Tuesday, May 13, 2014

Friday, May 9, 2014

Final Four

The Final Four is set! Who will be the champion of 2014?

Voting ends at noon on Tuesday.

Final Four:

Wednesday, May 7, 2014

Elite 8

It's time for the regional finals! Which proteins will make the Final Four?

Voting ends at noon on Friday. Contact arnoys_at_calvin_dot_edu if you'd like to participate in the voting.

Linus Pauling Regional:

Dorothy Crowfoot Hodgkin Regional:

Christian Anfinsen Regional:

Max Perutz Regional:

Monday, May 5, 2014

Sweet 16

After a tough first round, many very good proteins have been left behind. Such is the nature of a single knockout tournament.

Here are the matchups for the Sweet 16. Voting ends at noon on Wednesday. Contact arnoys_at_calvin_dot_edu if you'd like to participate in the voting.

Linus Pauling Regional:

Dorothy Crowfoot Hodgkin Regional:

Christian Anfinsen Regional:

Max Perutz Regional:

Friday, May 2, 2014

clickable matchups for the first round

Anand Divakaran, author of the winning Protein of the Year 2013 entry, holds the Jane Richardson Cup. This was the breakthrough year for nitrogenase after it had been eliminated in the Final Four in 2012.

If you are interested in participating in the voting, please submit your request to arnoys_at_calvin_dot_edu.

The bracket is here!

Thursday, May 1, 2014

stories of the bracket

Jane Richardson was trained as a philosopher and a physicist but soon turned to studies of protein structures. She developed a means of representing α-helices and β-sheets in tertiary structures that is now the standard for protein structures, and she has continued her work as a pioneer in protein structure study and representation. She is now a member of the National Academy of Sciences, among other awards. In honor of her beautiful illustrations that have become the standard for understanding structure/function relationships, the prize for Protein of the Year is named “The Jane Richardson Cup.”

suggested links:

Linus Pauling won a Nobel Prize in Chemistry in part for predicting the structures of α-helices and β-sheets in proteins. He won a second Nobel Prize in Peace for his work on nuclear disarmament and the Partial Test Ban Treaty which limited above ground nuclear testing . He was close to a third prize for the structure of DNA, but Watson and Crick beat him to it.

suggested links:

Dorothy Crowfoot Hodgkin was a pioneer in x-ray crystallography, and many of the early protein crystallographers credit her work as a forerunner for theirs. She solved the first structures of vitamin B12 and insulin, among other things, and she won a Nobel Prize in Chemistry for this work in 1964.

suggested links:

Christian Anfinsen won a Nobel Prize for his elegant experiments demonstrating that the information necessary for ribonuclease folding was contained in its amino acid sequence. We know that this holds for other proteins, though sixty years later we still do a poor job of predicting a protein’s structure from its sequence.

suggested links:

Max Perutz is another giant in protein x-ray crystallography, having solved the initial structures of both oxy- and deoxyhemoglobin and proposing the Perutz mechanism by which hemoglobin switches between the R state and T state to bind and release oxygen. Along with John Kendrew, he received the Nobel Prize for his work in studying the structures of globular proteins.

suggested links:

Proteins in Red Shirts

What will the first round look like? A few of our proteins will need opponents from outside of our class.

If you don't know the reference, check out What's in a name.

Wednesday, April 23, 2014

Assignment #5: due Thursday, May 1

Finish your blog. That's it. This assignment is worth the remaining 45 points.

Remember, your classmates will be using your blogs to determine which protein should be Protein of the Year 2014. Students will be asked to evaluate more on your posts than on the protein itself. How informative is your blog? How easy is it to read? How well have you incorporated images and any relevant reactions? How much effort have you put into it?

Once again, points will be fairly generous, but with the following caveats:

  • This is a firm deadline. If your blog is incomplete at this date, there will be deductions. If you do not have proper citations by this date (see below), you will receive a 0.
  • All figures must be properly cited to receive credit. If you made an image with PyMol or jmol, you must tell us the software you used and the PDB code. If you captured an image from the web or from printed material, you must provide a proper citation for it.
  • Cite where you found information as well, whether it be the primary literature, your textbook, wikipedia, etc. This is the reason you summarized journal articles for a previous assignment.
  • The work must be your own.
  • Typos should be cleaned up as best you can, especially if someone has pointed this out in a suggestion.
  • The bracket will be announced on the following day.

Sunday, April 13, 2014

Assignment #4: Dues Tuesday, April 22

This assignment is worth 10 points.

Go to our signup page on Google docs to find the list of blogs. Then evaluate and leave constructive comments on at least the three blogs linked directly beneath yours; if you're at the bottom of the list, loop back around to the front. Feel free to comment on as many additional blogs as you would like. Failure to complete this assignment by the deadline will result in a loss of 10 points.

Remember, though, that this is the place for constructive comments rather than trash talk. Those who follow these directions will receive the full 10 points. Those that don't...really...why wouldn't you want 10 easy points?

Thursday, March 6, 2014

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.

Monday, February 17, 2014

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.

Monday, February 10, 2014

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:
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:

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.