1. What does PDB stand for, and what information is stored in the PDB?
2. Describe what information is provided in each column of a standard PDB file.
3. If you haven’t already done so, download and install Deep View (Swiss PDB Viewer) onto your computer: http://www.expasy.org/spdbv/
Next, visit Dr. Gale Rhode’s Deep View tutorial site:
http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/index.html
Practice using Deep View by working through the various tutorials (especially, 1-6 and assignment 1). After you have completed the tutorials (and assignment 1), obtain 1ZIN from the PDB.Briefly, for 1ZIN create a view similar to this one:
Put in words, you must create a view that displays alpha-helix 201-216 – complete with hydrogen bonds and residue labels and with the helical backbone and side chainscolored according to residue properties – within the context of the larger protein, displayed as a ribbon and colored according to secondary structure. Remember to render the final structure as a high quality image.
When you are done, copy the picture into yourword document that you will turn in to be graded.
Next, calculate the phi, psi and omega angles for residues 201-216. Include your results in the same word document.
In the same document, be sure to provide the following information:
9a. the PDB code and name of the protein.
9b. a brief description of the function of the protein.
9c. a short discussion about the overall 3D structure of the protein.
9d. a short discussion about the physical, chemical and structural properties of helix 201-216, especially considered within the context of the larger protein.
4. Suggest a destabilizing mutation and stabilizing mutation to helix 201-216. Briefly explain why your proposed mutations are predicted to be destabilizing and stabilizing, respectively. Provide pictures of your two mutant proteins (analogous to question 9, above).