochemical quality of a protein structure can be assessed.
• To introduce the concepts of fold recognition and secondary structure prediction.

Objectives

After this lecture you will:

• understand how dihedral angles are measured;
• know the steps involved in comparative protein modelling;
• understand how fragment-fitting and rotamers are used in the modelling process;
• know several criteria that are used in assessing the stereochemical quality of a protein;
• be aware of the concepts of fold recognition and secondary structure prediction, and the situations where these methods could be applied.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line.
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A short discussion of state-of-the-art techniques in protein structure prediction, and their applications, is given in: Baker, D., and Sali, A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96. (David Baker's publication list)

Rob Russell has written A Guide to Structure Prediction that includes practical advice and links to useful software.

Several of the figures shown in the lecture were taken from Professional gambling. This is an updated version of the article: R.Rodriguez, R. and Vriend, G. (1997) "Professional gambling", in Vergoten, G. and Theophanides, T. (eds.) Proceedings of the NATO Advanced Study Institute on Biomolecular Structure and Dynamics: Recent Experimental and Theoretical Advances.

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, including the rules for measuring torsion angles in protein structures.

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.

Extensive lecture notes and slides on structure prediction prepared by Johan Leckner for earlier courses at CTH/GU are available on-line.

Protein structure prediction: a practical approach, edited by Michael J.E. Sternberg, contains a collection of articles covering several of the areas mentioned in this lecture.

Principles of Protein Structure, Comparative Protein Modelling and Visualisation has material from an internet course on protein structure and modelling.