Protein Portraits






         The aesthetic alchemy of life

Archive for Student posts

May 9, 2017

OMSI Exhibit — Must see!

Filed under: 2017 posts,Student posts @ 10:48 am

Raha is just back from visiting the Art of Brick exhibition at OMSI (in Portland).  Check it out!

May 4, 2017

Standalone 3D viewers for proteins

Filed under: 2017 posts,Student posts @ 10:18 am

The widely used pymol is available here. Highly recommended for adjusting your view as you work on your protein portraits projects.

Modeling Hemagglutinin

Filed under: 2017 posts,Student posts @ 9:30 am

The Protein: Hemagglutinin (HA), a protein involved in the viral infection process. Specifically, HA helps cells internalize the virus and eventually the viral RNA.

Structure: Hemagglutinin is a trimeric transmembrane protein that extends from the surface of viruses. There are two types of chains in the enzyme, which we can call HA I and HA II. HA I (shown in blue) sits on the top of the protein while HA II (shown in yellow) is partially covered by HA I at first. There are also various carbohydrates on the Hemagglutinin surface. The viral strain (H1,H2, etc) can change if the location of the carbohydrate chains on the HA surface changes.

Hemagglutinin extending from virus surface

You can view the various hemagglutinin structures on PYMOL using the following PDB IDs:

  • 1RD8 – uncleaved hemagglutinin from the 1918 influenza virus
  • 1RUZ – the active form of hemagglutinin from the 1918 influenza virus

Mechanism of Action: 

Video 1 shows the whole influenza virus infection process

Video 2 (skip to minute 4) shows the membrane fusion process

The blue portion of the protein targets sialic acids, which are part of some glycoproteins found on the cell membrane. Once the virus is docked on the cell membrane surface the cell internalizes the entire virus via endocytosis and begins releasing acids meant to digest the endosomal contents. However, the acids actually help activate conformational changes in Hemagglutinin, which allow the red portion of the protein to attach to the endosomal membrane. The yellow portion of the protein then moves up the the protein and brings the viral and endosomal membranes together. The viral RNA can enter the cell after the two membranes fuse together.

Hemagglutinin conformational changes

Modeling Ideas:

Some combination of these

1.Different colored flowers made of tissue to represent the different parts of the protein joined together by pipe cleaners or wire or something similar since the protein looks like a flower bouquet from certain angles. And tissues are the only cold/flu related material I can think of.

2. Tissue flowers for the HA I portion and then spiral bracelets to represent the alpha helices on the inside. Show conformational changes by moving the different pieces. Use a safety pin/bobby pin structure to pull two “membranes” (pieces of cloth?) together to represent the fusion of the viral and cell membranes.

3. Play-doh model of the three different stages?

Tissue carnations

Spiral bracelet

May 3, 2017

Copper: Wilson’s Disease Protein or Hemocyanin

Filed under: Student posts @ 1:38 pm

Image result for wilson's disease protein modelWilson’s disease is a rare disorder in which too much copper accumulates in your liver, brain or organs in general. The liver is not able to filter out copper properly. I would focus Wilson copper ATPase, also known as the Wilson’s Disease Protein. My medium would be copper wire, and I am thinking of making either a human figure or using wire on a canvas.

Hemocyanin2.jpgPDB 1hcy EBI.jpg

I am leaning towards this one slightly. Hemocyanin is a protein that transports oxygen throughout the bodies of some invertebrate animals. These metalloproteins contain two copper atoms that reversibly bind a single oxygen molecule (O2). If I chose the molecule Hemocyanin, I could also use copper wire and contrast a metal model of a snail.

May 2, 2017

Let’s visit the Linus Pauling Collection

Filed under: Student posts @ 10:22 am

Chris Petersen will host a tour of the collection on Tuesday of Week 8 (May 23) at 10 am.  We’ll meet at the library 5th floor (Special Collections).

Read about Pauling’s discovery of the alpha helix here.

 

April 18, 2017

KlpA Kinesin can walk backwards!

Filed under: 2017 posts,Student posts @ 11:23 am

This was news a few months ago but the Weihong Qiu lab in the Physics/Biophysics lab observed and reported that kinesin can walk backwards. It was previously thought that kinesin could only walk forward, in fact the Hoogenraad Lab video on kinesin even mentioned that it could only walk forward.

 

Here is the post on the Physics webpage; A biological motor that switches gears from forward to reverse

 

Also here is a funny animation for myosin on a single strand of actin by Erin Craig (CWU).

 

 

 

Erythrocruorin

Filed under: 2017 posts,Student posts @ 9:56 am

Let me introduce Erythrocruorin, giant hemoglobin made from earthworms. This hemoglobin is HUGE, it is comprised of 144 globin chains and its skeleton is comprised of 12 globin chains. Each of these chains can carry oxygen and with its 3-fold symmetry, the real reason I noticed it, it kinda acts like a rock tumbler or a rattler. The oxygen rattle around bonding randomly in its skeleton structure but never being allowed to escape. Maybe this is more like one of those cat/dog toys containing a treat. Tell me what you think!

 

April 16, 2017

Tobacco Mosaic Virus

Filed under: 2017 posts,Student posts @ 7:04 pm

TMV is the first virus to be discovered and is found to be mostly made of protein. It is supposed to be very stable and can survive for years within a cigar or cigarette.

TMV’s helical shape kind of reminds me of tubulin and how it forms dimers to make microtubules. Though they do not form in quite the same way, they both have the ability to rapidly assemble and disassemble which reminded me of this origami paper tower below. It’s a dynamic structure that can be squished or stretched out (a decent representation of the rapid assembly/disassembly).

 

April 13, 2017

Actinomycin

Filed under: 2017 posts,Student posts @ 10:08 am

Actinomycin, discovered in Streptomyces antibioticus in 1940, is the first natural antibiotic that has anti-cancer activity. Unfortunately, actinomycin does not specifically kill cancer cells, so it too toxic for general use. This molecule works by intercalating into the DNA double helix and interfering with topoisomerase activity. Topoisomerases, which untangle and reduce tension of DNA strands in cells, break down DNA before making topological changes and reassembling the DNA. Actinomycin and other intercalating drugs prevent topoisomerases from reassembling the DNA after it has been broken down. Actinomycin (shown as the green/blue structure in the figure below) is composed of two parts:

  1. a flat ring (shown in green) that resembles DNA bases, and
  2. two cyclic peptides composed of unusual amino acids (shown in blue)

 

Actinomycin intercalates between the bases in a DNA helix

To represent actinomycin artistically, we can use a half unraveled bracelet  to represent DNA with a knot or bead to represent actinomycin and the effect it has on DNA. We could also used a half tangled slinky to represent DNA with something jammed in between the layers to represent actinomycin.

                                                           

April 12, 2017

Proteasome

Filed under: 2017 posts,Student posts @ 9:46 pm

Proteasomes break down other proteins. They help keep the cell free of damaged proteins as well as allowing the cell to  recycle parts of proteins that it no longer uses. In this image, the yellow and red core is where the proteins are broken down. The blue ends recognize ubiquitin tagged proteins and starts pulling them in, while the pink part unfolds them and passes them in to the core.

This protein reminded me of a pencil sharpener, especially the twisted core in the middle. The core reminded me of the center of a classroom pencil sharpener, and the outer parts of the protein are kind of similar to the holes in a pencil sharpener that only let the right size of pencil through. If you attached two pencil sharpeners back to back and put on a casing that looked more like the protein shape, you could have a fairly accurate representation of a proteasome that would also be able to sharpen two pencils at the same time.

Image result for pencil sharpener inside

P-Glycoprotein

Filed under: 2017 posts,Student posts @ 8:55 pm

This is the P-Glycoprotein found in many cells of the human body. It’s role is to search for toxic molecules and eject them from the cell to be disposed. Using ATP, the P-Glycoprotein targets mostly hydrophobic toxic molecules in its deep opening and then changes shape to allow the molecule to escape outside of the membrane. The protein can target hundreds of toxic molecules from as small as 10 atoms to as large as hundreds of atoms.

In order to artistically portray this protein, one could have two small seesaw shapes with the seats facing each other. The seesaws would shift at the same time to connect on the other side.

Sodium-Potassium Pump

Filed under: 2017 posts,Student posts @ 5:46 pm

Sodium-potassium pumps create and maintain electrochemical gradients, pumping potassium ions into the cell and sodium ions out of the cell. The established gradient is a crucial part of sending electrical nerve signals and regulating the osmotic pressure in cells. When the axon of a nerve cell experiences a depolarization in membrane potential, sodium-potassium pumps are responsible for reestablishing the resting potential of the membrane. This allows the axons of nerve cells to be prepared to transmit the next signal.

Since sodium-potassium pumps are partially responsible for the transmission of electrical nerve impulses, one way to represent the protein would be in such a way to resemble a lightning bolt. It might be unique to sculpt the protein with wire and small LED lights in the shape of lightning to represent one of its key functions.

April 11, 2017

Aquaporin: Wat-er an amazing protein!

Filed under: 2017 posts,Student posts @ 11:50 am

Aquaporin creates a channel for water molecules to pass through a membrane, so this molecules pops up when talking about osmosis. Aquaporin can be found in many organisms, from bacteria to eukaryotes and is made up of 4 identical chains.  The molecule itself is somewhat stationary with some rotation in the membrane, but the water molecules allow us to visualize how the function of the aquaporin is important.

When visualizing this molecule, there are a few different approaches that can be made. From the video above, you can see the bounciness of the water molecules as they pass through the aquaporin molecule. This reminds me of an arcade or carnival game that has the floating balls and you have to knock the balls down with a bigger ball or a sack. When the bigger ball misses and passes through the floating balls, there is a bounciness that can occur due to the gust of wind or movement. The aquaporin molecule in this case would be the machine that blows the balls up in the air and allows it to bounce.

Similarly, this model reminds me of a kinetics ball that can expand and allow things to pass through it (such as a bouncy ball) or a filter or colander that strains and separates.

Week 2 Animation Assignment

Filed under: 2017 posts,Student posts @ 10:23 am

This week please post a protein example from the Molecule of the Month and include an idea of how the dynamics of that protein could be conveyed artistically!

Here’s a quick rundown of the artwork we looked at on Tuesday when we were discussing the portrayal of action:

Hang on!

June 22, 2016

Play this game to help researchers!

Filed under: 2016 posts,Student posts @ 4:58 pm

Hi all,

I wanted to say thanks for a great semester, and wanted to share this cool game I found! Foldit is a protein folding game was developed by the University of Washington. As more people play the game, researchers at UW can see more unique approaches to protein folding and gain a better understanding of it. (In case the link above doesn’t work, here it is again: http://www.gamesforchange.org/play/foldit/)

Have a great summer!

Vy

May 25, 2016

Filed under: 2016 posts,Student posts @ 11:50 am

Protein Portraits 2016

May 23, 2016

Google Doc Caption

Filed under: 2016 posts,Student posts @ 11:51 am

Below is the link for art captions. Please ensure your caption and PDB picture stay on one page. Once you are done, remember to put your project and name in the ballot on the last page.

https://docs.google.com/document/d/1mApN-EBO76QV3N_XFD6QjF_qgeStUoz_0j-K3cLXpnU/edit?usp=sharing

May 17, 2016

Ideas for Keratin potrayal

Filed under: 2016 posts,Student posts @ 1:00 pm

52d36ac9503c0ca563a86fedd1b50874 2014-01-30 08.40.48 Curling-Ribbon IMG_3986_small2 nsmb.2330-F1 spiral_scarf_v1

Here are some interesting possibilities for my protein (keratin) portrait. I’m thinking about using wool as a medium, since wool is a type of keratin. Tomorrow in class I’d love to share my goals for the project and brainstorm with you all!

May 15, 2016

Comic Book Panels

Filed under: 2016 posts,Student posts @ 5:09 pm

IMAG0071

So, if you guys were to read a comic at a presentation, how much context/background story would you feel comfortable with before getting bored? I presently have about 10 panels.

May 13, 2016

3D painting!

Filed under: 2016 posts,Student posts @ 5:26 pm

I just found out that Google has made 3D painting a reality. I think this would make the art of making a protein portrait easier. As their website states: “Your room is your canvas. Your palette is your imagination. The possibilities are endless.” I also really like the fact that this product is sustainable; you can create so many things using very few material products. I guess my only concern with this is how you would be able to present your art work.
Check it out! (Don’t forget to press play): http://www.tiultbrush.com/

May 9, 2016

Medium for my project

Filed under: 2016 posts,Student posts @ 3:33 pm

hannahfish

This is my paining/art piece from years ago.  For my project, I will be using this method: I will be using acrylics to paint the molecule and then after putting several layers of it, I will then pour blank paint/ink all over the paper.  After a couple of minutes, I will then use a sponge to rinse off the ink.

Microbial Cross-stitching

Filed under: 2016 posts,Student posts @ 9:59 am
May 8, 2016

Hopeful for the Instamorph

Filed under: Student posts @ 3:15 pm

I played around with the Instamorph this weekend. The major challenge is the heating and reheating necessary when cutting. It is very malleable immediately after heating and becomes hard (at least with thin pieces) in a few minutes. When hard, it is slightly flexible, but not brittle (it seems pretty indestructible). And… I made an alpha helix!!

IMG_20160508_150905684

 

 

May 7, 2016

Gluten

Filed under: 2016 posts,Student posts @ 12:34 pm
Tags:

Articles About the Structure of Gluten

The structure and properties of gluten: an elastic protein from wheat grain

Structure and Function of Gluten Proteins

Circular Dichroism and Nuclear Magnetic Resonance Spectroscopic Analysis of Immunogenic Gluten Peptides and Their Analogs

Optical Rotatory Dispersion, Circular Dichroism, and Infrared Studies of Wheat Gluten Proteins in Various Solvents

My biggest hangup right now is interpreting what the data in these papers means and how I’d put it in a visual form. I realize it’s open for some interpretation, but I want to strive for SOME accuracy. I’m definitely going to use gluten as the medium because it has some interesting properties that make it worth utilizing to depict its structure.

Experimenting with My Medium

Gluten Project Experiment

What I’ve found by playing around with gluten is that it’s stickiest and most elastic when mixed with tap water. However, if too much water is added, the elasticity is lost and the mixture segments into smaller bits. Here it is mixed with excess water:

excess_water

Solutions, Baking vs Air-Drying

One of the first things I tried was mixing it with oil (left), vinegar (second from left), some water (second form right), more water (right). Then I baked it to see what would happen (bottom). After baking, the sample with oil got really crumbly, but the others stuck to the board without issue. The variations in water quantity were the most beneficial to play around with. I’ve decided a against baking because it sort of smooths out the surface, causes some bubbling, and I don’t really like that – I’d rather have the rough texture minus the bubbles.

before_baking_IMG_0053-001 after_baking_IMG_0058-001
This picture shows the gluten with different quantities of water after they have air dried, rather than baking.

hydrated_then_dried_IMG_0065

After reading this article about bread chemistry, I decided to experiment with salt water. I started out making a super concentrated salt water and mixed it with the gluten and the consistency is more granular – it’s not elastic at all. Even by diluting the salt water, the mixture just lacks elasticity when salt is involved.

Planning the Piece

I’m also trying to think of contexts, and I’m stuck in a more artistic mindset so I’m envisioning a wheat field, or the inside of a person’s intestinal tract, but I could also do something more abstract looking. Without knowing much about the structure of gluten, I’m leaning more toward the abstract layout. I want to use the stretchiness and natural shapes that emerge from pulling the gluten over the board. Maybe utilize the different textures of the gluten when mixed with excess water, little water, and/or salt water. Here’s a sketch of what I’m thinking:

gluten_project_sketch_IMG_0087

I have an 8″ x 10″ cradled wood panel because the gluten adheres really well to wood and I think it’s going to be a nice surface to work on. I have tubes of watercolor paint that can be easily mixed with the water I add to the gluten, so I should have lots of flexibility with colors.

paint_board_File_000

Since the gluten I’ll be working with will be hydrated, I think using blues for the “holes” and a warm color, such as orange or sienna, for the web-like part will provide some context to the piece. Below is just a sample I did to see how well the paint mixes with the gluten.

less_water_plus_pigment_File_005

Once I get the gluten layered on the board I can come back in with paints and add in details to explain the amino acid sequences of some of it or mark out hydrogen bonds, etc.

IMG_0069-001

Feedback, suggestions, whatever! Let me know what you think.

***Update 5/10****

First layer done; wet, then after drying:

 

 

 

 

 

image image

Update 5/23/16

May 4, 2016

Book Sculpture

Filed under: 2016 posts,Student posts @ 12:27 am

My current idea is to turn a book (The Linus Pauling Catalogue, which I got at OSUsed!) into my art piece. Specifically, I intend to cut the pages in layers (like so:

https://www.google.com/imgres?imgurl=http%3A%2F%2Fviola.bz%2Fwp-content%2Fuploads%2F2012%2F12%2F%25E2%2580%259CAnimal-Story%25E2%2580%259D-Book-Sculpture.jpg&imgrefurl=http%3A%2F%2Fviola.bz%2Fbook-sculptures-by-jodi-harvey-brown%2F&docid=i2LnNCaFz0-EnM&tbnid=sj1Xir1dqRzw9M%3A&w=500&h=372&hl=en-us&client=safari&bih=729&biw=1024&ved=0ahUKEwiijvSz6L_MAhVN1WMKHaHEBnc4ZBAzCEcoRDBE&iact=mrc&uact=8

and the 8th one on http://www.hongkiat.com/blog/book-paper-sculptures/) to show normal and sickle cell hemoglobin, since they were the subject of some of Pauling’s research.

I may also include a collage aspect, interspersing pictures in the layers of hemoglobin. Here is an example of the collage style I want to achieve: http://craftycreativegal.com/james-giant-peach-book-sculpture/.

May 2, 2016

Another cool post (I think! ;)

Filed under: 2016 posts,Student posts @ 11:22 pm

An amazing glowing gown worn by Claire Daines (have to scroll down a bit to see the gown glowing)–maybe an inspiration for anybody who wants to delve into their protein portraits from either fluorescence or fashion side, or both!
https://www.thewrap.com/claire-danes-met-gala-glow-in-dark-gown-zac-posen/

Inspiration for fluorescent protein enthusiasts: New Jellyfish Discovered!

Filed under: 2016 posts,Student posts @ 10:57 pm

Here is a link to an article that talks about the recently found species of jellyfish in the Mariana Trench: http://www.smithsonianmag.com/smart-news/deep-sea-researchers-spot-mysterious-jellyfish-near-mariana-trench-180958961/?utm_source=facebook.com&no-ist

Here is a live-stream of the expedition that led to the discovery of this jellyfish (off topic, but live streams are pretty cool! :D): http://oceanexplorer.noaa.gov/okeanos/media/exstream/exstream.html

Found my medium: InstaMorph

Filed under: 2016 posts,Student posts @ 11:17 am

Clear Worbla Rose

InstaMorph Groot Sculpture

Over the weekend, while watching youtube videos, I discovered the world of thermal plastic art! Worbla is sheet thermal plastic while InstaMorph (there are many other names for this) is pellet thermal plastic you heat in water and then mold. I started searching different applications of InstaMorph. It is used in a lot of Cosplay, but also for basic utilities for fixing mechanical devices that are broken.

InstaMorph Cosplay Mask

I wasn’t sure how feasible it would be to use it as a medium at first, but then I saw a finger splint that looks like an alpha helix! The different components, when shaped, can be reformed if more hot water is added. For my project, I will make the different secondary structure components separately, then I will reheat then to create the tertiary structure.

The medium has also made me reconsider my protein choice. Doing a transmembrane protein that is very complex will be very hard to scale correctly.

April 21, 2016

Insulin depiction by Dorothy Hodgkin

Filed under: 2016 posts,Student posts @ 7:36 pm

http://www.margaretalmon.com/wp-content/uploads/6a0105362f4359970b0120a859270a970b.png

 

This is a color diagram showing the crystal structure of insulin as depicted by Dorothy Hodgkin, the woman we talked about in class Wednesday. I love how much it looks like a true artwork.

Click to go to Margaret Almon's mosaic blog. Beautiful!

Click to go to Margaret Almon’s glass mosaic web blog where she comments on “Art in the Atoms”. Beautiful!

April 20, 2016

Agar Art

Filed under: 2016 posts,Student posts @ 8:07 pm

Agar ArtAgarArt_ThankYou1

I have attached a few pictures from Agar Art events I helped organize this year through the Department of Microbiology (inspired by the ASM Agar Art Contest). I wanted to share them because I think it’s a really cool and unique way to combine art and science to create something amazing. The images were used to create greeting cards and the Microbiology Student Association might use them to make coasters.

 

Polymer Clay

Filed under: 2016 posts,Student posts @ 1:07 pm

I thought this technique might be something some of you may like to try. Could be turned into something wearable such as earrings 😉

Using Protein Shapes as Outlines

Filed under: 2016 posts,Student posts @ 12:44 pm

Here’s an interesting idea that people may want to consider. Rather than focus specifically on the protein and its function, we could instead find shapes in the protein structure  and use them to create drawings of things important in our lives, such as family or hobbies. Here is a blog showcasing what I mean.

https://maykayart.wordpress.com/

Beauty of Microscopy Blog

Filed under: 2016 posts,Student posts @ 11:11 am

From ZEISS Microscopy, “Confocal microscopy of mouse brain, detail” “Depth coded projection (colour) image of mouse hippocampus sections of thy1-GFP line. Stained with GFP and imaged with ZEISS ELYRA PS.1 with LSM 780 confocal option. Tiling & stitching with ZEN software generates hi-res confocal maps, make sure to download in full resolution and zoom in. Sample courtesy of Yi Zuo, Molecular, Cell and Developmental Biology (MCDB) Department, University of California Santa Cruz. www.zeiss.com/elyra”

Mouse Hippocampus sections of thy1-GFP line

I discovered a blog called the Beauty of Microscopy a while back when I wanted to find a cool science wallpaper for my computer. There are some really great images of microscopic perspectives.

natureofnature:

Confocal microscopy of plant tissues

Confocal microscopy of plant tissue

i-heart-histo:

Have A Very Micro Christmas!
A growing snowflake by Kenneth Libbrecht
i-h-h

Growing Snowflake

April 19, 2016

Can the class see this post?

Filed under: 2016 posts,Student posts @ 11:34 pm

I believe tomorrow is 4/20/2016

Inspiration: art that depict symmetric/circular structures

Filed under: 2016 posts,Student posts @ 9:12 pm

http://www.thisiscolossal.com/2016/01/hypnotic-new-kinetic-sculptures-by-anthony-howe/

Since there are so many people who like circular protein structures in this class, I thought I would share this link with y’all! Check out some mesmerizing kinetic sculptures designed and made by Anthony Howe. Although his work is not inspired by protein structures, I feel like he is inspired by objects that are symmetric and intricate, like some of the proteins we have seen. Also, going along with the idea of art that portrays the function of a protein, I think that if he were to create kinetic sculptures based off of protein structures, he could use his art to theorize the movements/change in configurations that enable proteins to function!

April 17, 2016

For the Crocheters and Knitters

Filed under: 2016 posts,Student posts @ 10:06 pm

Check out these crocheted structures: http://jpolka.blogspot.com/

March 30, 2016

The Best Scientific Image Of The Year Was A Hand-Painted Watercolor of Ebola Virus by David Goodsell

Filed under: 2016 posts,Student posts @ 12:12 pm

Check it out!

April 15, 2015

Mondrian in Cake Form

Filed under: Student posts @ 7:37 am

At the San Francisco Museum of Modern Art, you can buy cakes and other desserts in the cafe that are inspired by works of art in the museum. Seeing as we talked about Piet Mondrian, and how his paintings look like aperiodic crystals, I thought I would share his work in cake form.

Mondrian cake by Caitlin Freeman at SFMOMA. Photo by Charlie Villyard.

Mondrian cake by Caitlin Freeman at SFMOMA. Photo by Charlie Villyard.

Here’s an article about the chef who created this cake, as well as multiple other art-themed desserts: http://openspace.sfmoma.org/2010/05/collection-rotation18/.

Art, cake, potential physics of life- what more could you want in a dessert?

-Lauren Pittis

April 5, 2015

Example post. X marks the spot

Filed under: Student posts @ 2:26 am

K.Sharpton chromosome

This is an example post.

This is also a great example of an artist’s view of a chromosome! Krista Shapton is the artist.  Her work can be found at kshapton.com

June 1, 2014

A Protein Progression

Filed under: Student posts @ 11:13 pm

Just a small update on my project. I just powered through 4 leaves and 1 petal of Rubisco, and it’s not taking as long as I thought, which is awesome! Hopefully I can power through another 7 and assemble it before Wednesday, but so far so good!

get-attachment

Next Page »

© 2017 Protein Portraits   Powered by WordPress MU    Hosted by blogs.oregonstate.edu