BIOL398-01/S10:HIV Structure

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=== Working with Protein Sequences In-class Activity ===
=== Working with Protein Sequences In-class Activity ===
<!--* This week we will begin to learn how to analyze protein structures.  For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
* Chapter 2:  Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition).  The example worked through in the book uses the sequence of an enzyme called dUTPase.  Follow the book example yourself and then work through the example again, this time using the HIV gp120 envelope protein instead.
* Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition).  The example worked through in the book is the epidermal growth factor receptor.  Work through this example and then do it again with the HIV gp120 envelope protein instead.
* Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition).  In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein.  Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence.  Since you were working with just a portion of the entire envelope protein, you may get some strange results.  Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means.  Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found [ here].
* Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition).  Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT.  We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.-->
=== Preparation for Week 8 Journal Club ===
=== Preparation for Week 8 Journal Club ===

Revision as of 13:33, 23 February 2010

BIOL398-01: Bioinformatics Laboratory

Loyola Marymount University

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  1. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, and Hendrickson WA. . pmid:9641677. PubMed HubMed [Paper1]
    Kwong et al. (1998) link to full text

  2. Stanfield R, Cabezas E, Satterthwait A, Stura E, Profy A, and Wilson I. . pmid:10368281. PubMed HubMed [Paper2]
    Stanfield et al. (1999) link to full text

  3. Stanfield RL, Ghiara JB, Ollmann Saphire E, Profy AT, and Wilson IA. . pmid:14592768. PubMed HubMed [Paper3]
    Stanfield et al. (2003) link to full text

All Medline abstracts: PubMed HubMed

Week 7

Working with Protein Sequences In-class Activity

Preparation for Week 8 Journal Club

The class will be divided into groups of 3 or 4. Each group will create and present a Journal Club (in class in Week 8) on the Kwong et al. (1998), Stanfield et al. (1999), or Stanfield et al. (2003) articles. The groups will be:

  • Kwong et al. (1998):
  • Stanfield et al. (1999):
  • Stanfield et al. (2003):

In preparation for the Journal Club, each individual will do the following assignment on their individual Week 7 Journal page.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.
  2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).

Week 8

  • Journal Club presentations in class.

Week 9

  • Project work session

Week 10

  • Project presentations in class.
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