Assignment

Today you will be given a peptide sequence and will be asked to propose a function and a structure based on sequence homology.

• Work through the Chapter 7 tutorial on Sequence Allignment from Stryer's Biochemistry website.
• You will be given a sequence of a peptide that was found at a crime scene. It turns out, the sequence for this peptide has never been observered before, suggesting that it comes from an organism that has never been observered before. Please propose a structure and a function for this peptide and propose what kind of organism is might be derived from .
• Do the following with your assigned peptide sequence
  • Create an evolutionary tree that includes your unknown peptide and which suggests what type of organism it might have come from.
• • • Use BLAST to search the "nr" database for homologous sequences
    • Select several sequences that are highly homologous along with some that are further down the list, about 10 in all, and create a phylogenetic (Distance) tree. Use the "BLAST Name" to label your tree.
    • Right-click on the try and save an image of your tree.
  • Create a proposed structural model for your peptide
    • Use BLAST to search the "pdb" database for homologous sequences. This will limit the search to proteins for which there are structures available.
    • Save an image of the sequence alignment to the sequence with the highest homology (lowest E value).
    • Obtain the pdb coordinate files for the two proteins that had the best (lowest) E values from the BLAST search of the "pdb" database.
    • Use BBEdit to edit the pdb files to include only the chain that your peptide is homologous to.
    • Use SwissPDBViewer superimpose these two structures.
    • Use SwissPDB Viewer to load your raw sequence, align it, and to thread it into a proposed structure using the protein with the highest homology score as your reference protein.
    • Save your folded sequence layer as a pdb file.
    • Use Jmol to create a snapshop of the structure of your protein as a cartoon colored by structure.