Protein Portraits

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 clip from the dashboard showing you which button to use. Position your screen cursor where you want the picture to be inserted in your post, press the red-circled button, and follow your file system to the location where you stored the image. (I usually get an error if I try using the “Flash loader”. If that happens to you, try the “Browser loader” instead. I have hardly any idea what that means, but as long as it helps me bend the universe to my wishes…). The button that finally posts the image is near the bottom of the loader screen. Play around. It didn’t work smoothly for me the first time, but I finally caught on.

PS  Our blog site is allowed 50 MB of storage space, so please try to keep the images fairly small.

Have fun.

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 Protein Workshop so he sort of has a wink and a smile.  What do you think?

Wikepedia reference

Journal reference

Tubby classification

PS The color of the chain, running from blue toward red, corresponds to the direction of the sequence, from N-terminus toward C-terminus.

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 viral diseases.

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 SW 2nd Street – Corvallis
Phone
(541) 757-0042

The Arts Center
Art Studios / Framing / Galleries

Contact:
Sara Swanberg
700 SW Madison Ave. Corvallis
Phone
(541) 754-1551

New Morning Bakery
Bakeries

Contact:
Ann or Joel
219 SW 2nd Street – Corvallis
Phone
(541) 754-0181

The Book Bin
Books / Magazines / News

Contact:
Bob Baird
215 SW 4th Street – Corvallis
Phone
(541) 752-0040

Old World Deli & Pub
Delicatessen

Contact:
Ted
341 SW 2nd Street – Corvallis
Phone
(541) 758-3527

Old World Deli & Pub
Delicatessen

Contact:
Ted
341 SW 2nd Street – Corvallis
Phone
(541) 758-3527

Benton County Fairgrounds
Fairgrounds

Description:
The Fairgrounds offers year-round events, building rentals for meetings, parties, and animal-related events, as well as RV/Boat storage, horse boarding, and RV and tent camping.

Contact:
Scott Stoller
110 SW 53rd Street – Corvallis
Phone
(541) 766-6521

Edge Design
Graphic Design / Printing / Typesetting

Description:

Edge Design specializes in:

* Web development
* Branding and identity
* Marketing collateral
* Product packaging
* Content development
* Sustainability

Contact:
Ian Russell Johnson
300 SW 2nd Street
Phone
(541) 753-4003

First Alternative Natural Foods Co-op
Groceries

Contact:
Donna Kaiser, Marketing Manager
1007 SE 3rd Street Corvallis
Phone
(541) 753-3115

Stoker’s VitaWorld
Health Services & Fitness

Contact:
Wesley Stoker
215 SW 3rd Street – Corvallis
Phone
(541) 754-8487

Majestic Theatre
Meetings & Banquet Facilities

Contact:
Tim Flowerday, Executive Director
115 SW 2nd Street – Corvallis
Phone
(541) 766-6976

American Dream Pizza & Crowbar
Pizza

Contact:
Mike OBrien
214 SW 2nd St. – Corvallis
Phone
(541) 753-7373

University Hero Sandwiches
Restaurants
211 SW 5th St.
Phone
541.754.7827

+The Vibe Internet Cafe
+The Interzone Cafe
+Odd Fellows Hall

Also, I would STRONGLY recommend looking into getting the artwork displayed at the DaVinci Days festival this summer! 🙂

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 find the presentation at all esoteric…

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 important enzyme from my biology classes.

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 to antibiotics.

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”.

I took a look at Amyloid-beta precursor protein, a membrane protein that functions in neural growth that can become degenerate and cause plaques to form, which leads to neuron death, and can give rise to Alzheimer’s.  I also took a look at myoglobin, the oxygen binding protein that is prevalent in muscle cells.  Both of these proteins have distinctly different shapes, which gives rise to their very different properties.

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 easy for them to put up a new post.  If  you run into that same difficulty, just leave the answer to your weekend assignment as a comment on this post.  OK?  Now go have fun exploring David Goodsell’s Molecules of the Month.

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 post, please post the names of the two proteins you chose to read about on Molecule of the Month.

-I’m going to get that hardware problem licked, or we’ll change to a different room.  My goal:  No presentation glitches for the rest of the term!