Q1
Aspartic proteinase enzymes are a family of enzymes involved in a number of important biological processes. In animals the enzyme renin has a hypertensive action through its role in the renin-angiotensin system. The retroviral aspartic proteinases, such as the HIV proteinase, are essential for maturation of the virus particle and inhibitors have a proven therapeutic record in the treatment of AIDS. The lysosomal aspartic proteinase cathepsin D has been implicated in tumorigenesis and the stomach enzyme pepsin, which plays a major physiological role in hydrolysis of acid-denatured proteins, is responsible for much of the tissue damage in peptic ulcer disease. Since aspartic proteinases also play major roles in amyloid disease, malaria and common fungal infections such as candidiasis, inhibitors to these enzymes are much sought after as potential therapeutic agents.

• Locate within the Protein Data Bank the 3-D structure of an aspartic proteinase enzyme. State what your chosen entry is, and download the coordinates for the structure to use with Rasmol to investigate your chosen structure.

• Identify, using an appropriate bioinformatics program, the active site residues for your chosen PDB entry. Show the output generated by the program used.

• Using the program rasmol or Swiss-PDB Viewer produce an image of the structure that you think clearly illustrates the major structural features within the enzyme and clearly shows the location of the active site residues. State the commands used within the selected program to obtain your image.

• Discuss which types of bioinformatics tools that could be used to design inhibitors for aspartic proteinase.

20 marks

Q2
Cytochrome P450s are a family of proteins involved in phase I drug metabolism reactions. They are highly expressed in the liver, in the endoplasmic reticulum membrane. In this question you will explore the use of protein-protein interaction databases to find out what other proteins P450s interact with and whether the potential partnerships could have biological significance.

• Use the UniProt file for human cytochrome P450 2D6 as your starting point. Summarise the key structural features of P450 2D6 including how it is able to bind to the ER membrane, and structural features of the active site.

• Use a range of PPI databases to identify possible protein partners. Summarise your findings.

• From your searches select three proteins with different activities that interact with P450 2D6, describe the evidence for the interaction and discuss whether these interactions could be relevant to P450’s ability to metabolise drugs. Wherever possible select proteins for which there is experimental evidence for the interaction.
25 marks
Q3

Using the human sequence for the 509 amino acid protein Tyrosine-protein kinase Lck (Uniprot sequence entry P06239) determine the domain present within this protein sequence, using the Pfam domain database. State the domain and the amino acids within the domain.
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 an in-depth discussion of the models obtained, the templates used by the program, and the 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 which clearly shows the main features of the model.
25 marks

Q4
In lecture 6 on RNA informatics you were shown an analysis of RNA structure across the 3′ UTR of interleukin 2 (IL-2). Many other cytokines also carry an AU-rich element sequence, including interleukin 6 (IL-6). Micro-RNAs are known to target some cytokine mRNAs. In this question you will explore the interaction between the mRNA of IL-6 and a micro-RNA miR-365. It has been shown that miR-365 inhibits expression of IL-6 through this interaction.

a) Retrieve the sequence files for human IL-6 and five other species. Align the 3′ UTRs of the six mRNAs and identify on your output potential AU-rich sequence elements.

b) Retrieve the two files containing the sequence of miR-365 from the miRNA database www.mirbase.org. Run the complete sequences of the RNAs on Mfold and show the predicted structure of the RNAs. Calculate the folding energy per base and comment on your findings.

c) Model the binding of the mature sequence of each miRNA (this is given in the miRBase file) with the 3′ UTR of IL-6 mRNA. Assume that the miRNAs will bind to complementary sequences in the IL-6 mRNA, but not necessarily with complete complementarity. You will have to use alignment software to map complementary regions. Describe the procedure you followed, discuss the output with reference to a diagram of the alignment.

d) On the basis of your models predict which miRNA would be inhibitory and explain why. Does the mechanism involve the AU-rich element of IL-6?

30 marks

 

 

 

Sample Solution

Sample solution

Dante Alighieri played a critical role in the literature world through his poem Divine Comedy that was written in the 14th century. The poem contains Inferno, Purgatorio, and Paradiso. The Inferno is a description of the nine circles of torment that are found on the earth. It depicts the realms of the people that have gone against the spiritual values and who, instead, have chosen bestial appetite, violence, or fraud and malice. The nine circles of hell are limbo, lust, gluttony, greed and wrath. Others are heresy, violence, fraud, and treachery. The purpose of this paper is to examine the Dante’s Inferno in the perspective of its portrayal of God’s image and the justification of hell. 

In this epic poem, God is portrayed as a super being guilty of multiple weaknesses including being egotistic, unjust, and hypocritical. Dante, in this poem, depicts God as being more human than divine by challenging God’s omnipotence. Additionally, the manner in which Dante describes Hell is in full contradiction to the morals of God as written in the Bible. When god arranges Hell to flatter Himself, He commits egotism, a sin that is common among human beings (Cheney, 2016). The weakness is depicted in Limbo and on the Gate of Hell where, for instance, God sends those who do not worship Him to Hell. This implies that failure to worship Him is a sin.

God is also depicted as lacking justice in His actions thus removing the godly image. The injustice is portrayed by the manner in which the sodomites and opportunists are treated. The opportunists are subjected to banner chasing in their lives after death followed by being stung by insects and maggots. They are known to having done neither good nor bad during their lifetimes and, therefore, justice could have demanded that they be granted a neutral punishment having lived a neutral life. The sodomites are also punished unfairly by God when Brunetto Lattini is condemned to hell despite being a good leader (Babor, T. F., McGovern, T., & Robaina, K. (2017). While he commited sodomy, God chooses to ignore all the other good deeds that Brunetto did.

Finally, God is also portrayed as being hypocritical in His actions, a sin that further diminishes His godliness and makes Him more human. A case in point is when God condemns the sin of egotism and goes ahead to commit it repeatedly. Proverbs 29:23 states that “arrogance will bring your downfall, but if you are humble, you will be respected.” When Slattery condemns Dante’s human state as being weak, doubtful, and limited, he is proving God’s hypocrisy because He is also human (Verdicchio, 2015). The actions of God in Hell as portrayed by Dante are inconsistent with the Biblical literature. Both Dante and God are prone to making mistakes, something common among human beings thus making God more human.

To wrap it up, Dante portrays God is more human since He commits the same sins that humans commit: egotism, hypocrisy, and injustice. Hell is justified as being a destination for victims of the mistakes committed by God. The Hell is presented as being a totally different place as compared to what is written about it in the Bible. As a result, reading through the text gives an image of God who is prone to the very mistakes common to humans thus ripping Him off His lofty status of divine and, instead, making Him a mere human. Whether or not Dante did it intentionally is subject to debate but one thing is clear in the poem: the misconstrued notion of God is revealed to future generations.

 

References

Babor, T. F., McGovern, T., & Robaina, K. (2017). Dante’s inferno: Seven deadly sins in scientific publishing and how to avoid them. Addiction Science: A Guide for the Perplexed, 267.

Cheney, L. D. G. (2016). Illustrations for Dante’s Inferno: A Comparative Study of Sandro Botticelli, Giovanni Stradano, and Federico Zuccaro. Cultural and Religious Studies4(8), 487.

Verdicchio, M. (2015). Irony and Desire in Dante’s” Inferno” 27. Italica, 285-297.