Find Your Protein Exercise Resource
This exercise is designed to help you understand and investigate some of the basic physical properties of proteins as determined by their primary sequence. The goals of this exercise are:
You will look up the ascension number of a particular protein and examine its database entry. There is a lot of information in this entry that may be unfamiliar to you. Don't panic! You are new to biochemistry and these documents contain a lot of information. You will be looking for some basic information: the number of amino acids in the protein, the original authors of the paper that described the discovery of the protein or cloning of the gene for this protein, the primary amino acid sequence, and some information about the the biological purpose or activity of this protein. One of the challenges of this assignment is to examine and explore this document to find the information you need to complete the assignment. To give you an idea of what you will be seeing and doing see the information below.
For a copy of the FYPE assignment handout click here
To find your accession number click here.
Looking up your accession number
1. Go to the UniProt Database webite http://www.pir.uniprot.org/search/textSearch.shtml
2. Search the database for a particular UniProtID. To do this pull down the menu under 'Select field and insert query below:" and select :UniProt UIDs/ACs. Your screen should look like this:
3. Enter your accession number into the box and click on "Search"
3. An entry for your protein should come up on the next screen. An example is shown below. Click on the link in the first column to get the entry page for your protein.
4. Use the information in the entry to answer the questions listed in your handout.
Finding your pI
1. Go to the ExPASy PI/MW calculator http://www.expasy.org/tools/pi_tool.html
2. Enter the primary amino acid sequence of your protein in the box. You may cut and paste from the UniProt entry for your protein. Do not enter your protein's ID into the box, paste in the sequence.
Looking up References
Go to the PubMed database on the NCBI website. Use the search boxes at the top of the screen to search for your protein in the literature database.
For the question that asks you to describe the function of the protein, I would like you to do more than just list or restate what is listed in the 'Function' section. At least try to put it in your own words or get more information so that you can describe what the protein does. Clicking on the keyword links in the "keyword" section will give you some more basic information.
Also, the proteins that you have been assigned are proteins or enzymes that have been of interest recently or are involved in metabolism, a disease or a cellular process that you should know. You may try looking in a textbook to find more information.