AS6056 Bioinformatics & Molecular Modelling
Semester A 2013
Assessment 2 – Data Analysis
PLEASE READ
Illustrate all of your answers FULLY, including ALL details of what you did, at what websites, and why. Include all relevant output from online programs/servers as appropriate to provide evidence of what you did. Accession numbers of all sequence files must be given. Any references used should be cited in your answer.
Q1
Hepatitis C is a serious disease that affects about 200 million people worldwide. No anti-Hepatitis C Virus (HCV) vaccine or specific anti-viral drugs are available today. Non-structural protein 3 (NS3) of Hepatitis C virus is a bifunctional serine protease/helicase, and the protease has become a prime target in the search for anti-HCV drugs.
Locate within the Protein Data Bank the structure of the NS3 protease domain of the Hepatitis C Virus complexed with an inhibitor. Download the coordinates for the structure and use Rasmol to investigate the structure.
(a) Identify the active site residues for your chosen PDB entry.
(b) Produce an image of the structure that you think clearly illustrates the major structural features within the complex.
(c) Identify those interactions which exist between the inhibitor and the enzyme. Illustrate with appropriate images how the inhibitor binds close to the enzyme active site.
(d) Discuss how molecular modelling studies could be carried out to design improved inhibitors for the NS3 protease domain of HCV.
30 marks
Q2
You are told by a colleague that a new web-site has appeared which predicts targets for microRNAs, URL www.targetscan.org. You are asked your opinion of the website.
a) Decide on three criteria to assess the website and write a brief summary of the usefulness of the website to bioinformaticians, based on those three criteria.
b) Use the web-site to find the miRNA(s) predicted to interact with the mRNA of human transferrin receptor 1 and write a brief summary of your findings.
c) Retrieve the mRNA / cDNA sequence of human transferrin receptor (TfR) from the EMBL / ENA file X01060 and identify the IREs in the mRNA. You can use 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. Summarise your findings.
d) Using an RNA folding programme, plot the local folding of the 3′ UTR of the human TfR in the following regions:
i) The binding site of the miRNAs
ii) The first two IREs
iii) The region between the second and third IREs.
Discuss your findings in relation to the expectation that (i) and (iii) are single-stranded and (ii) has significant secondary structure.
[Note: plots of local folding of RNA were discussed in the lecture on RNA Structure and Function, slides 60 and 62. It is recommended to use a sliding window of 20 bases and calculate folding energies every 5 to 10 bases.]
40 marks
Q3
Using the 509 amino acid Tyrosine-protein kinasefrom Homo sapien (Uniprot sequence entry P06239) determine the domains present within this protein sequence, using your choice of domain database.
Run homology modelling for this sequence using SWISS-MODEL to obtain a 3-dimensional structure for this sequence.
DISCUSS, in detail, the results of the modelling that you obtain, including a discussion of all output generated.
Download the coordinates of what you consider to be the best 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 the secondary structure predicted for that model.
30 marks
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