Assignment 2 (50 points)
This assignment will be dedicated to protein analysis
The goal of this exercise:
* To learn about the basic protein structure prediction tools available on the WWW.
You will take a protein sequence, and predict features related to its primary, secondary
and tertiary structures.
*To get experience with phylogenic programs
* To use some of the important modeling WWW servers
Part-1: Sequence analysis (Sub-cellular localization)
1. From NCBI or SwissProt databases pick proteins that allow you to test the following
purposes:
-Signal peptide (secretory pathway)
-Chloroplast
-Mitochondria
-Peroxisome
-N-glycosylation
-Transmembrane domains
-GPI-anchoring
-Hydrophobicity
2. Use the websites from today’s lecture
3- Submit:
*Graphical presentations whenever is possible.
* Discuss and interpret your data and indicate which program did you use.
Part-2: Phylogeny analysis.
1. Pick a protein sequence. Use your favorite protein sequence, or pick any random
sequence, or use what you used in Assignment 1. Save it as FASTA format.
2. Search Swiss-Prot or NCBI using BLAST search program
3- Pick randomly between 10 and 15 sequences (proteins). Submit the list of these sequences
(not the sequences).
4-Using this web-based program (http://align.genome.jp/ ), perform several trees.
-Submit three types of trees.
-Answer:
*What the difference between the methods that are used to create the trees?
* Discuss your trees.
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Part-3: 3-D fold prediction.
We will be visiting these websites. The easy one to work with is the first (PHYRE), but I
encourage you to try the two other sites.
Protein Homology/analogY Recognition Engine (Phyre)
(http://www.sbg.bio.ic.ac.uk/phyre/html/index.html) for tertiary structure
modeling
PredictProtein for secondary structure prediction
(http://www.predictprotein.org/newwebsite/submit.html)
UCLA Fold Recognition (http://www.doe-mbi.ucla.edu/Services/FOLD/)
1. Fetch these 2 protein sequences from NCBI: Here are the entries:
AAV51943 and At3g46550
* Report some details about the proteins
* For further processing, save the protein sequences on you computer as
FASTA format.
2. Create a 3-D model for your protein sequences
* Go down the page of the SwissProt entry to "direct submission to SwissModel".
Or go to Phyre website and submit your sequences.(I recommend to try both sites)
* You will get by mail (SwissModel) the coordinates for the proteins.
Or you can wait and get them for directly from the interactive web
(Phyre at http://www.sbg.bio.ic.ac.uk/phyre/html/index.html)).
* Report the %identity and length of alignment between your query and the template.
* Is it above the threshold required for safe homology modeling?
* Submit a picture of the model for each protein that you can view via Jmol program.
* What secondary elements can you identify?, at what positions ? (You may want to
use the backbone representation only. For that, go to the 'control panel' window and
unselect the 'side' option of amino acids). You may wish to do that in the classroom
with our help...
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