Homework #4 Chem4110 Fall 2012 Due Friday September 28th

This homework assignment is designed to increase your familiarity with protein databases, searches of those databases, and how to find out interesting information about particular proteins and their relationships with others in the database. We will be looking at the citrate synthase enzyme from human mitochondria for this assignment, which is encoded by the CS gene. But you are encouraged to investigate other proteins that may interest you using the same techniques used for this homework assignment.

1. Perform a search for this protein in the Universal Protein Database (UniProt).

2. Find the 13 following pieces of information for this protein (A through K):

• The UniProt accession number (Entry code)
• Number of amino acids
• Sequence status
• Protein Existence status
• Number of amino acids in mature enzyme (not including the mitochondrial transit peptide)—Use this mature enzyme for all of the following:
• Number of acidic residues
• Number of basic residues (Arg and Lys)
• Number of Cys residues
• Molecular weight
• Molecular formula
• Isoelectric point
• Extinction coefficient at 280 nm
• Sequence of amino acids in FASTA format

Hint: You may need to browse around the site to find things. Look for pull-down menus and buttons to click to find the information you need once you get to the page for the selected protein.

3. Run a BLAST search with your protein(complete, including transit peptide) to identify other proteins that are closely related. (Basic local alignment search, with default settings)

4. For the 5 most closely related proteins, give the following information (Don’t include redundant sequences):

A. The Entry code for each

B. The organism each comes from

C. The percent identity for each protein

5. Perform an alignment of these five proteins with the human sequence, and print out the alignment. (Just use the default settings.)

Also, give the number of residues that are not strictly conserved among these six proteins.

Place all this information in an organized format in a Word document (Use the numbering and letters for each piece of information as described above). Make sure to attach your alignment that you printed out. The assignment is worth 40 points.

Enjoy!