Mini Assignment # 4 This assignment is due February 10th, 2025 Make a figure with the following subpanels: Retrieve the Alphafold 2 model of Pseudechis australis basic phospholipase A2-PA5 from the Uniprot website for the protein sequence.
The model can be found lower down in the page, above the sequence itself. All of the following should be separate panels in a single figure, arranged as a 2×2 grid, assembled in Inkscape or a similar program.
Keep the size of the protein and orientation consistent between panels (you can use get_view/set_view, and save scenes as you go, as you might find that you need to use a slightly different view later). Use a white background, maximum detail, with no shadows, at high resolution (at least 1000 pixels per image).
Everything should be ray traced, and look crisp and professional, as in a paper. A) Using the MSA you developed for assignment #3, make a Consurf figure of the publicly available Alphafold 2 model of Pseudechis australis basic phospholipase A2-PA5, coloured by sequence conservation in Consurf. Do not use Consurf’s auto generated MSA, make sure to give it the one you have hand curated.
You can use any reasonable colour gradient for Consurf, as long as you describe it in the panel (Default cyan/magenta is fine too). It’s generally a good idea to keep neutrally conserved as white. Orient the molecule so that the most conserved surface faces the viewer, with the longest axis of the protein vertical. Label key active site residues to the extent that they are visible in the image (see below).
B) Perform a DALI search of the PDB using Pseudechis australis basic phospholipase A2. Superpose this structure on the top hit, using DALI for the superposition. Show a single chain of each as a cartoon, along with any bound ligands. Choose colours that contrast but don’t clash. Show only a single protomer shown for each protein. In the accompanying caption, note the Z-score, sequence identity, rmsd and aligned length. What is the oligomeric state of the protein you are superimposing on? C) Phospholipases use a membrane lipid as their substrate. Using OPM, predict the orientation of Pseudechis australis basic phospholipase A2 in the mammalian cellular membrane. Using information from papers from known homolog structures (part B), identify any key catalytic residues. Make a third figure, in the same orientation as the other two, showing the protein as a cartoon trace. Show disulfide bonds, active site residues, and any residues that extend into the plane of the membrane as sticks, side chain only. Colour each group of residues with the carbon atoms a distinct colour, and heteroatoms as their default colours. Show the cartoon of the protein in a fourth colour – white is a good default choice. Show the plane of the membrane as yellow transparent spheres. Make a second panel showing the protein in the plane of the membrane; this panel should be at 90 degrees to the first view – you can go back and adjust this view. Label the shown residues.
Provide an appropriate caption for each figure panel, explaining what you are showing, including which sequences were used to generate the Consurf figure. Make sure that AC are clearly marked in the figure.
