[toc]Protein structure determination using X-ray crystallography is the major experimental technique in Structural Biology. This module will provide an in-depth introduction to diffraction techniques, covering the basics of symmetry, diffraction and methods for measuring the diffraction pattern, as well as the mathematical techniques for solving and refining a crystal structure. No similar module is offered at this level anywhere in South Africa.
Lecturer
Dr Muhammed Sayed, Department of Biotechnology (UWC), is a protein crystallographer who completed his post-doctoral studies under Professor Tom Blundell at Cambridge University. He will supervise the web-courses in protein structure and protein crystallography. His goal is to develop protein crystallography as a practical discipline.
Main Outcomes
The aim of this section of this module is to introduce students to the principles of X-ray diffraction and the elucidation of crystal structures. It is intended to underpin and to accompany students’ independent study of the Protein Crystallography web-based course. On completion of this module, students should be well prepared for the module on “Protein Crystallography” later in the course.
The ability to:
- crystallize proteins,
- collect and process crystallographic data,
- determine space groups,
- solve structures by molecular replacement,
- solve structures by isomorphous replacement and multiple anomalous dispersion techniques
- display structures
- build models of proteins using experimentally determined maps
- use standard crystallographic software
Main Content
- Crystals
- Crystal growth
- Periodicity and unit cells
- Symmetry
- Symmetry elements, point groups and space groups
- Diffraction
- Introduction to diffraction of waves
- The reciprocal lattice
- Diffraction by crystals; Bragg equation
- Fourier transforms
- Obtaining the diffraction pattern
- Instruments
- Data collection strategies
- The phase problem
- Deriving a trial structure
- Direct methods
- Patterson method
- Isomorphous replacement
- Anomalous scattering
- Refining the structure
- Fourier and least-squares methods
- Analysis of structural parameters
Online Lectures
- Introduction to X-ray crystallography (2003, Susan Bourne)
- Secondary structure prediction. Chou & Fasman (1974) (Muhammed Sayed)
- Tertiary Structure Prediction Methods (Muhammed Sayed)
- Basic Principles of Protein Crystallography
- Strategies, Optimisations, Non-Standard Methods
- Symmetry
- Why X-rays?
- Obtaining the diffraction pattern
- The Phase problem
- Protein Structure, Evolution and Function – Lecture 2 (Muhammed Sayed):
file missing: /lectures/sayed/Prot1B03Lect2.ppt- Notes – Part 1. Secondary structure
- Notes – Part 2. The supramolecular organisation and functions of fibrous proteins
- Protein Structure, Evolution and Function – Lecture 3 (Muhammed Sayed):
file missing: /lectures/sayed/Prot1B03Lect3.ppt - Protein Structure, Evolution and Function – Lecture 4 (Muhammed Sayed):
file missing: /lectures/sayed/Prot1B03Lect4.ppt - Protein Structure, Evolution and Function – Lecture 5 (Muhammed Sayed):
file missing: /lectures/sayed/Prot1B03Lect5.ppt- Notes. Protein structure and functions
Assessment
Tutorial worksheets will be handed out at regular intervals. These must be completed and handed in by the specified deadlines. A 2 hour examination will be given at the end of the module. The worksheets and exam will count 40 and 60% respectively.
Tutorials
References
A number of helpful books are available in the UCT and UWC libraries. Useful introductory texts include:
[bibliplug category=”PC” keywords=”pc-intro” order_by=”ln”]
The International Union of Crystallography website (mirrored at www.gh.wits.ac.za/iucr-top/) has numerous useful articles.