Instructions for Writing Assignment CHEM 431A Winter 2006:

 

Purpose:                      To acquaint the student with methods for prediction of protein function based on sequence identities.  To familiarize the student with basic bioinformatics tools.

 

Assignment:               Pick one protein sequence and identify a minimum of two other protein sequences that show at least 20% identity.  Print out a comparison of the protein sequences.  Indicate regions of identity, functional motifs, and potential post-translational modification sites.  Describe an overall assessment of the role of each protein in the cell.  This includes the biochemical reaction that the protein is primarily responsible for and the biological outcome of a mutation in the gene that codes for the protein.

 

Websites to use:        http://www.ncbi.nlm.gov (use this as the home page to get information on your gene).  You can get to PubMed from here, which is useful for obtaining research and review articles related to your protein.

 

http://www.ncbi.nlm.nih.gov/PubMed (use this page to get more references on the protein you are interested in)

 

http://www.ncbi.nlm.nih.gov/omim (use may use this site to initiate your search for the protein sequence you are interested in).  On this page you should choose Search the OMIM Database. 

 

Copy (Ctl C) your protein sequence of interest.

 

http://www.ncbi.nlm.gov/BLAST (select a protein basic BLAST search)

 

Paste your protein sequence of interest.

 

Look at the Results and determine which genes have the highest score of identity.

 

Scroll down to inspect each pairwise alignment.  Copy protein of different species into a new MSWord document.  Convert to Courier 10 pt font and select landscape view.  This gives you the consensus sequence and two genes of alignment.  Repeat to get one other gene of interest.  Use MSWord for editing.

 

You can paste each of three protein sequences into the ClustalW program (found at http://www2.ebi.ac.uk/clustalw/).  This program will align all of your sequences.

 

http://myhits.isb-sib.ch/cgi-bin/motif_scan (use this page to inspect your protein sequence for post-translational sites and functional motifs).

 

Title Page

 

                Top center of page: Name of protein you are interested.

 

                Example: An analysis of “human K-ras protein”

 

                Middle of page:    Name of student

                                                                Date

 

                Bottom of Page:    CHEM 431A

                                                                California State University at Los Angeles

                                                                Professor Jamil Momand

 

1.        Text should be typed double-spaced, using 12-point font size, with 1” margins (top, bottom, sides).

2.        The text should be 2-5 pages in length (not including the title page).

All pages, except the title page must be numbered at the bottom, center.

 

Introduction

 

                Present background information on the protein of interest.  Why is this a protein of interest?

 

Results

 

                Show the protein sequence alignment of a minimum of three gene products.

                Create a box around the areas that show the highest degree of identity.

Mark those sequences that constitute potential post-translational modification sites.  Name the type of post-translational modification predicted to occur (phosphorylation, methylation etc.).

Mark those sequences that could be functional motifs or domains (nuclear localization sequence, leucine zipper).

 

Overall Assessment

 

Answer the following questions. What is the dominant biochemical activity that your protein is predicted to carry out.  Which sites on the protein contribute to the process directly?  Which sites contribute indirectly?  How does the biochemical activity relate to its biological function?  What is expected to occur to the organism if the gene of the protein is inactivated?

 

References

 

Author, year, title, source, volume and page numbers.

 

Reference websites as well.