Structures:

The remainder of this part of the course consists of increasingly more realistic, and thus increasingly more complicated, YASARA exercises on protein structures or small parts thereof.

Today more even than the other days in this course it is much more important to do that what you do well than to finish all exercises.

When you see a structure, ask yourself if all residues are behaving well according to the rules given in this course so far:

• Are there prolines, glycines, etc., in turns?
• Are most residues in the core hydrophobic ?
• Are about half of the surface residues hydrophilic ?
• Are there more than average AMELK residues in helices ?
• Are there more than average VITWYF residues in strands ?
• Are strands alternatingly in-out, and hydrophobic hydrophilic ?

We will start with some very simple molecules that we made up for simplicity so you can get used to the visualisation software. The later exercises involve real molecules, solved by X-ray crystallography. When you work with a real molecule, please look up what its function is, and a few more things you can find about it.

• From which species does it come?
• Where in that species does it perform its function?
• How is it regulated?
• Which residue is disobaying most what you learned so-far?
• What does the PDB file-header tell you about this protein?
• Try to think of a few more relevant things that you can explain given the 3D structure.

Use Google!

If you haven't gone through the YASARA introduction help movie yet, this is the moment to do it. See under YASARA a few steps earlier in this course.

Question 56: The questions to answer here are:
1) Can you find the structures in the Exercise files list in the little Miscellaneous window?
2) Figure out how to Save (for example) the file HYPOTHASE.pdb from the Exercise files section onto your Desktop.
3) How do you enter it into YASARA?