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
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.