Week 9 Individual Journal William P Fuchs

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?

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

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.

Externals

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Assignments

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Useful Links

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