Protein Portraits

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.

These are two views of the different ends of the mechanosensitive channel that I posted last week

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 [...]

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 [...]

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 [...]

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 [...]

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.

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).

I chose this orientation because it shows the simplicity of the prion, which is somewhat misleading to its crucial function.

This is my artistic 3D rendition of the calcium pump (a membrane protein). I chose this orientation because I loved the way it enhances the beauty of the bottom alpha helices!

This weekend you should: Choose a protein Render its image in 3D using the tools in the protein data bank Orient the protein with as much artistic flair as you can muster, and Post the image as a jpg picture. That last step might be a little tricky the first time.  Below is a a [...]

Hi all, I wanted to practice posting the image of a protein, so I looked for a protein with a name that might suggest a sense of humor.  I found Tubby… a very important protein involved in the development of the nervous system.  They have named a whole topology after “him”.  I oriented him using [...]

I researched the Dengue Virus (tropical virus), which changes shapes when in acid, and Alpha – Amylase, which begins the process of starch digestions.

Hi guys! I’m having trouble finding how to view the protein rotationally (as phil did in class). Can anyone clue me in on how to do this through the molecule of the month website? Thanks and see ya in class tmw!

The proteins I looked at were caspases and collagen. I chose collagen because it is the most abundant protein in our body and its properties allow us to maintain structure in our bodies. I chose caspase because it plays a very important role in apoptosis, which needed to stop the development of some cancers and [...]

Here’s a brief list of venues in town I think might be interested in hosting out Protein Portrait art exhibit… Art in the Valley Art Studios / Framing / Galleries 209 SW 2nd St. Corvallis Phone (541) 752-0811 Pegasus Frame Studio & Gallery Art Studios / Framing / Galleries Contact: Bill or Paige Shumway 341 [...]

I chose to examine Acetylcholinesterase and Green Fluorescent Protein (GFP, and my, my, how varied are their purposes… from regulating brain function to making animals glow in new and exciting colors. I like the set up of the site very much. There’s a lot to look at and a lot to learn, but I don’t [...]

Every rendering is a depiction, but not every depiction is a rendering

I read about fatty acid synthase, which makes  fatty acids for the body, and the tobacco mosaic virus, which causes the death of the tobacco plant and is cylindrical.

For my molecule of the month research I looked at the catabolite activator protein and DNA ligase. I chose the catabolite activator protein because I thought it was really pretty. I liked the symmetry that it had and the variation between textures in the molecule. I chose DNA ligase because it was a familiar and [...]

I looked at carbonic anhydrases (soluble) and multidrug resistance transporters (membrane) – very cool! We studied alot about carbonic anhydrases in bb45X series mainly because of how fast/efficient its enzymatic activity is at making carbonic acid. MDR transporters are found in bacteria and as you can probably tell by their name, they pose a problem [...]

The two proteins I looked at were insulin which basically tells organs to take glucose out of blood and store it after having a meal when sugar levels are higher in the body and Alcohol Dehydrogenase which converts a potentially dangerous molecule – alcohol – to “mere foodstuff”.

Molecule of the Month

I took a look at fibrin, which is necessary for blood clotting. I also looked at ATP synthase. I was excited to see it looked like the simplified version in my biology book! Very neat.

As stated in the syllabus, the main question of our course is What does a protein look like?  And guess what?  That question has received an answer!  What do you think? One technical note for the weekend:  I’m still working out some of the bugs on this blog.  Even though I have granted some of your classmates author privileges, it hasn’t been [...]

I read about T-cell Receptors and Prions. We encountered both in BI 212, so I figured I’d check them out again. Pretty cool!

Our Wednesday action items were: -Everyone should come up with a good nickname. -Email me your official university email address.  I’ll sign you up for the blog.  You’ll receive an email invitation to join blogs.oregonstate.edu/psquared.  After you sign your life away, go to your user profile and give yourself your nickname.  Then for your first [...]