BIO2B03 - Biochemical Interactions Between Molecules In Cells - Medical Science Assignment Help

Assignment Task -

Question 1:  Create a clearly oriented view of your protein-ligand interaction.  Save an image of this interaction and create a figure (with figure caption beneath) that describes your image.  Make sure to label your figure appropriately. Be sure to include the citation of the original article that published the crystal structure, together with the PDB number in your figure caption.

Question 2: Identify all the hydrogen bonds that exist between your protein and ligand.  Make sure that when doing so, you set your hydrogen bond cut-off at 3.0 Angstrom. Be sure to have these hydrogen bonds inserted as hatched lines between your protein and ligand. Create a figure (with figure caption beneath) that describes your image.

Question 3: How many hydrogen bonds do you find? Report the names and amino acid number of the amino acid residues in your protein that are forming these hydrogen bond interactions with your ligand. What do you hypothesize may be the importance of these interactions in the protein: ligand binding? What role do you think that these types of non-covalent interactions may have when it comes to the Kd or Ka value for this protein: ligand interaction. Be sure to include a full citation to primary literature that supports your hypothesis.

Question 4: You and your group members are part of a research team that is looking to explore the important of these non-covalent interactions on protein-ligand binding, pathway activity and overall outcomes on cellular processe.

• Select 2 amino acid residues that form hydrogen bonds with your ligand and using the mutagenesis Wizard menu, carryout a site-directed mutagenesis of these 2 residues. That is, replace them with 2 other amino acids in your primary protein sequence on PyMOL.  You must make sure to replace these 2 amino acids with ones that have different properties (eg. if a hydrophilic amino acid is in the original primary sequence, replace it with a hydrophobic amino acid, if a charged amino acid is in the sequence, replace it with an uncharged amino acid etc). From the amino acids that you identified in Question 3 above, which are you replacing and why? Report the names and properties of the amino acids before and after you replace them.
• Carry out the mutagenesis of the 2 amino acids (from a) on your PyMOL protein structure. Make sure to toggle through and get the appropriate rotamer of your amino acid mutant.  Once you have done so, re-run the hydrogen bond analysis tool to show the number of hydrogen bonds between your now mutant protein and the ligand. Create a figure (with figure caption beneath) that describes your image.
• Hypothesize what may be the effects of each of these mutations alone and together on the Ka and Kd of this protein: ligand interaction. Be sure to include a full citation to primary literature that supports your hypothesis
• Do you believe that these mutations may have effects on other protein-protein interactions that your protein may have in the cell?  Are there any signaling pathways that may be disrupted or augmented given these interactions? Outline and describe the main role that is played by your protein in their respective pathway. Be sure to include references that provide evidence for what pathway(s) your protein may belong to.

Question 5: Look through the literature and find a common mutation within your chosen protein that is related to a disease. Briefly describe where the mutation is located, including the amino acid residue number and mutation type. Be sure to include references that support the information that you have obtained.

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