Alex A. Cardenas Week 8

Chapter 2

Retreiving protein sequences for envelope glycoprotein gp160 (pp. 42-51)
Went to www.expasy.org/sprot/.
Envelope glycoprotein gp160 was typed into search box and retreived. The description of envelope glycoprotein gp160 can be found [here].
- Entry Name - ENV_HV1C4
- Primary Accession Number - P05879
FASTA format was viewed (FATSA - a sequence alignment-and-database-scanning program). New window appeared with all amino acids in the protein sequence.

Protein sequences retrieved by advanced search methods. Clicked on advance search tab and typed in envelope glycoprotein gp160.

Reading a SWISS-PROT entry (pp. 110-123). The link can be found [here].
Went through steps in deciphering the envelope glycoprotein gp160 swiss-prot entry. Information on entry name, primary accession number, protein name, gene name, etc., can be found in the link above.
8 References were found in the article.
The Cross references - not all cross references were displayed online as they were in the book as seen below in the picture:

ORFing DNA sequence. Retrieved sequence from clicking on FASTA in UniProtKB and posted it in open reading frame finder. DNA sequence is displayd as 6 parallel horizontal. There are 6 possible translation frames: +1, +2, +3 on on reverse --> -1, -2, -3.
ORF displayed the following

Working with a single protein sequence.
Followed link www.expasy.org/tools/#primary and clicked on the ProtParam link.
- Accession number was entered for gp120 sequence. N and C terminus boxes left blank in order to analyze the whole sequence.
- Submitted amino acids 266-288 in order to show molecular weight, extinction coefficient, and estimated half-life.
  - Molecular weight - 2547.8
  - Extinction coefficient - As there are no Trp, Tyr or Cys in the region considered, your protein should not be visible by UV spectrophotometry.
  - Estimated half-life - 100 hours.
Looking for transmembrane segments in the next sectional exercise. Followed www.expasy.org/cgi-bin/protscale.pl and entered accession number into the search box, selecting the appropriate boxes for properties and widow size. Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41). Shown below in the picture taken from the webpage.

Interpretation of the graph below was taken into account. Followed the steps it gave in order to find the threshold value, which was found to be around a score of 1.

Finding transmembrane regions using link www.cbs.dtu.dk/services/TMHMM-2.0. Entered FASTA format of sequence into the corresponding box.
- Highest probability of transmembrane region being found is amino acids 21-43,523-545, 604-626, and 690-712 --> as seen in the picture below.

PROSITE patterns being looked for in next exercise --> followed link www.expasy.org/tools/scanprosite/ and entered accession number into box. Unchecked Excluded motifs with a high probability of occurrence box (to have small patterns be meaningful and not overlooked) and checked do not scan profiles box. The picture below shows the hits by pattern with a high probability of occurrence and when dragging mouse over the bottom portion, it corresponds with the highlighted portion in the amino acid sequence.

Found domains with InterProScan by following the link www.ebi.ac.uk/InterProScan/ and entering in sequence. And InterProScan results are shown below.

With Motif Scan --> found domains by following myhits.isb-sib.ch/cgi-bin/motif_scan. and entered in sequence and selected the PROSITE motif box because it gives a much quicker answer and is a lot smaller than Pfam.
More practice with these exercises will help in drawing more conclusions about the protein.

Working with Robert and Zeb.
V3 loop conformation is the main area of study and comparing these regions with those who developed AIDs and those who did not. We will investigate these different conformations and how they compare with the given numbers such as CD4 T cell count, ratios, etc.
Rapid progressors sequences will be compared to moderate and non progressors. Subjects of interest are 1, 3, 4, 10, 11, and 15. Moderate progessors of interest 6 and 13.