Find a primary literature review describing the protein/enzyme.
Find and load a pdb file in Swiss pbdviewer
If there are several types of enzymes select the best picture.
Find the active site if identified.
Get the protein sequence from NCBI or other data base.
Blast (using blastP) the data base and retrieve 5 sequences from other organisms and align them in the BioEdit program**. (You should already have Bioedit working). Highlight conserved amino acids.
In your structure find the conserved amino acids and identify where they are (highlight them on the structure. Pick 5 areas of identity and if possible describe their function. Determine if other structures of the same protein exists with substrates or inhibitors bound. Locate the small molecule binding site in the protein and report which amino acids in the aligned sequences that interact with the small molecule(substrate, inhibitor or modulator).
You should have at least three primary research articles that you reference more may be helpful. Write a five page description of your project. Support your data with graphs pictures and alignments (not included in the page limit).
A 5 page double spaced written report and as many figures as required is minimum for a grade. Reference all literature used and use a bibliography that is compatible with the journal Cell Minimum of 3 references. Remember-do not copy the text. This is plagiarism and a zero will be assigned if plagiarized. Use your own words to explain. To find out how to use cell references go the web page for Cell- Instructions for authors. And get examples from there.
If your enzyme or protein is part of a multi subunit complex or interacts with other proteins instead of small molecules, describe the interaction motif and treat the other protein binding site as a small molecule binding site. Report the interaction sites as describe on the previous page. Any other interesting facts, biochemistry and superfamily relationships please include.
Grading will be on the degree of detail and completeness of the project. This assignment is a learning tool so spend quality time in the completion of it and demonstrate your own initiative in the scholarship of the project.
** When aligning the sequences pick homologous sequences that are some what distant at least 20% sequence dissimilar. If you pick E. coli and use Salmonella or Shigella which are very closely related there maybe no differences in the sequences to determine conserved and non conserved domains. When using BlastP select sequences down the list (select 500 hits). With lower BLAST scores.

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.