?Locate within the Protein Data Bank the 3-D structure of an aspartic proteinase enzyme

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AS6056/AS6007 Bioinformatics & Molecular Modelling Data Analysis For all questions illustrate your answers fully, describing what you did at every step and providing input/output illustrating what input/output was obtained. You need to include, embedded, within your submitted work all relevant output from online servers, as appropriate, as well as a written dialogue to fully illustrate what work you carried out. For all parts describe how you obtained your data by stating the bioinformatics portal used and the search strategy. Please quote accession numbers of all database files used. 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

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Author Since: November 30, 2020

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