The tutorials are meant as self-study! They are for updating/refreshing
your knowledge about amino-acids and protein structure.
Answers to the question have to be given back to me.
Tutorials day1: Visualising structural information
This exercise is aimed at getting you acquainted with the way amino acids, secondary
structure elements and whole structures are visualised with computer graphics. It will also
give you a basic idea about the way the main structural databases are used.
The tutorials use Jmol as a java-based viewer (works in Windows, OS X and LiNUX/UNIX )
1 Amino acids.
Go to http://www.rpc.msoe.edu/cbm/jmol/amino.php
This tutorial aimed at refreshing your memory on amino acids and their properties. It will also
provide an idea on the way amino acids are represented graphically.
2- Learn to analyse a structure. Go to
http://proteopedia.org/wiki/index.php/Intro._to_Protein_Structure
Here a lot of topics are gathered with each their own graphical information. The ones to
explore are “secondary structure”, “phi and psi angles” and “ramachandran plot”. Other topics
will also give a lot of information.
On protein architecture:
http://biomodel.uah.es/en/ enter biomodel-1 and follow the flow on the right side panel.
3 Concepts of protein folding
Go to http://cbm.msoe.edu/includes/jmol/concepts.html after you have finished the amino
acid tutorial. This tutorial will look at the basic concepts of folding in case of a beta-globulin.
Questions will be asked in a self-quiz manner and 5 more proteins.
a) Some questions to answer:
b) Can you see a difference in the proteins?
c) Which ones seem different and why?
Try to find a reason for the differences (think about function and environment).
Also a very good tutorials can be found at http://www.umass.edu/microbio/chime/
Day 2
Tutorial: Protein structure characterisation:
In this tutorial we will try to use the knowledge from talk on database use to analyse a protein
structure. Find a structure (1C1H, ferrochelatase in complex with N-methylmesoporphyrin ) in
the PDB (www.rcsb.org) . Using the visualisation tools of the PDB, answer the following
questions:
1- How many -helices are there in the structure?
2- How many -sheets and how many -strands in each sheet (if there are any)?
4- How many domains are there in the structure?
5- Go to the protein classification site SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/). How is
this protein classified (class, fold, superfamily, family)?
6- Go to PDBSUM (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ ) and search for the
same entry. Answer the questions:
a- What is the connectivity scheme for the secondary structure elements within each domain.
b- At the end of the page you will find
Ligand: MMP - N-methylmesoporphyrin
and
LIGPLOT of interactions
Click on this and then on the symbol for Rasmol (
)
The graphics will show the interaction with the inhibitor N-methylmesoporphyrin.
Take a look at the type (charged, hydrophobic, etc) of amino acids that interact with the
inhibitor. What interactions are dominating? Describe by your own words the way the
inhibitor is bound to the protein.
Day 3
1-How to use SwissPDBviewer
Follow basic tutorial here:
http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/index.html
Followed by Homology Modelling document.