Atrolysin, the venom of the Crotalus atrox, better known as the western diamondback rattlesnake,
is very nasty. It is responsible for the largest number of deaths by snake bites in the United States of America
per year. The venom, a metalloproteinase, is an enzyme that breaks down the protective coating of blood vessels. This causes serious internal bleeding in the victim, leading to death.
Needless to say, a suitable antidote is urgently needed.
In this
bioinformatics practicum, we will design such an antidote by looking at the 3D structure of atrolysin
in a number of exercises. You can use this form (Word | PDF) to write down you answers.
The spatial structure of a protein is very important for its
function. Understanding it is the key to solving problems caused by
malformed proteins (like we find in many hereditary diseases) or,
like in our case, by unwanted malignant proteins in our bodies. You
need some background knowledge of protein structure, amino acids and
molecular interactions like hydrogen bonds for this practicum. If
you think you do not have sufficient knowledge (yet), you can refer
to the theory section for a quick introduction.
Explain why systematically mutating all the amino acids of a protein, one by one, can resolve which amino acids are important. Answer
In enzymes, the most important amino acids are located in the active site of the protein. This is where the actual enzymatic reaction takes place. Later in this practicum, we will look for the active site of the venom. But let's start with some basic exercises in 3D visualisation.
Yasara is a graphics program used to visualise and manipulate protein models. It was developed by Elmar Krieger, mainly at the CMBI. If Yasara is not installed on your computer yet, go to the software section to see how to do that.
After the practicum, you will have a chance to look at several other
interesting proteins. You can also use the program to make nice
pictures for reports and science projects. An elaborate description can be
found in the section More in 3D.
Start Yasara (help). In Yasara, you can load a polypeptide using the menu on the top left of the window: File > Load > Complete scene. Choose the file introduction.sce and click OK.
You can now see the structure of the peptide with sequence Asp-His-Arg-Gly-Gly-Met-Lys-Tyr in the so-called ball and stick representation. Individual atoms are shown as balls, connected
by sticks representing the atomic bonds.
Note: the hydrogen atoms are not represented because that would make the model much more complicated.
Below, you can see a 2D representation of the same peptide.
You will notice a "cloud" around the peptide. This represents the Van der Waals
surface. This surface shows how much space the atoms actually occupy: there is barely any empty space between adjacent atoms.
If you move your mouse cursor along the bottom of the Yasara screen, the sequence bar appears. To keep this bar visible, click on the blue pushpin at the left end of the bar.
When you click on a residue in the sequence bar, the Cα-atom of this residue will flash. If you push Ctrl while you click on the residue, the protein will rotate and zoom so that you can clearly see the Ca atom.
You can manipulate the protein by holding the mouse buttons and moving your mouse. Try the following:
The atoms are coloured by atom type. If you click on an atom, extra information about this atom will appear on the left side of the window.
