Week 9 Individual Journal William P Fuchs
HIV Amino Acid Sequence Project
Question
Prediction
Target Clones and Visits
Rationale for Selections
In Class Activity
Purpose
To discover and implement various amino acid tools for the analysis and reconstruction of the protein structures of HIV.
Methods
Convert a nucleic acid sequence to a protein
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- 5'3' Frame 1 was the correct sequence because there was no stop codon in the reading frame.
- Check the derived sequence with the actual data set to test the accuracy of the read.
Investigate gp120 further and find entries for that protein
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- I got 206,278 hits
- Use the accession number "P04578" to narrow the search
- What types of information are provided about this protein in this database entry?
- Names and Taxonomy, Subcellular location, Pathology and Biotech etc.
Next, use the predict protein server to analyze the V3 region from Markham et al. paper
- test an amino acid sequence
- How does this information relate to what is stored in the UniProt database?
- This program analyzes composition of the protein and gives a more numerical analysis of the protein and its characteristics.
Download the structure file for the journal club paper
- Open the file with the Cn3D software and have the tool reconstruct the protein from the data.
- Find the N-terminus and C-terminus of each polypeptide tertiary structure
- Identify the secondary structure sites
- Do those sites match up with the protein predictor?
Results/Discussion
Data and Files
- This figure presents multiple reading frames of one of Subject 10's clones
Acknowledgements
I worked with Matt Oki in developing the scope and direction of the amino acid project as well as developing the question, prediction and subject selection sections. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.William P Fuchs 18:18, 25 October 2016 (EDT)
References
- Week 9 Assignment Page
- Provided guidelines and instructions for this week's individual journal.
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Assignments
Useful Links
- Bio Class Page
- BIOL368/F16:People
- Will Fuchs
- Link to LMU: http://www.lmu.edu/