Courtney L. Merriam Week 9

Purpose

The purpose of this experiment was to

Methods and Results

Defining Your HIV Structure Research Project

What is your question?
Make a prediction about the answer to your question before you begin your analysis.
Which subjects, visits, and clones will you use to answer your question?
Justify why you chose the subjects, visits, and clones you did.

HIV Structure In-class Activity

Convert your DNA sequences into protein sequence using NCBI Open Reading Frame Finder
- How do you know which of the six frames is the correct reading frame?
- Once you have done one example, you can obtain the rest of the protein sequences from the BEDROCK HIV Problem Space.
Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgeable (UniProt KB) .
1. If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
2. Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
3. What types of information are provided about this protein in this database entry?
We are going to use the PredictProtein server to analyze just the V3 region from Markham et al. (1998).
- Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit.
- Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
Download the structure file for the paper we read in journal club from the NCBI Structure Database
The files can be opened with the Cn3D software site. Answer the following:
1. Find the N-terminus and C-terminus of each polypeptide tertiary structure.
2. Locate all the secondary structure elements. Do these match the predictions made above?
3. Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.

Data and Files

No files or data was used for this assignment.

Conclusion

Acknowledgments

I collaborated with Avery Vernon-Moore and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.