Designing an antivenom in 3D (2)
Working with Yasara
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, ask your teacher for help.
Exercise 2:
Start Yasara. 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. Above, 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 Ca-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:
- Left: Rotate
- Middle: Translate
- Right: Zoom
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.
Exercise 3:
- Look up which types of atoms (elements) can be found in proteins, using this list of amino acids.
- Look at different atoms in Yasara and find out which elements are coloured red, dark blue, green, and light blue.
Exercise 4:
In the representation that you see now, covalent bonds are shown as short sticks of a specific colour. Explain the difference between the yellow and white bonds.
Exercise 5:
The 3D structure shows three of the four different types of interactions that are important for protein folding.
These different interactions are represented by green, blue and orange sticks.
- Which interaction belongs to each colour?
- Locate these interactions in the 2D representation of the peptide.