A. The protein Fatty acid 2-hydroxylase processes lipids (fats) in the human body.
An entry corresponding to this protein can be found in the UNIPROT database
under the ID# Q7L5A8.
1. Use PROSITE to predict the domains/sites of this protein.
▪ How many domains are predicted? What is the function of each domain?
▪ How many disulfide bridges does the protein have?
▪ Does it have any relevant sites (i.e., active sites or some other sites)? If yes, how many sites and what kind of sites are each?
2. Assume that the secondary structure of the protein is not known. Use
JPRED4 to make a prediction. In the results page, consider only the
consensus prediction (hint: check what the acronyms mean).
▪ Between helices and sheets, which is obviously the dominant motif type?
▪ How many instances of helices and sheets were predicted for each and how many motif counts were predicted in total?
▪ Chronologically jot down and number each motif. (For example: Motif 1 - Sheet, Motif 2 - Sheet, Motif 3 - Sheet, ...)
▪ View the results in SVG. Provide a screenshot of the results summary.
3. Assume that the tertiary structure of the protein is not solved. Use SWISS
MODEL to build a model. If there are multiple results, consider only the model
who has the highest coverage.
▪ How many predictions did the tool give? What is the %coverage of the
one you are considering?
▪ Between helices and sheets, which is obviously the dominant motif type?
▪ How many instances of helices and sheets were predicted for each and
how many motif counts were predicted in total?
▪ Chronologically jot down and number each motif. (Hint: to determine
model's terminal amino acid, check the section of your result card labelled
Model-Template Alignment)
▪ Provide a screenshot of the 3D model.
▪ Compare your notes on the chronological order of each motif from
JPRED4 to SWISS MODEL's. Comment on how well they match (or do
not match).
