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:

http://kinemage.biochem.duke.edu/lab/richardson/richardson.php

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:

http://pauling.library.oregonstate.edu/

http://nobelprize.org/nobel_prizes/chemistry/laureates/1954/

http://nobelprize.org/nobel_prizes/peace/laureates/1962/

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:

http://nobelprize.org/nobel_prizes/chemistry/laureates/1964/hodgkin-bio.html

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:

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1972/anfinsen-bio.html

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:

http://nobelprize.org/nobel_prizes/chemistry/laureates/1962/perutz.html

Proteins in Red Shirts

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

I give you Proteins in Red Shirts.

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

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.

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?

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.