Assignment #3: Due Tuesday, April 8

What makes your protein the best? Convince us.

Submit a post to sell your classmates of the beauty of your protein, with an emphasis on its biochemistry. Include structures, reactions, references, and anything else you need to make your case. Though you should consider this your final version, you will get the chance to respond to the comments from your classmates before your final submission enters the brackets.

This assignment is worth 30 points. You will be evaluated by your peers on the basis of your protein's biochemistry.

Assignment #2: Due Friday, March 21 (though it won't be late until Tuesday, April 1)

The due date falls right before spring break, but you may take more time if you choose. It's your decision if you want to do it right away, wrap it up before spring break, or devote time to it over spring break.

For your second assignment, worth 10 points, you need to find and summarize articles describing your protein from the biochemical literature. Find information that tells us something interesting about the biochemistry of your protein. What does it do? Does it catalyze a reaction? If so, write out the reaction (you don't need to show structures yet). What does it do for a cell or the organism? Are there diseases associated with it? If you're looking for examples, check out some of those posted in the Virtual Protein Museum, the Protein Data Bank Molecule of the Month site, or the Protein Structure Initiative Featured Molecules page.

You must find a minimum of 3 articles, at least one of which must be a primary research article (you may use review articles for the others). Then you should write a one paragraph summary of the most interesting items from the article--remember, your goal is to convince your friends and family of the beauty or amazingness of the biochemistry of your protein. Include a link to the article in your blog post.

Where should you look?

• The Protein Data Bank page for your protein will have a link to the article linked to the structure.
• Another good place to look is the PubMed site. You can look for review articles here, too (these will be a great source of the interesting features of your protein); you can then look for a primary article from the references listed in the review. To look for reviews, select the [Limits] tab and then scroll until you find the [Reviews] tab. For further instructions on PubMed, click here.
• Highwire and Google scholar are other great sources for articles. Once you find an article, you can also get a list of other articles that have cited it. This may also help you find reviews.
• You need not read the whole article--take a look at the abstract and the introduction (which will have more citations) to see what the authors found about your protein.

If you have selected a protein featured at either the Protein Data Bank Molecule of the Month page or the Protein Structure Initiative Featured Molecules page, you must also cite the source on your blog page.

Post on the Google docs sign up when you have finished.

Assignment #1: due Monday, March 3

For your first assignment, you must explore different ways to represent your protein and then post pictures to your blog. Provide the PDB number for any structures in your post. 

Try cartoons, space-filling representations, sticks. Highlight prosthetic groups. Change the colors by secondary structures, chains, chainbows, etc.Use at least two different background colors (under the [Display] pulldown, and examine different use of [color space] from [Display].

Post 5 different representations by the end of the day on March 3. Your assignment is not complete until you have posted your blog address on the Protein of the Year sign up page on Google docs.

Protein of the Year assignment overview

For your Protein of the Year assignment you will need to convince your classmates that your protein is fantastic due to its biochemistry. Your goal is to add your name to the coveted Jane Richardson Cup alongside the previous years' winners Ian Robertson, Alex Harris, and Anand Divakaran. To do so, you will generate a web page via Blogger that will show off your protein. Though some proteins can make a convincing case on their own with their structures, you will want to enhance your case by pointing out what makes your protein the best. Though you need not follow the template, feel free to examine the pages for these proteins to give you an idea of what to show:

• ribonuclease inhibitor
• GFP
• rhodopsin
• alpha-hemolysin
• chaperonins like GroEL-ES 

Each student will pick a unique protein (first come, first served), which you will post on Google docs. You will not be able to choose any of the following proteins already in the Hall of Fame: ribonuclease inhibitor, alpha-hemolysin, anthrax toxin, salmonella needle complex, nitrogenase, or hemagglutinin. I have posted a Google document for your sign up starting at 5:00 PM on Wednesday, Feb. 12, and student choices will be awarded in the order in which you have signed up. Let me know ASAP if you cannot access the signup.

In the meantime, each of you should start your own blog on blogger (you should be able to find instructions from this page...let me know if you're having trouble), and then make sure that you're able to post comments. Look around for proteins of interest, whether they be from the Protein Data Bank, your research, the textbook, etc., and find a backup or two in case someone chooses your protein before you.

Here are a few links you may find useful:

• RCSB Protein Data Bank
• the beginnings of my Virtual Protein Museum; there are several proteins here whose pages are incomplete. You may use this as a starting point for your own page (though your work should be original)
• Proteopedia

For resources, you may use the Molecule of the Month site from the Protein Data Bank, Proteopedia, primary literature, this link from our Moodle page with highlights from protein crystallography, wikipedia, other web pages, etc., but all of your work must be original. Plagiarism will be dealt with according to Calvin policy; if you are in doubt, please ask. More details, including deadlines, will be coming soon.