Internal Code:1AJHEB
TASK
What is the nature of these proteins, and what organism do they belong to? And what is their common function? Your answer should be a brief paragraph. Looking specifically at E2F4, find the regions of the following:
1. DNA binding region
2. Dimerization domain
3. HCFC1-binding-motif
A crystal structure of E2F4 in complex with DP1 has been solved (check Protein DataBank - PDB; complex code 5TUU). Using VMD, indicate which chain is E2F4 and DP1,and indicate the dimerization domain region Each chain should be rendered in a different colour (and the dimerization region) and the complex in Surf mode. Your figureshould have an appropriate figure legend and key. You might need to check the publicationfor more information. Show the complex in an appropriate orientation (NOT default).
Determine the average MW, pI, charge, and predicted localisation (k-NN) of all 6proteins given in the table above (E2F1-E2F6) using the bioinformatics tools you have Learnt.
Using the appropriate bioinformatics tool, list the predicted profiles, patterns, andmotifs (with the appropriate sequence range in numbers) for E2F4. Include a visual representation of the profiles and Protein kinase C phosphorylation site only.
Write a brief paragraph describing the Protein phosphorylation in general, (includesome of the different motifs or consensus sequence that are recognised forphosphorylation). Use references where needed.
You are asked to generate antibodies against E2F4, but you are not sure if you shouldmake monoclonal or polyclonal antibodies. In a paragraph, describe the difference between the two types (monoclonal and polyclonal antibodies), then name a couple of their advantages and disadvantages
Use the antigenicity prediction tool to determine the best epitope for E2F4 for generating the antibody, and calculate the MW of that sequence alone. Your answer should have a screenshot of the graph with peaks only.
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