| Country : | Australia |
|---|
Assignment Task:
Protocol:
Use PyMOL, to explore the structures that you have been provided. Use the questions below to guide your exploration. The following toots in PyMOL are likely to be useful in your exploration:
1. Representing the protein as solid surfaces and c- alpha and ribbon traces
2. Locating and colouring by accessibility to solvent
3. Measuring distances
4. Computing hydrogen bonds
5. Aligning structures to be able to compare them easier
Questions:
Note: every question requires an image or multiple images from the symbol in the answer. You must do your own work.
1. Which amino acid residues (E. coli and/or maize, say which one) do you think define the active site of the enzyme and why are these residues important? Include a picture of the active site showing the residues that define it
2. Which amino acid residues do you think to define the inhibitor binding site? Include a picture of the active site showing the residues that define it.
3. What type of inhibitor (competitive, etc.) do you think aspartate and malate might be and why?
4. If the structures do represent inhibited and uninhibited structures can you explain why the active site of one might have a higher affinity than the other? (think about the binding of the substrate, accessibility of the binding site)
5. There are a number of highly conserved residues within PEPC, including ARG456, GLUS66, ASP603, ARG647 and ARG759 (residues in 11QO_DCDP.pdb), which are found to be a part of the binding site. Looking at these residues what R chain properties do you think are important and why might some of these be so conserved? Would it be possible to mutate ARG759 to another residue and maintain functionality (i.e. binding of ligand)? What type of residue could ARG759 possibly be replaced with? Show a possible replacement of this residue (including the number of possible rotamers and percentage of probability for the most likely rotomer for that mutation).
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