Assignment task: Analyzing 3-dimensional shape of 2 different proteins:
Part 1: The first protein you will analyze are prions. Answer the following questions about prions. You can use Google searches to assist the acquisition of information just make sure you cite the source or sources.
A. What is the function of prions?
B. What disease does prions cause and what role do prions play in development of this disease? What are the different ways in which humans get this disease?
Part 2: Now let's explore the structure of this protein. You will need to use the Protein Data Bank (PDB) website. Click to open the website. In the search site at the top put in 1HJN (this is an important fragment of the protein). This will bring up the structure of wildtype (non-disease causing) human prion protein.
A. Click on "sequence". How many amino acids make up the listed fragment of human prion protein?
B. Click on the "genome". What chromosome contains the prion gene?
C. Now let's analyze the structure. Click on "structure summary". What is the molecular weight of this protein fragment?
D. Now click on "structure" below the structure diagram. Scroll to the bottom of page and select a different viewer (JSMOL). Click and view the different structure styles. Go back to the ribbon structure and click and drag the structure to rotate the protein. What secondary elements do you see? Include how many helices the protein contains and how many strands the beta sheet has.
E. Click the back arrow at the top of the page to exit this page. Now go to the literature description. Write down the specific amino acids (numbers) that are involved in the make up the helices and the beta sheet.
F. Now let's explore the structure of a fragment of the misfolded prion protein that may cause the aggregates that lead to the disease state. In the search site of the PDB website, type 6PQA. Explore the structure of this important fragment of the protein. How has the structure changed from the wildtype version you just analyzed? Now review the literature section. What type of method was used to produce this predicted structure?
Now search for information regarding current hypothesis of how infectious prions cause the disease. Briefly describe this hypothesis. Site your reference(s).
Search the Web for the structural formulas of lysine, glycine, and valine - can you draw a chemical structural formula of KGV tripeptide?