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 retrieved the FASTA sequence for the fragment:NLTDNAKTIIVHLNESVEINCTRPFNNTRTSXRIGPGQVFYRTGDITGSIRRAYCEINGT
KWNKVLXQVTEKLXEH
- 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.
- SCREENSHOT for ORF:
