Sequence and Structure Analysis of a Peptide Sequence

Assignments:

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.
• Do the following with your assigned peptide sequence
• • Create a list of know proteins that are homologous with your unknown peptide sequence
    • Use BLAST to search the "nr" database for homologous sequences
    • Use to search the "pdb" database for homologous proteins having known structures.BLAST
  • Using the CATH classifications, propose a class, architecture, topology and homology superfamily for your protein.
  • 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 SwissPDBViewer superimpose these two structures.
    • Display only the backbones, color one structure red and the other blue.
    • Use the Mac OS's Preview application to grab a jpeg image of the superposition.
  • Using the standalone version of Jmol, create a model of the protein that had the best E value from the search of the "pdb" database.BLAST
    • Model the protein as a cartoon colored according to structure. Show any ligands present as spacefilled and colored according to element type (cpk).
    • Create a jpeg image file of the mode directly from Jmol

Handin:

Create a Word document that contains the following:

1. Your name
2. Your sequence in FASTA format
3. A description of what an "Expect (E) value" is
4. A description of what is found in the "nr" database.
5. The sequence allignments for the top two hits from the "nr" database, i.e., those which have the two lowest Expect (E) values.
   1. Include a description of each along with their corresponding E values.
6. The sequence alignment for the top two hits from the "pdb" database. These are the hits for which 3-dimensional structures are available.
   1. Include a description of each along with their corresponding E values.
7. The CATH classifications for the top two hits from the "pdb" database.
8. A jpeg image showing the superposition of the top two hits from the "pdb" search
9. A jpeg image showing the cartoon representation of the top hit from the "pdb" search

---

[Chemistry Dept.] [Chem 406]

---

Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu