Zrusso Biol 368 week 9
From OpenWetWare
HIV Structure Project
- Convert your DNA sequences into protein sequences.
- How will you do this?
- How will you know that it was done correctly?
- 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?
- 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?
- 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.
- Download the structure files for the papers we read in journal club from the NCBI Structure Database.
- 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.
- 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.
- 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?
- 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
- Background that led you to ask your research question
- Your question
- How you answered your question, method/results
- Interpretation of your results; answer to your question
- Discussion and interprettion of your results in light of the new paper you found.
- Upload your slides to the OpenWetware wiki by the Week 9 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.
- Use these Presentation Guidelines when preparing your PowerPoint slides.
- Your presentation will also be graded on the following Guide to critiquing talks.
- Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
