Protein Portraits

Here is the link to the video I showed in class:

http://www.youtube.com/watch?v=PjdPTY1wHdQ

Dynein is a motor protein complex involving many different proteins. Some PDB IDs for different sections of dynein are as follows:
LC8/IC/TCTEX complex: 3FM7
IC/LC7 complex: 3L7H
Heavy Chain(Legs): 3VKG

While I was working on my project this weekend, I came up with a new idea! Instead of myosin and actin I am now looking at EMILIN-1. This protein is responsible for the formation of elastic fiber. This gave me the idea to create a toy similar to silly putty, flubber! I used to love to play with this stuff when I was a kid.  The protein structure is pretty cool too!

I’ve narrowed my protein choice down to 1JNV. It’s an ATP Synthase protein from E. Coli.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1JNV

In the CATH classification system, the “Mainly Beta” parent node (at the C level) has a child node known as “Sandwich” (at the A level) whose representative domain structures include over 18,000 known structures.  That’s a lot of sandwiches.

Looking through the numerous topological children nodes of Sandwich (at the T level), I notice three representative sandwich topologies that seem especially ripe for being turned into toys by applying a little bit of evolutionarily-inspired tinkering.  These are the Neurophysin II Chain A topology (CATH code 2.60.9) , the ATP synthase epsilon chain domain 1 topology(phew, that’s a mouthful! easier to say CATH code 2.60.15), and the Gamma-B crystalline domain 1 topology (CATH code 2.60.20).

What’s fun about these three domain topologies?  Let’s tinker…

Why it is good to tinker (according to Francois Jacob)

In 1977, Francois Jacob, fresh from his pioneering studies of gene transcription with Jacques Monod, delivered a stimulating lecture on the topic of Molecular and Evolutionary Tinkering at UC Berkeley (later published in Science magazine). Jacob pointed out how important it is in any type of design effort to begin with a picture of how a thing works since if you want to understand or improve the thing the most common route to success is to tinker with the existing picture.

We should listen to Jacob.  As we build our protein projects, let’s unleash our instincts to tinker

More quotes from Jacob’s 1977 lecture

• “To produce a valuable observation, one has first to have an idea of what to observe, a preconception of what is possible.  Scientific advances often come from uncovering a hithertounseen aspect of things as a result, not so much of using some new instrument, but rather of looking at objects from a different angle.”  (p. 1161, my italics)
• “[Tinkering] has several aspects in common with the process of evolution. Often, without any well-defined long-term project, the tinkerer gives his materials unexpected functions to produce a new object. From an old bicycle wheel, he makes a roulette; from a broken chair the cabinet of a radio. Similarly evolution makes a wing from a leg or a part of an ear from a piece of jaw. Naturally, this takes a long time. Evolution behaves like a tinkerer who, during eons upon eons, would slowly modify his work, unceasingly retouching it, cutting here, lengthening there, seizing the opportunities to adapt it progressively to its new use.” (p. 1164)
• “It is at the molecular level that the tinkering aspect of natural selection is perhaps most apparent. What characterizes the living world is both its diversity and its underlying unity. The living world contains bacteria and whales, viruses and elephants, organisms living at -20C in polar areas and others at 70C in hot springs. All these objects, however, exhibit a remarkable unity of chemical structures and functions. Similar polymers, nucleic acids or proteins, always made of the same basic elements, the four bases and the 20 amino acids, play similar roles. … New functions developed as new proteins appeared. But these were merely variations on previous themes. … The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information. The appearance of new molecular structures during much of biological evolution must, therefore, have rested on alteration of preexisting ones.” (p. 1164)

I was thinking of building a protein/proteins by folding paper into shapes like these

http://www.rcsb.org/pdb/explore/explore.do?structureId=3S4G

http://www.rcsb.org/pdb/explore/explore.do?structureId=4AED

This origami structure is made up of flowers glued together. The virus looks like it has flowers embedded too!

I am going to make a series of 5 or so T-shirts with chemistry-cat style puns on them using common proteins that people who don’t know a ton about science will (hopefully) still get. I’ll include a simple line drawing of the structure on the shirt as well.

I love doing jigsaw puzzles so I decided that I would create a protein jigsaw puzzle. 

 I loved DIY projects when I was a kid. In particular, there were these books which showed you how to make little critters from pipe cleaners, beads, etc. My idea is to make a similar book, but with instructions of how to make a protein out of pipe cleaners.

Similar to this, but with a protien theme

I was excited to find the protein luciferase, which produces light and is found in fireflies.  The colors can change depending on the amino acid attached to the protein.  This fits well with my idea for lights and colors.

I finally have an idea! So one of the proteins I’ve been looking at on the Molecule of the Month site is the tobacco mosaic virus. It was the first virus to be discovered, and it is the cause of disease in tobacco plants. I think it has a really interesting structure. It is composed of a helical RNA strand which encodes 4 proteins. I was thinking of making one of those bead maze toys that you see in doctors’ offices. I could make it out of wire which would be the RNA strand and the beads could be proteins. 

Since I was thinking about creating an active/outdoor toy, I thought it would be cool to choose a protein that is related to exercise and physical activity.  Myosin and actin, and their role in muscle contraction, came to mind. If you go to the link below and play around with the 3D structure, it kind of looks like a person kicking a soccer ball!  http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=1m8q

BMAL2 is a circadian clock protein found in humans, dimerizing with CLOCK. It helps modulate many hormonal feedback mechanisms, and is an essential part of functional sleep/wake cycles and endogenous rhythms. I think it would be fun to either make a floating pool toy or some sort of pop-up educational book. 

I think it would be cool to model ATP synthase as a carousel toy like this one. If you twist the top “motor” it causes the bottom “motor” to spin and produce ATP.

Dynein is a motor protein that can walk across microtubules, transporting cargo across the cell. My portrait idea is to create a puppet of dynein that can walk.

So I found a really interesting group of proteins on the molecule of the month website, called the circadian clock proteins.  These proteins create our 24-hour internal cycle that involves when we get hungry, tired, etc. Thanks to the circadian clock proteins, our internal clock knows when the days get shorter and longer, when the seasons change and what time of day it is. One of these depictions even looks kind of like a clock.  I think these would lend themselves well to a protein toy as well!

Hi everyone,

Below is the link for the “Juego de la Liga”. You can just watch the first 2 min of the video

This was my favorite childhood toy… Barbie’s very own, luxurious camper van! Shockingly, all the furniture, sleeping bags, extra outfits etc. fit into it when folded. I think making a protein-themed toy with some of the same features would be really cool.

Growing up, my favorite toys were any I could bring in the pool and bathtub, especially the floating islands!

My favorite toy was lite-brite!

My favorite toy growing up was Silly Putty.

My favorite toy was my stuffed dog, Lucky.

Like Madison, my favorite toys were my beanie babies!

When I was little, I loved the original Polly Pockets.

My favorite toys when I was little were my Barbie dolls.

When I was little my favorite toys were stuffed animals. I collected Beanie Babies.

Some of the architectures new to CATH since 1997:

From: Nucleic Acids Res. 2009 January; 37(Database issue): D310–D314.

“CATH (class, architecture, topology, homology) is a hierarchical protein domain classification (1) where domains are classified manually by curators, guided by prediction algorithms (such as structure comparison). Each protein structure is decomposed into one or more chains which in turn are split into one or more domains before being classified into homologous superfamilies according to both structure and function. At the Class, or C-level, the domains are classified simply on the basis of their secondary structure content [whether they are mostly α-helical (Class 1) or β-sheet (Class 2), contain a significant percentage of both secondary structure elements (Class 3) or contain very little secondary structure (Class 4)]. The domains within each class are then sorted according to their architecture—that is similarities in the arrangements of secondary structures in 3D space. Each architecture (A-level) is further broken down into one or more topology, or fold, groups (T-level), where the connectivity between these secondary structures are taken into account. The domains are then classified into their respective homologous superfamilies (H-level) according to similarities in sequence, structure and/or function. Clustering performed at the H-level (>35% sequence identity and above) then produces one or more sequence families for each of the homologous superfamilies (S-level).”

I enjoyed playing with play-doh as a child.

As a child I used to enjoy playing with legos.

This set of the twenty amino acid side-chains doesn’t have the names listed.  You can quiz yourself to help you learn the names and predict the chemical properties of these different structures.  Example:  Which are the hydrophilic side-chains?  Which of these might tend to mover away from water and gather together in the same way that oil droplets coalesce into larger oil drops?

I love everyone’s projects they are all sooo beautiful! I had a lot of fun in this class and just wanted to say thank you all for making it so much fun. :] Congrats to the seniors who are graduating! Also, if you guys aren’t doing anything on Friday at 4, it’s my accapella group’s last show. It’ll be either outside the bookstore if it’s sunny, or inside the MU on the main steps if it’s rainy. I’d love to see you guys there (you can hang out with Casey!) There’s also a chamber choir concert on Friday, but let’s get real, that’s no fun.

Thanks for everything guys,

:] E

Finally finished.

Hi Connie, when are you going to set up tomorrow so I know when to bring the easel?  I have a meeting at 9.  But 10 and after I should be good to go.

Sorry, I totally forgot about making this blurb until today.

Author: Elvis Nguyen
Blurb:
Where would we be without ribosomes? Ribosomes are biological structures in the cells consisting of 2 subunits and made up of lots of RNA and dozens of proteins. It reads incoming mRNA transcriptions and translates them into beautiful polypeptide chains. No other proteins would be possible without the “Mother of all Proteins.”

Protein: Integrase
Protein Data Bank ID #: 1K6Y.
Artist: Erica Puopolo

The HIV/AIDS pandemic has had a large impact on our world in the past thirty years, it is estimated that there are upwards of 35 million people living with HIV/AIDS and over 25 million have died AIDS related deaths. When the virus enters the body it attaches to the CD4 receptor of the helper T-cell. In my model, the globe is represents a T-cell that has already been infected by the virus, it is covered in pictures of people, showing that HIV has left no gender, age, or ethnicity untouched. This was also meant to put faces to the pandemic, when a disease is as widespread as HIV/AIDS it becomes easy to see it’s inflicted as mere statistics, but I think it is important to remember that every person infected is a mother, a father, a sister, a brother, a daughter, a son, or a friend to someone.  The syringe represents the CD4 receptor which HIV has used to enter the cell, the syringe is also symbolic of the large role that IV drug has played in the spread of the virus. Red and black viral DNA is being combined with the blue and yellow host DNA by integrase, which seals the fate of the cell. It is now a viral DNA lead workshop, and will begin replicating and releasing more viruses that will degrade the very immune system that is trying to fight against it.