J'aime C. Moehlman's Week 8

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Analyzing Protein Structure

  • This week we are using the Bioinformatics for Dummies book in order to analyze the protein structure of gp120.

Chapter 2: Retrieving Protein Sequences for the HIV gp120 Envelope Protein

  • Searched the protein knowledge base for the gp120 protein.
  • Picked envelope glycoprotein 120 with the accession number of A0A897, its entry name is A0A897_9HIV1.


  • We then conducted an advanced search to retrieve a protein sequence.

Chapter 4:Reading a SWISS-PROT entry

  • As seen in the screen shot above we know that the protein name is envelope glycoprotein 120
  • The gene name is env
  • We looked at the reference section and it shows that there is only one reference which doesn't imply major significance.
  • The cross reference page link to entries within other databases:
    • Screen shot from EMBL sequence database:
  • The keywords for the gp120 protein are; envelope protein and virion.
  • In the features section we see non-terminal residues at positions 1 and 76.

Chapter 5:ORFing your DNA sequence

  • Picked the DNA sequence from Subject 10 at visit 4 at clone 1.
  • compared to the SWISS-PROT entry the orf sequence shows very small differences in the sequence.

Chapter 6: Working with a Single Protein Sequence

Predicting the main physico-chemical properties of a protein

  • We used the expasy tool page in order to carry out a primary structure analysis.
  • We used the accession number A0A987 from Swiss-Prot into the ProtParam.
  • ProtParam generated the parameters of the entire gp120 sequence that we selected.
  • The results include many things, such as; how many amino acids there are in the sequence, the molecular weight, the overall number of positively charged residues, and the total number of negatively charged residues.

Digesting a protein in a computer

  • We pasted the gp120 seguence into the ExPasy website again in order to cut the protein.

Looking for transmembrane segmenting

  • We used the accession number A0A987 again and put it into the ExPASy ProtScale site and conducted a full range analysis.
  • The image was retrieved in GIF format.

Interpreting ProtScale results

  • A piece of paper was used to help us locate the strongest peaks on the graph.
  • We determined that there were four important transmembrane regions.

Running TMHMM

  • We generated the TMHMM results by using a FASTA sequence of the gp120 protein.

Looking for PROSITE patterns

  • Used the accession number A0A897 to determine which proteins we wanted to be scanned and then started the scan.

Finding domains with InterProScan

  • We again used the same gp120 protein segment that we have been using throughout the entire assignment.
  • We used the our class textbook to interpret the results that were generated by the InterProScan.

Finding domains with the CD server

  • We used the same FASTA gp120 protein sequence.
  • This image shows some of our results:

Finding domains with Motif Scan

  • We pasted the FASTA sequence into the Input box.
  • Selected PROSITE to conduct the search that we wanted.
  • With the results, we saw different things: including a matches map, a list of matches, and a matches details section.

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