# BIOL368/F11:Week 9

BIOL368: Bioinformatics Laboratory

Loyola Marymount University

This journal entry is due on Wednesday, November 2 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

## Individual Journal Assignment

• Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
• Don't forget to add the "BIOL368/F11" category to the end of your wiki page.

### HIV Structure Project

To answer your question posed in the Week 8 Assignment, you will need to do the following:

1. Convert your DNA sequences into protein sequences.
• How will you do this?
• How will you know that it was done correctly?
2. Perform a multiple sequence alignment on the protein sequences.
• Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
• How do you account for this?
3. Which of the procedures from Chapter 6 that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?
• How are they applicable?
4. Chapter 11 contains procedures to use for working with protein 3D structures. Find the section on "Predicting the Secondary Structure of a Protein Sequence" and perform this on both the entire gp120 sequence and on the V3 fragment that we are now working with. You will compare the predictions with the actual structures.
5. Download the structure files for the papers we read in journal club from the NCBI Structure Database.
6. These files can be opened with the Cn3D software site that is installed on the computers in the lab (this software is free, so you can download it and use it at home, too.) Familiarize yourself with the software features (rendering and coloring) with both the gp120 peptide and ternary complex structures. Alternately, you may choose to use the Star Biochem program to do this portion of your work. Answer the following:
• Find the N-terminus and C-terminus of each (poly)peptide structure.
• Locate all the secondary structure elements. Do these match the predictions you made above?
• Locate the V3 region and figure out which sequences from your alignment are present in the structures and which sequences are absent.
7. Once you have oriented yourself, analyze whether the amino acid changes that you see in the multiple sequence alignment would affect the 3D structure and explain why you think this.
8. The journal club papers we read are quite old already for a fast-moving field. Using the Web of Science (or PubMed or Structure) databases, find at least one more recent publication that has a structure of gp120 (V3) in it and download the structure file to view. What additional information has been learned from this new paper?
9. Your presentation for Week 10 will be formatted similarly to the previous HIV Evolution Project. In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
• Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
• Title slide
• Outline slide
• Discussion and interprettion of your results in light of the new paper you found.

## Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F11:Class Journal Week 9 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page; this should be part of your template.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F11" category to the end of the wiki page (if someone has not already done so).

### Reflection

1. Which project was more interesting to you: studying the evolution of the HIV virus or studying the structure → function relationship? Why?
• Note that I'm not asking about the tools you used, but the scientific problem studied.
2. What was the best part of working with a partner on this project? What was the worst part? Has this changed since your last project? Why or why not?
3. Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project?