Week 9 Individual Journal William P Fuchs

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HIV Amino Acid Sequence Project


  • Will there be a visible protein sequence change that correlates with a decline in CD4-T cell count?


  • Given that the amino acids of the clones of subject 10 are changing simultaneously there will be an observable drop in CD4-T cell count in response to the ongoing changes in the clones' proteins.

Target Clones and Visits

  • Subject 10 all clones all visits

Rationale for Selections

  • We are trying to see differences in change of protein sequence and CD4-T cell decline and we believe that the rapid progressives will exhibit the strongest relationships.

In Class Activity


To discover and implement various amino acid tools for the analysis and reconstruction of the protein structures of HIV.


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?
    • Yes it would seem so

Data and Files


  • This figure presents multiple reading frames of one of Subject 10's clones.


  • Figure of protein reconstructed from the data of Kwong et al. 1998

Scientific Conclusion

The various programs assisted in a comprehension of the analyzable amino acids.


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)



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  1. Bio Class Page
  2. BIOL368/F16:People
  3. Will Fuchs
  4. Link to LMU: http://www.lmu.edu/