Bioinformatics and molecular modelling
Instructions:

Lipase is an enzyme that the body uses to break down fats in food so they can be absorbed in the intestines.
Locate within the Protein Data Bank the 3-dimensional structure of a lipase. Download the coordinates for the structure and use Rasmol to investigate the structure.
(a) Using Rasmol produce an image of the 3-D structure of lipase that you have downloaded that clearly illustrates the catalytic site of the enzyme. Making reference to the PDB reference code of your protein detail those commands you used in Rasmol to produce your image.
(b) Discuss how an understanding the 3-dimensional structure of the active site of enzymes allows researchers to design inhibitor molecules using molecular modelling techniques and discuss the methods used.
25 marks
For the 461 amino acid protein Elongation factor 1-alpha (Uniprot sequence entry P19039) identify which domains are present within this protein. Detail the starting and ending amino acids of each domain.
Run homology modelling for this protein using SWISS-MODEL to obtain a 3-dimensional structure for this sequence.
Show and discuss in detail, the results of the modelling that you have obtained, detailing the information provided in the output file and the validity of the model that is obtained.
Download the coordinates of the model obtained as a protein databank (*.pdb) file and create an image of your modelled structure using rasmol or Swiss-PdbViewer. Include your image together with a discussion of both the secondary and tertiary structure of the model obtained.
35 marks
Q3
In lecture 8 we discussed small elements of RNA folding found in the transferrin receptor (TfR) mRNA called Iron Responsive Elements (IREs). Five copies of these elements are found in the 3′ UTR of TfR mRNA.
(a) Retrieve mRNA / cDNA sequences of human, chicken, rat and mouse transferrin receptor mRNA and identify the IREs in each mRNA. Use the EMBL files X01060 (human), X13753 (chicken), M58040 (rat) and BC054522 (mouse) and refer to the paper “Chicken transferrin receptor gene: conservation 3′ noncoding sequences and expression in erythroid cells” Nucleic acids Research vol 17, p3763, 1989 posted on WebLearn to help you.
(b) Draw a diagram showing the positions of the IREs in each mRNA 3′ UTR. Align the five IREs from human TfR and separately align the IREs from the different species in sequence, i.e. align the first IREs from the four species, then the second, third, fourth and fifth. How much conservation of the IRE sequence is there i) within a species and ii) between species?
(c) ?Use an RNA folding program to calculate folding energies of the chicken IREs and show images of each folded IRE.
(d) Calculate folding energies of human, rat and mouse TfR IREs (no need to show images of the folded RNAs) and compare them between the species. Comment on your findings.
(e) Compare the sequences between the second and third IREs on the
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Referencing Requirements:
It has to be done by person in uk as the domains should show uk address.

 
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