updated bracket--Sweet 16

Two match-ups went to overtime, and two others were decided by the slimmest of margins. Here is where we start seeing the tense contests!

Round 2

Linus Pauling Regional:

Hemagglutinin vs. troponin

IgG vs. phosphofructokinase-1

telomerase reverse transcriptase (TERT) vs. calmodulin

triose phosphate isomerase vs. botulinum toxin

Dorothy Crowfoot Hodgkin Regional:

Fibrin vs. dystrophin

luciferase vs. DNA polymerase I

Light-induced protochlorophyllide reductase vs. dicer

Lysozyme vs. glutamine synthetase

Jane Richardson Regional:

Anthrax toxin vs. Divalent ion metal transporter (DMIT)

neuraminidase vs. antifreeze protein

aquaporin vs. HIV-1 protease

Bacteriorhodopsin vs. nitrogenase

Max Perutz Regional:

Albumin vs. Na⁺/K⁺ pump

NO synthase vs. hemoglobin

dipeptidyl peptidase vs. DNA ligase

Mechanosensitive channel of small conductance (MscS) vs. RuBisCO

Background information on the bracket namesakes

Linus Pauling won a Nobel Prize in Chemistry in part for predicting the structures of α-helices and β-sheets. He won a second Nobel Prize in Peace for his work on nuclear disarmament. He was close to a third 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. 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

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

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

Protein of the Year 2011: matchups with links

Linus Pauling Regional:

Hemagglutinin vs. malate synthase

Concanavalin A vs. troponin

COX1&COX2 vs. IgG

β-secretase vs. phosphofructokinase-1

ubiquitin vs. telomerase reverse transcriptase (TERT)

p-glycoprotein vs. calmodulin

triose phosphate isomerase vs. actin

HIV-1 integrase vs. botulinum toxin

Dorothy Crowfoot Hodgkin Regional:

Fibrin vs. bifunctional enzyme

Xanthine oxidoreductase vs. dystrophin

Lactate dehydrogenase vs. luciferase

Cytochrome P450 vs. DNA polymerase I

Light-induced protochlorophyllide reductase vs. insulin

Dicer vs. pepsin

Lysozyme vs. Tol C

Riboflavin synthase vs. glutamine synthetase

Jane Richardson Regional:

Anthrax toxin vs. catalase

Divalent ion metal transporter (DMIT) vs. major histocompatibility complex (MHC)

Histones vs. neuraminidase

β-propeller vs. antifreeze protein

prions vs. aquaporin

HIV-1 protease vs. cytochrome bc1

Bacteriorhodopsin vs. choleratoxin

Cadherin vs. nitrogenase

Max Perutz Regional:

Albumin vs. isocitrate dehydrogenase

Na⁺/K⁺ pump vs. thrombin

Inteins vs. NO synthase

Hemoglobin vs. methylmalonyl CoA mutase

Alcohol dehydrogenase vs. dipeptidyl peptidase

Leghemoglobin vs. DNA ligase

Mechanosensitive channel of small conductance (MscS) vs. kinesin

DNA helicase vs. RuBisCO

Links to your classmates' blogs

324a

Links on Life: Pictures of Dicer

Tyler Veldkamp

Emily Diekema_Mechanosensitive Channel of Small Conductance (MscS)

Chelsey Knapper_Awesome Possum Protein

Jared Scripture

Lauren Bylsma_Lauren's Protein of the Year!

Evan Sonderman_Botulinum Toxin

Anna Kim_Tryptophanyl-tRNA Synthetase

Alyson de Walle_choleratoxin

Ian Robertson_A Protein for All Seasons

Katie Faber_All About IgG

Paul Meppelink_Thrombin

Keith Van Dusen_HIV-1 Protease

Frank Carr_My Biochem 324 Protein

324b

Alex Cortez_The Bifunctional Enzyme

Eric Prins_Riboflavin Synthase

Melanie Holtrop_Phosphofructokinase-1

Alex Batt_Troponin: Protein of the Year

Amanda Erwood_Protein of the Year

Betsy Hansen_Albumin

Adam Driscoll_Protein of the Year (2011)

Jacob Artz_Dipeptidyl Peptidase

Gill Morris_Nitrogenase

Alex Wrobel_Protein of the Year--Beta-3 Alcohol Dehydrogenase

Lauren Manck_Bacteriorhodopsin

Josh Stuive_Divalent Metal Ion Transporter

Stacey De Haan_Triose Phosphate Isomerase

Jake Baker_HIV-1 Integrase: Biochem 324 Protein of the Year

Samantha Vue_Beautiful World

Dan Tiesman_Hemoglobin, Protein of the year

Brandon Burkhart_Protein BioLog

Alex Verseput_Aquaporin

Lindsay Rios_DNA Polymerase I

Milton Herrold_Malate Synthase

Allison Sterling_Major Histocompatibility Complex

Chris Bouma_Protein Assignment

Cheri Ackerman_RuBisCo

Dan Oram_Glutamine Synthetase

Christie Timmer

Adam den Boer_Fibrin

Amanda Harris_DNA Ligase

Steve Griffith_biochem: Pics of Lysozyme

Assignment #3: Due Wednesday, April 27

What makes your protein the best? Convince us.

Submit a post to sell your classmates of the beauty of your protein. 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.

Assignment #2: Due Friday, March 18

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 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 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 is another great source 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 here when you have finished.