Subject : Bioinformatics
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:
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.
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).
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