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 one or
several of the following purposes:
-Signal peptide (secretory pathway)
-Chloroplast
-Mitochondria
-Peroxisome
-Transmembrane domains
-GPI-anchoring
-Hydrophobicity
2. define potential posttranslational modifications
3. Use the websites from today’s lecture
4. Submit:
*Graphical presentations whenever is possible.
* Discuss and interpret your data and indicate which program you used.
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://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/ ), perform several trees.
You can also look for another program:
http://evolution.genetics.washington.edu/phylip/software.serv.html#servers
-Submit three types of trees.
-Answer:
*What the difference between the methods that are used to create the trees?
* Discuss your trees.
1
Part-3: 3-D fold prediction.
We will be visiting these websites. The easy one to work with is the first (PHYRE), but feel
free to try the two other sites.
Protein Homology/analogY Recognition Engine (Phyre2, NEW!)
(http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index ) for structure modeling
 http://swissmodel.expasy.org/
 http://www.robetta.org/submit.jsp
1. Use 2 protein sequences from NCBI
* Report some details about the proteins
* For further processing, save the protein sequences on your computer as
FASTA format.
2. Create a 3-D model for your protein sequences
* go to Phyre website and submit your sequences.
* You will get by email the link to the results of the modeling.
* Report top template information.
* How many residues out of the sequence have been modeled? Confidence?
* 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? Can you attempt to
change the presentation of the molecule?
2