MD Problem Set
Lysozyme
1) Go to the PDB and find the entries for Lysozyme.
You will see many entries. Pick one with an entry number that contains the day and month of your birth.
If you were born on the 10th of November, you could choose 110L. Obtain and read the header of the pdb entry,
which contains information on the protein (mutations, ligands, source, etc) slong with crystallographic information.
2) What is the resolution of your Lysozyme structure?
Find an entry with better data. Give the entry ID.
Find an entry with worse data. Give the entry ID.
3) (Omit this question, the data does not seem to be readily available) Look at the crystallographic data.
What information does that provide to you? (hint: not much)
4) Pull the coordinate file into a visualization program.
How many alpha-helices and beta-strands are there?
5) List 3 charged amino acid residues other than Arg.
6) For each of these charged residues, is the charge buried or solvent exposed?
7) Use excel for the following:
a) For the atoms (from #4) with formal charge of 1 or -1, make a table with the following columns:
residue #, residue type,
atom#, atom type, x coordinate, y coordinate, z coordinate.
b) Use the Pythagorean Theorem to calculate the three pairwise distances.
c) Using a simple electrostatic treatment, and assuming the dielectric of the medium is 78, calculate the pairwise electrostatic potentials.
d) Using a simple electrostatic treatment, and assuming the dielectric of the medium is 4, calculate the pairwise electrostatic potentials.
e) Which assumption do you think is most realistic? why?
8) Find the web page of someone actively involved in macromolecular simulation research. Give the PI name, the link and a 3 sentence critique of their home page.