THE GALLERY - Examples
Example Course Material
Page currently under construction!
Students are warned that they may struggle on the course without some
knowledge of the fundamental disciplines involved. Prerequisites are listed in
Some teaching material on these prerequisites is available through the course
pages. As an example, see some
geometry prerequisites provided by Stefan Sack.
- molecular biology
- organic chemistry
- internet and computing
Here is a quick
Introduction to the Amino Acids
Introductory material includes an introduction to the basic structure and
geomety of proteins. The two most important elements of protein "secondary
structure" are covered in detail.
Oliver Smart at
Birkbeck has produced an excellent overview of
molecular forces . WARNING! - this section is complex, mathematical, and
A comprehensive section on
protein secondary structure by Kurt D. Berndt includes to a link to an email
server for the program
PredictProtein . This predicts the secondary structure of a protein based on
its sequence similarity to other proteins of known structure. Its use is free to
academics and students.
The overall structure of proteins, divided into classes, is covered in detail.
These pages contain links to many examples of protein structures, taken from the
Protein Data Bank at Brookhaven, USA.
Proteins are classified into "folds" using a system based on their overall topology.
There are very many fewer known folds than known structures. Folds are further
classified into structural classes - an example is
Links are available to two databases of protein structure classification:
The final part of the course examines ways in which proteins
interact with each other and with other large molecules in cells.
SCOP - Structural Classification Of Proteins
CATH - Class, Architecture, Topology and
Material describing a number of protein families in detail is planned. Some of
the first example families are:-
- Cytokines are "extracellular messengers"; when they bind to receptors
embedded in the cell membrane, signals are transmitted into the cell.
Author: Simon Brocklehurst.
- Proteases break down other proteins by selectively cleaving peptide bonds.
There are several families of proteases. The metalloproteases bind a metal ion -
often zinc - in the active site. Carboxypeptidase A and thermolysin are well-known
Author: Daniel Barsky
- The small hormone, insulin, was one of the first proteins to be
crystallised and solved. It can associate into dimers (two molecules) and
hexamers (6 molecules).
Insulin is not, strictly speaking, a "protein family"; this section, with
impressive inline graphics, is included here in recognition of the part played by
in the development of protein crystallography.
Authors: Raj Gill and J. Walshaw, University of London.
- AVI Movies
- These molecular animations, contributed by
Andrew Booth of the
BioNet Teaching & Learning
Technology Project, are in the form of .avi files. You will need a viewer such
as Media Player to view them. They are large files, between 0.5 Mb and 8 Mb.
Example subjects are the transition between oxy-and deoxy-haemoglobin, and the transmembrane
helices of rhodopsin with a chromophore bound.
- A movie from Joel Sussman, Richard Gilliland, and Daniel Ripoll, showing
how substrate moves into the active site of acetylcholinesterase.
Henry Brzeski of Strathclyde University has written a
tutorial to illustrate the use of the molecular graphics program
RasMol to study the lac repressor /
operator complex and its interaction with DNA. [To run the tutorial, you need a
Web browser configured to start up RasMol automatically when a Protein Data
Bank file is imported.]
Lectures and Conferences in BioMOO
Neuroscience Journal Club
- Transcript of a recent discussion of a paper in Experimental Neurology held at
BioMOO, with participants from 3 continents. An archive of journal club transcripts can be found
A lecture and question and answer session on sequence analysis given by Dr. William Pearson as
part of the GNA Virtual School of Natural Sciences course on Bioinformatics (June '95).
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