Bobak Seddighzadeh Week 8

Question

The question that me and my partner decided to tackle is: What specific sequence changes in the V3 domain of HIV-1 play a role in altering its structure significantly enough to affect its function?

Procedure and Results:

Ch 2:

Retrieving protein sequences:

1. First you must retrieve protein sequences form the web. You can use a host of sites such PubMed, but Bioinformatics for Dummies suggests using ExPASy instead because its a good site for protein information as well as being easy to use.
2. Go to http://www.expasy.org/sprot
3. Type in gp120 + envelope protein + HIV-1 in the search windown and then click the search button. A list of relevant protein sequences should be shown.
4. Click the link to your protein sequence that's relevant to your query
5. Scroll to the bottom right of the screen and click on the FASTA format link

Ch 4:

Deciphering the EGFR Swiss-Prot entry:

1. Go to http://www.expasy.org/sprot
2. Type in the Swiss Prot ID P00533 in the search window at the top of the page
3. Click the go button to reveal the general information about the entry and name and origin of the protein. Also included are the references, comments, keywords, features, and the sequence.
4. Do the same thing for gp120 protein accession number P04578.

Ch 5:

ORFing your DNA sequence

1. Go to www.ncbi.nlm.nih.gov/gorf/gorf.html
2. Go to biology workbench and retrieve sequence in txt format from one of your subjects
3. Copy and paste the sequence in the input box
4. Click the OrfFind button
5. To examine the ORF's more closely click, click the corresponding rectangle in the graphical display
6. Compare this ORF to the ORF to gp120 protein you found earlier

Ch 6:

Predicting the Main Physio-chemical properties of a protein

1. Go to http://www.expasy.org/tools/#primary
2. Click the ProtParam link near the top
3. Enter your sequence from the gp120 protein by copy and pasting the sequence or entering the accession number
4. Click the compute parameters button. Then press submit and proceed to analysis
5. Save results:

Looking for transmembrane segments

1. Go to www.expasy.org/cgi-bin/protscale.pl. The ProtScale page duly appears.
2. Enter the accession number P04578 in the small search box.
3. Scroll down and select the radio button next to Hphob./Kyte & Doolittle. You do this because ProtScale gives you a large rannge of properties to choose and test on your protein. This one is appropriate for predicting transmembrane helices.
4. From the Window Size pull-down menu, choose #19
5. Press submit butotn at the bottom of the page