2012 Protein Portraits Show
Our projects are on display in the Honors College Lounge (Strand Agricultural Hall Room 032). We’ll keep most of them up through at least part of Finals Week (until about June 13 or 14). Come take a look and fill-out a ballot to vote for your favorites:
- On Monday, we clocked-in our two remaining student presentations. Coincidentally, each spent time discussing biological clocks, including the rhythm mechanisms that keep butterflies flying and humans humming.
- And on Wednesday, it’s time for the 2012 Protein Portraits Show!
- Last week’s presentations walked us through dynein, stretched our imaginations with EMILIN, clarified our thinking about crystallins, and cast a bright light on luciferase.
- This is a short week. We’ll hear about a couple more proteins on Wednesday and then we’ll wrap up our student presentations next Monday.
- And showtime is coming up next week, on Wednesday! Here’s the official announcement:
Mark your calendars – BB399H Protein Portraits competition
Students enrolled in BB399H will display their Protein Portraits projects Wednesday of Week 10, June 6, from 9:00 a.m. to 5:00 p.m. in SLUG 2 (StAg 032). This year’s theme is “So it’s a protein: What’s fun about that?” Please come see these works of molecular art+science+fun and fill out a ballot to vote for your favorite(s). The winners will be announced right here in our course blog.
- Last week we enjoyed classroom presentations telling us about the fun side of four proteins: 1) the coat proteins of tobacco mosaic virus, 2) AMP-activated protein kinase, 3) the coat proteins of icosahedral viruses, and 4) the reverse transcriptase of human immunodeficiency virus.
- This week we will learn about another four fun-tastic proteins.
- Our illustrious volunteers will lead discussions on the science and fun of their chosen proteins.
- We will make plans for our end-of-term show.
- On Monday, let’s begin our project design reviews by discussing everyone’s progress in choosing one or more specific proteins as their project theme. By “specific”, let’s narrow the choice down to a representative PDBID.
- Let’s also set up a schedule of student talks about each project, leading up to our end-of-year show. Let’s aim to to fill the remainder of our calendar with about two talks each Monday and Wednesday through the end of the term. Any volunteers for this week?
- Thanks everyone for posting your fun and interesting ideas, from clocks to carousels, from tobacco virus roller coaster beads to lightning bug tail lamps. I’m looking forward to discussing all our project ideas this week!
- Let’s plan to review the protein science behind our projects and discuss how this science can be turned into memorable toys that push the envelope to infinity and beyond. Move over Mr. Potato Head! There’s a new brand of bioassemblies in town
- Good news. About a third of our class (maybe half?) has zeroed in on a potential protein project. Others have a tentative idea. This week we’ll firm up those ideas and plans. Hopefully by next Monday everyone will have a preliminary design.
- On Monday and Wednesday let’s also look into the scientific studies behind several proteins of interest. One suggestion I heard at the end of the class last Wednesday was to discuss the bcl2-bax system which normally is involved in cell death and when messed up can trigger tumor cell growth and is therefore a challenging protein system from the point of view of our thematic question of “what is fun about that?” But if anyone can find the fun in bcl2-bax, we can!
The bcl2-bax complex, in all-American colors.
This week we’ll talk more about protein structure. Of course!
- One very helpful subject of discussion will be 2-D topologies of 3-D proteins. A topological diagram can be as useful as a rotatable 3D computer model if you are trying to make sense of how a chain travels through a molecule. Below are examples from Jane Richardson. Note how her topo diagrams readily highlight the differences between superficially similar alpha-beta class proteins:
- We should also talk some more about the multi-domain and oligomeric-structure of big protein molecules. We’ll discover where each of us lands on the scale of inspiration: Will you depict a small protein by showing its details, or will you smudge out the detail and portray a big protein?
- Some of you may want to talk about the mysterious process by which proteins change shape, including the transition from their unfolded state(s) to their native folded structure seen in static PDB models. Given that proteins probably wiggle a lot more than a stationary model suggests, we face a question of artistic design: How much interpretational leeway does an artist have in adjusting the shape of a protein to achieve an inspired pose while staying within reasonable scientific boundaries?
- A related topic is the depiction of moving proteins. We know that many proteins (including cooperative multi-subunit proteins, motor proteins, and proteins involved in energy metabolism) are involved in highly dynamic processes: Wouldn’t it be nice to get that kinetic feeling across in a fun, working model of a protein? Justin may have an opinion on this matter .
- Finally, let’s make sure everyone is up and running as a blog author. We should begin posting ideas about our protein portraits projects.
This week we will continue talking about the chemical structure of proteins. You don’t need to memorize all twenty amino acid side chains, though sometime in the future it will help you to know those details. But to build models you need to understand protein chains. Here’s a quick re-cap of what we looked at with our “jump rope model” of a protein chain:
- Each protein chains is a linear polymer having two distinct ends (N and C). The units (the 20 aa’s) are joined by peptide bonds. The “sequence” of a protein chain is given as the list of amino acids in its chain, from N to C.
- The amino acids can be described according to three generic characteristics — Is the side-chain oil-like? Is it wettable by water? Is it positively or negatively charged? In addition, some of the amino acids play special roles. For example, a cysteine can form a cross-link with another cysteine. Glycine is special because it has such a tiny side-chain. Proline is special because its side-chain is locked into a small ring that restricts flexibility.
- Chains wind around in a 3-D arrangement that is dictated by the character of the amino acids. As the amino acids interact, they enforce this shaping of the chain. We call this process “protein folding”. The final shape that is adopted by the protein is generally very complicated. Protein scientists use all kinds of specialized nomenclature to describe the resulting “protein fold”.
- Protein chains often make abrupt turns called “hairpin turns”. Less abrupt turns are also common. Turns allow a protein to fold back upon itself so that we end up with something with a complicated three-dimensional shape.
- A few types of regular “secondary” structures crop up again and again (alpha helices, beta strands). Various sorts of weak interactions (such as hydrogen bonds) add up to help stabilize such secondary structures.
- Multiple chains can pack together to give “multimeric” proteins. A myoglobin molecule, for example, has but one chain. A single hemoglobin molecule has four. Fibrous proteins (keratin, silk and collagen, for example) are built of many many chains wound together in specialized registries.
On Monday we will start looking at some of the many 3D possibilities that result from the general tendency of proteins to fold into complicated shapes. Here are some of the themes we’ll examine VISUALLY:
- A protein’s “tertiary structure” is the complete, atom-by-atom description of its three-dimensional shape. At first glance, tertiary structures are typically too complicated to absorb, but as you stare and compare, you eventually begin noticing simpler features and elements that help you to understand the protein as a recognizable, unique natural formation. Think about the first time you saw a ring-tailed lemur: Is it a fox? No. A cat? No. Maybe there’s a little bit of raccoon there, in the eyes, or … maybe … a primate? …
- To begin honing our ability to recognize and understand protein shapes we will make heavy use of the PDB, the internationally famous and wonderful Protein Data Bank.
- Our first step into the PDB will be through David Goodsell’s superb Molecule of the Month portal. Check it out.
- Mystery Molecule Quiz: Can you name the protein shown below? It is the March 2012 Molecule of the Month!
Welcome to BB407H Protein Portraits, a colloquium course in the Oregon State University Honors College. I teach this course differently every time because you guys are always different. This time, over the next ten weeks, we will each create an origninal answer to a question inspired by the following dialogue in Big, the movie where Tom Hanks plays a toy-loving kid named Josh:
JOSH (studying the thing while raising his hand) I don’t get it.
PAUL (frowning outside the picture) What exactly don’t you get?
JOSH It turns from a building into a robot, right?
JOSH Well what’s fun about that?
That is our basic question.
When might this question come up?
Imagine you are talking to a friend, a relative, or perhaps someone you’ve recently met. The conversation moves to an important topic: It’s a protein. It’s made out of amino acids. It does important things.
Well what’s fun about that?
We will each find an answer. Ten weeks. You can do it!
Our plan for week 1
We’ll jump into the scientific realm in a big way. Because to make proteins fun, we need to be experts on, yes, the anatomy of proteins. That means we’ll need to come up to speed fast, in week 1, on the chemistry of amino acids and the ways amino acids stick together to give a four-tiered hierarchy of structural possibilities — primary, secondary, tertiary and quaternary structure — that covers the ground from protein molecules that aren’t much more than little squirts floating around in water all the way up to gi-normous proteins as big as a micron in length — a thousand nanometers — stretching from here to there in the most unusual places.
Experts? ”Connoisseurs” might be a better word, though harder to spell.
I know what you’re thinking. You don’t have any idea what you’ve just signed up for, do you? What is this gentleman asking me to do on my Mondays and Wednesdays? So read the syllabus.
Also, as it slowly sinks in, as you begin to realize you are being asked to go back in time to the days when you were just a kid, maybe a good option is to dig out those old toys of yours, the ones that are still in the back of your closet back home. And in the mean time, check out these ticklishly intriguing examples of protein portraits left to us by one of the great toy sketchers, Irving Geis, 1908-1997. Test yourself by asking: What’s fun about that?
(Irving Geiss drawings ©2000 Howard Hughes Medical Institute)