Protein Portraits

Hey P-Squared Pals! I have no idea what protein I want to do yet, but I can’t stop thinking about all the crazy sorts of materials we can come up to use for our models: yarn or wire or leaves or plastics or candy or umm banana peels? Haha, so many options!

Hi everyone, I have finally signed everyone up as an author.  You should each now try to author a new post.  Log in with the username and password you received by email.  Change your profile if you want  to give yourself a nickname to serve as your public display name. Then write a sentence or two and publish to the blog.  It is possible that the first time you post and/or leave a comment, I will be coaxed to give approval (a spam prevention measure), but after that you will be able to post and comment to your heart’s content.

In case I’ve confused you, here are the manual’s directions for writing a post:

To write a post:

1. Log in to your WordPress Administration Panel (Dashboard).
2. Click the Posts tab.
3. Click the Add New Sub Tab
4. Start filling in the blanks.
5. As needed, select a category, add tags, and make other selections from the sections below the post. Each of these sections is explained below.
6. When you are ready, click Publish.

I had no idea what to put for the title or what to even post. First thing that popped into my mind. Yay!

Minhazur

P.S. All of you are beautiful, don’t let anyone tell you otherwise 😛

And I’m watching Royal Pains. Good show, by the way.

Most biology and biochemistry textbooks have a table showing the twenty amino acids found in proteins.  Here’s a figure you can use to quiz your knowledge:

On Monday we’ll meet each other, share a few stories, and fill in some details in our course syllabus.

I have set up your exhibits in the library of the Biochemistry and Biophysics Department (second floor Ag Life Sci Bldg). Come by and take a look if you have a chance.

You can pick up your protein anytime.  Those that are left with me will come in handy next year.

Have a nice summer.

Phil M.

Thank you BB399H students for sharing your creations.  You have proven beyond any doubt that there is more than one way to look at a protein molecule!  Thanks also go to all those who attended the show, including Kevin and Indira, our illustrious judges.

I will post photos of the show in the near future (thank you Gilda for your camera work).

Good luck next week with your final exams.

Best regards,

Phil McFadden

Hey Guys!

The tables are now set up for our show in SLUG 2. There are three tables on the right hand side of the room as soon as you walk in. Feel free to put up your protein whenever. I also put up a couple fliers – but still tell all your friends to come! See you all at 11am tomorrow!

Professional Judging Guidelines:
1. Scientific Insight
2. Artistic Merit

“Between Ourselves” Judging Categories:
1. Most creative materials
2. Most effort and/or most complex
3. Most desperate-looking molecule

… see you at the UHC Thesis Fair!

A celebration of undergraduate research at OSU.

When: Wednesday, May 20, 11:30 a.m.-1:30 p.m.

Where: Gallery and Rotunda of the Valley Library

Protein Portraits will return to its regular schedule next week!

I’m making a last minute change to my protein, by moving from the blue variant to the green fluorescent protein.  It’s not much of a change because I can’t tell the two apart with the naked eye.  Anyway, the protein is rendered at 1.9 angstrom resolution, has 264 amino acids, and has an 11 stranded beta barrel with a coaxial helix, which is where the light forming reaction takes place.

As far as design goes I plan on using aluminum cans and wire and I think I will use a box as a stand and for support when building.  I also plan on maybe lighting it up but I haven’t got any good ideas yet.

So basically, ferritin is composed of mostly alpha helices (4 lonand 1 short) with beta strands connecting them. Like we talked about the other day, some of the beta strands wrap around (because the helices go in the same direction twice) and are therefore longer than other beta strands. From what I can tell, ferritin is classified in the “Up-Down Bundle” domain.

Since this protein functions to bind calcium and iron, I want to represent that creatively in the structure that I build. This is why I am interested in doing a little metal working when I go home next weekend. My basic plan is to build the alpha helices on a scale of approximately 1 angstrum = 3 inches. This should give me a dramatic molecule slightly over 2 feet in length. For the iron and calcium ions, I’m thinking of attatching different colored lightbulbs and a battery to make a circut with the metal in the molecule that causes the bulbs to light up.

I also would like to show the ferritin protein in its functional structure (24 subunits put together) but don’t think I’m capable of such complicated metal work. So for this, I might just draw a sketch of the whole molecule or use a metal that can be easily bent.

The p53 protein (cellular tumor antigen) is an alpha-beta protein. It is composed of 4 alpha helices and 4 beta pleated sheets. I plan on using the following materials for the construction of my protein: faux flowers (plastic flowers), pipe cleaners, rocks, and these foam sheets that I am going to cut into beta pleated sheets. I found all of these supplies at the Dollar Store!

Zif268, also known as Egr1(Early Growth Response Protein 1) is a transcription factor. It can be found in the nucleus of the cell where it regulates transcription of genes required for cell differentiation and mitogenesis. Zif268 is composed of 543 amino acids with a molecular weight of 57.5 kDa. Its structure consists of three zinc fingers.

I plan to sculpt hands out of clay as the base/stand to hold the protein. And then I will replace some of the fingers of the hands with the ‘zinc finger’ structures with a stretch of DNA running through the center of the structure. I plan to make the protein and DNA out of wire. Does anyone have any suggestions on sturdy wire that is easy to bend?

So the “class” for my protein is mainly alpha (this is all according to the PDB). The architecture type is considered up-down bundles.  Additionally, I believe at one time I mentioned that I had gone to a craft store and found these fake twigs in the floral section that are bendable. I made some alpha helices from it and it worked really well! So I’m planning on going with that- for now at least.

Here are the three places we’ve talked about in class.  Please post a comment if you know of any others…

Creative Crafts & Frame Shop
934 NW Kings Boulevard
Corvallis, Oregon 97330
541.753.7316

 
Michael’s
1550 NW 9th St, Ste 106
Corvallis OR 97330-451
(541) 738-0109

Trump’s Hobbies
Timberhill Shopping Center
2401 NW Kings Blvd.
Corvallis, Oregon 97330
541-753-7540

I changed my protein. This is an important compound in vipoxin, which is the lethal neurotoxin found in the venomous viper species. This part of the venom is the toxic phospholipase inhibitor.

This is the interferon gamma protein. It plays a large role in the immune system because infected/stressed cells send it out as a cytokine “help me” signal. Last summer I measured the levels of this protein in mice with multiple sclerosis. This will most likely be the protein I choose for the art project.

This receptor is one of the most important in muscle movement. It is found on all postganglionic neurons and on muscles at neuromuscular junctions. It is also the main receptor found in the parasympathetic nervous system. It is a very elegant protein that has many alpha helices at the bottom, which resemble cigarettes.

Today let’s talk about the folding and unfolding of proteins.  We’ll get some insight into the flexibility of proteins, and along the way let’s rate (thumbs up/ thumbs down) some recent attempts at depicting protein flexibility.

GCSF folding

IL-1 receptor

HIV protease

villin

Inner life of the cell

This protein is a transcription factor commonly found in eukaryotic cells. The thing that caught my attention with this structure was the three subunits that have configurations known as “zinc fingers”. I plan to use this for my final product and I think it will turn out really well.

This is the molecule that I have chosen to represent for my final project. This is a ferritin molecule that is important in oxygen binding in hemoglobin. The molecule is made up of 24 identical protein subunits (pictured above).

This is a picture of the metal binding domain of the Amyloid Precursor protein.  This is one part of the amyloid protein and I’m still trying to find an aggregate picture of many of these proteins bound together to show their plaque-causing ability that is associated with Alzheimer’s disease.

To Do List:
-Protect DNA from damage
-Make proteins to halt DNA replication to repair the damage
-Or, if damage is too severe, recommend that the cell commit suicide
Such is the life of the p53 tumor suppressor

I chose this orientation because it shows the perfect symmetry of the p53 protein.

The Aqequora Victoria jellyfish glows green using a protein called the green flourescent protien (GFP) and the photo above is a blue variant of GFP.  Calcium ions in the Aqeuora bind to the protein, releasing the blue light.

Does anyone else see a pair of ballroom dancers in this one? You can almost see the love that ‘binds’ them… 🙂

This is one of the most common enzymes found in the cytochrome P450 mixed-function oxidase system, called CYP3A4. The P450 family of proteins is responsible for the metabolism of various compounds within the body such as drugs.  CYP3A4 is a really good model enzyme for this system because it is abundant in the liver where almost all detoxification occurs, however it is also found in the brain and other organs as well. This picture clearly shows the complex form of this protein and also gives a good view of the heme prosthetic group in the middle. This enzyme is the foundation for why toxic compounds do not build up in the body when pharmaceuticals are introduced.

Here it is finally, my protein, insulin. I like the view because it looks like two faces (one upside down) and shows all the different structures in insulin very well.

Here is another view:

My current protein of interest:

“Neurotrophins

August 2005 Molecule of the Month
by David S. Goodsell
Previous Features

Your brain is composed of 85 billion interconnected neurons. Individually, each neuron receives signals from its many neighbors, and based on these signals, decides whether to dispatch its own signal to other nerve cells. Together, the combined action of all of these neurons allows us to sense the surrounding world, think about what we see, and make appropriate actions.

Remarkably, this complicated structure is formed in nine short months as an embryo grows into a baby. Nerve cells start as typical, compact cells, but then they send out long axons and dendrites, connecting to other cells in the brain or even to entirely different parts of the body. Neurons in the growing brain test the connections with their neighbors, looking for the proper wiring. Half of the neurons are discarded during this process, in areas that get too crowded. The half that remain become the nervous system. Throughout the rest of life, these neurons typically do not reproduce, although they do send out more dendrites to neighboring cells as the nervous system grows or repairs damaged areas.”

Aminoacyl-tRNA Synthetases

I liked how this protein seemed symmetrical over the diagonal line that can be seen in the middle of the molecule. The diagonal space draws the attention to the center, just like the bright ions did in the membrane protein pictures.

PS – Disregard my last post. I just saved the file in a different format. I’m not sure why JPG didn’t work for me. But this one seems to work fine.

Hey Guys,

I’m having trouble uploading my molecule picture. When I try to upload it to the blog, I get a message about my image not being supported by blog security. Can anyone help me out?

Thanks!

This is the ranasmurfin protein.  It has an unusual name and it’s function is unknown.  I chose to just render the backbone because I liked how it eliminated enough clutter to emphasize the symmetry of the protein.  It’s a blue protein found from the foam nests of a tropical frog.  (The fact that it’s blue may be part of the “smurf” root in the name but I’m not sure)

This is a view of the 20S proteasome, a multienzymatic protein comples used to degrade damaged proteins. I liked this view because it is looking directly through the center of the barrel-shape of the protein.

I really like the symmetry of this protein. I also like how it kind of looks like a clock from this orientation. I’m very interested in trying to find a protein in which the function can be easily seen or interpreted in the structure.

Amyloid Beta Precursor Protein

I chose this orientation because it shows the protein’s one distinct alpha helix, and it also captures one of the protein’s characteristics- length.

This one looks very interesting if you move it around, each end has an interesting looking barrel leading to the center.  I chose this view because it reminded me of how viruses and bacteria are often represented in science video animations. (i.e. it has a box like “head” and multiple “legs” (actually alpha helix chains) that surround the lower center).