Proteins in the News

In this episode of Protein Portraits, we created visual companion pieces to go with proteins that have been highlighted by the press.  While every protein on earth is undoubtedly newsworthy to some degree or another, the following proteins actually garnered headlines.  Each student, acting as a reporter, referred the headline back to the protein databank (PDB) to learn enough about the protein’s structure to create a portrait that can help communicate the news made by the protein.  Hence, while fame may be fleeting, the historical achievements of these proteins is now immortalized by the 2023 Protein Portraits Colloquium.

1.  Reporter: Daniel Bacher

Researchers develop new modular vaccination kit for plants

Headline: Biologically and diagenetically derived peptide modifications in moa collagens

Flower Power – protecting plants with argonaute

Argonaute is a protein involved with siRNA silencing in a variety of molecules. I selected this protein based on its use in a new method of “vaccinating” plants against viral infections. My protein portrait went through many design phases. Inspired by the stem-like “legs” at the bottom of the argonaute to create something related to its use in plant science, my initial idea was to create something akin to a herbarium specimen, with plants mounted on paper in the image of the protein.

But I wasn’t happy with any attempts to complete this, so I transitioned into fashioning a wire model of the protein, with the intention of adding plant elements for the alpha-helices and beta sheets. This turned out to be challenging, and I had trouble getting the leaves to stick on the wire molecule. I ultimately had to go to plan C. Drawing on my earlier observation of the stem-like appendages at the termini of this protein, as well as the fact that my protein came from Arabidopsis thaliana, I used the extra wire I had to fashion the basal leaf rosette of Arabidopsis as a stand, and then used the protein to represent an Arabidopsis flower.

 

 

 

 

 

 

 

Reference:  Cleland Timothy P., Schroeter Elena R. and Schweitzer Mary H. (2015) “Biologically and diagenetically derived peptide modifications in moa collagens.” Proc. R. Soc.

2. Reporter: Emily Basler

Sunny D₃

Headline: Is feeding a raw meat-based diet worth the health risks?

Vitamin D₃ Hydroxylase, encoded by the gene VDH in Pseudonocardia autotrophica, is responsible for converting inactive Vitamin D₃ to hormonally active 1,25-dihydroxyvitamin D₃.
While Vitamin D₃ Hydroxylase can catalyze this two-step reaction in P. autotrophica, three enzymes are required to catalyze this reaction in mammals. The final enzyme, 1–hydroxylase, catalyzes the conversion of 25-hydroxyvitamin D₃ to 1,25-dihydroxyvitamin D₃. Deficiency in 1–hydroxylase, often caused by the improper implementation of a meat-based raw diet by a dog owner, can result in Vitamin d-dependent rickets type 1.

More closely related to the story, 1–hydroxylase was the original focus of this art piece. Encoded by the gene CYP27B1, it had been the focus of multiple Vitamin D-related gene expression experiments in my research. Unfortunately, the structure of 1–hydroxylase has not been determined, and thus my focus shifted from mammals to bacteria—the structure of Vitamin D₃ Hydroxylase had been solved. Thus, Vitamin D₃ Hydroxylase is the center of the wreath

its  helices represented by coiled ribbons and  sheets represented by arrows. Given that the reaction is light dependent, the protein is displayed on a wooden sun cutout. The dependence of the reaction on light is highlighted throughout the entire wreath—the ribbons are various shades of yellow and orange, bows are made of yellow and orange tubing, and small sun figures are present throughout. The research aspect of my experience with this protein type is brought in through the presence of strip polymerase chain reaction tubes and microcentrifuge tubes (each labeled to appear as if they’ve come straight from the lab). And, quite honestly, my favorite part of the wreath sits at the top—a 3D model of to 1,25-dihydroxyvitamin D₃.

Reference: Callahan, C. (2023, May 9). Is feeding a raw meat-based diet worth the health risks? DVM 360. https://www.dvm360.com/view/is-feeding-a-raw-meat-based-diet-worth-the-health-risks-

3. Reporter: Zach Bosworth

Arboreal Arthritis Avoidance

Headline: Cartilage Is Grown in the Arthritic Joints of Mice

Osteoarthritis is a disease that affects millions of people worldwide. Tissue engineered cartilage might be a path towards healthier joints and reduced pain. Aggrecan is a key proteoglycan that provides cushioning in cartilage.

I’ve been involved in an osteoarthritis lab at Oregon State for a while now. When searching for an article related to my protein of interest, I happened upon this article. Tissue engineering has been a recent interest of mine, so I couldn’t help but be interested by the intersection proposed in the headline. Aggrecan is a proteoglycan that provides much of the shock absorption and cushioning effects of articular cartilage. Osteoarthritis is characterized by an overactive enzyme (aggrecanase) and a decrease in the concentration of aggrecan, leading to more brittle cartilage and ultimately degradation. Each of the aggrecan core proteins are linked to a long hyaluronic acid chain and contain the functional glycosaminoglycans chondroitin and keratan sulfate. These negatively charged molecules lead to water swelling into the cartilage, ultimately leading to improved cushioning of the joints.

I ended up using modeling clay to depict my protein. Aggrecan is described as having a “bottlebrush structure”. Since the bottlebrush is a plant and legs are sometimes referred to as “tree trunks” (a bit of a stretch, I know…), I felt as though a hyaluronic acid trunk with aggrecan core proteins jutting off like branches would be an interesting representation. I also used feathers as “leaves” to represent the glycosaminoglycans that swell up to provide cushioning. I meant to add small pom-poms to represent a smaller set of glycosaminoglycans as well, but I couldn’t find an easy way to affix them to the structure.

Reference: Kolata, G. (2020, August 22). Cartilage is grown in the arthritic joints of mice. The New York Times. https://www.nytimes.com/2020/08/22/health/arthritis-cartilage.html

4. Reporter: Tara Conrad

Like Clockwork

Headline: Ticking Circadian Clocks

Circadian rhythms are 24-hour cycles controlling an organism’s physiology and behavior. The complex nature of circadian rhythms has engendered the idea that these cycles are reserved for higher-order, multicellular creatures. But this is far from the truth. A 24-hour ticking clock is now known to be of central importance to the physiology microscopic life. In cyanobacteria, a circadian clock drives rhythmicity of important behaviors such as photosynthesis and nitrogen fixation. Genes for photosynthesis are actively expressed during the day but are repressed come nightfall; during the midnight hours, nitrogen fixation ensues. It is an extremely robust, precise clock that maintains 24-hour periodicity even in periods of rapid cell division. Researchers now know that of central importance to these circadian rhythms is a protein known as KaiC.

This complex, hexameric protein interacts with other Kai proteins in a cyclic routine of phosphorylation and dephosphorylation. From dawn to dusk, KaiC slowly accumulates phosphates. From dusk to dawn, these phosphates are sequentially removed, and the clock is reset.

In this art piece, I have represented a simplified structure of just one of the subunits of KaiC. The secondary structure is interlaced with many alpha helices and beta sheets, which is represented with the alternating wire spirals and bends, respectively. Two domains are present, represented by the large and small globes. The six hanging ornaments are a reference to the six subunits of the complete KaiC protein.

The colors of the beads transition from bright yellow, to amber, and eventually to black, representing the change in KaiC’s activity with the addition of phosphates as sunrise progresses to sunset. Finally, the suspended copper disks in the center of the bead ornaments represent the pendulum that drives the precise rhythmicity of the grandfather clock.

 

 

 

Reference: Ticking Circadian Clocks. (2004, July 6). The New York Times. https://www.nytimes.com/2004/07/06/science/observatory-ticking-circadian-clocks.html

5. Reporter: Caleb Gerhard

Gelatinous Glow

I chose Green Fluorescent Protein (GFP) because of its unique, aesthetic protein structures. From Aequorea Victoria, the extraordinary, fluorescent beta-barrel structure of GFP is often used as a fluorescent marker of gene expression in living cells.

While GFP is an old discovery, the creation of new, brighter, different colored variations of GFP fascinates me, such as the red fluorescent mScarlet3 which had a record-breaking brightness. After much deliberation, I opted to create a wire sculpture of the Aequorea Victoria jellyfish with the GFP molecule incorporated into the tentacles, since the protein was first discovered in Aequorea Victoria. Manipulating wire and finding the resources I needed was quite a challenge, and the final product was not exactly my initial intention.

 

 

 

Reference: University of Amsterdam. (2023, March 27). Biologists develop new record bright red fluorescent protein. Phys.org. https://phys.org/news/2023-03-biologists-bright-red-fluorescent-protein.html

 

6. Reporter: Jeremy Hancock

Collagen, The Secret to Unlocking Our History

Headline: A New Study Says Humans Were in America 130,000 Years Ago

New data collected from analyzing collagen has given rise to the thought that we might have arrived in the Americas earlier than what was previously accepted.

I remember hearing about this finding last year and I wanted to dive deeper into the claim. Collagen consists of 3 left-handed polypeptide fibers that wind to form a right-handed triple helix. Collagen is a major structural component of bone, and thus we can use radiocarbon dating to determine the age of a bone. Radiocarbon dating works by analyzing the decay of the C-14 isotope which is absorbed into our bodies through our lifetime. I chose ceramics as my medium since I wanted to mimic the structure of collagen and combine this with the structure of a bone. Ceramics made this easy as I was able to build each individual part and then was able to join them together.

Reference: Yong, E. (2017, April 26). New Study Puts Humans in America 100,000 Years Earlier Than Expected. The Atlantic. Retrieved from https://www.theatlantic.com/science/archive/2017/04/new-study-puts-humans-in-america-100000-years-earlier-than-expected/524301/

7. Reporter: Camryn Lau

Bee-Lieve in the Future of Vaccines!

Headline: U.S.D.A. approves first vaccine for honeybees

Vitellogenin binds inactive disease-causing pathogens allowing for their transfer into a queen bee’s eggs thereby vaccinating entire bee colonies against American foulbrood.

Bees are a crucial part of human survival, pollinating the food we eat and maintaining the prosperity of various ecosystems. As these critical pollinators decline in number due to climate change, urbanization, diseases, and the increased use of pesticides among other things, there has never been a better time to help protect bee populations. In fact, in my hometown of Wilsonville, Oregon, nearly 50,000 native bees were killed when blooming linden trees were sprayed with a toxic pesticide. Given the importance of bees in sustaining life as we know it today, I was amazed to see that the USDA had approved a vaccine for bees to protect against American Foulbrood. Never before had I thought about giving vaccinations to insects–especially since their immune systems have not been widely understood. Given that tiny syringes are not used to administer these vaccines (rather dead versions of the bacterium that cause American foulbrood is incorporated into royal jelly and fed to queen bees), proteins play a critical role in providing this immunity for bees. Vitellogein plays a key role in enabling entire colonies to gain immunity from American foulbrood by acting as immune elicitors and carrying inactive Paenibacillus larvae (the bacterium causing American foulbrood) ingested by the queen and transferred into her eggs, creating larvae immunity. The vitellogenin protein itself is highly disordered with no fixed three dimensional structure. While the protein consists of one unique protein chain, it does contain several phosphate groups. Given the wide array of shape for vitellogenin, I decided to follow notion of structure following function by constructing a honeypot out of clay to symbolize the use of vitellogenin in honeybee vaccinations. On the sides of the pot are also phosphate groups along with small honeybees.

 

 

 

 

 

 

 

Reference: Tumin, R. (2023, January 7). U.S.D.A. approves first vaccine for honeybees. The New York Times. https://www.nytimes.com/2023/01/07/science/honeybee-vaccine.html

 

8. Reporter: Kyleigh Layman

Apolipoprotein! A protein solution to ALS

Headline: ApoA1 Identified as a Novel Target for ALS Therapy

This headline stood out to me because ALS is a deadly disease that attacks motor neurons that has no cure or known cause. ALS affects 18,000 people in the United States and research like this has the potential to improve the quality of life for many people. The utility of apolipoprotein to aid with ALS treatment is very promising.

Lipids are important for the maintenance and repair of neural cells and apolipoprotein has the ability to help limit the damage done by ALS. I felt the helix pattern resembled a spiral in crocheting. I chose to use blue and white because those are the colors used for ALS awareness.

 

9. Reporter: Rachel Mahler

The SOD of ALS

Headline: F.D.A. approves drug for rare form of A.L.S.

The misfolding of SOD 1 has been correlated as the cause of a type of ALS. My grandpa passed away from ALS, a motor neuron disease, whilst I was in high school. He had a passion for fine woodworking which inspired the idea to incorporate trees into my protein portrait, as well as a painting of the protein because growing up, my grandparents and I painted a lot when I was staying at their house. ALS causes one to over time lose the ability to control their muscles and movements. First with fine motor skills, and later down the line with eating and talking. The FDA recently approved a drug for trial that can treat a specific kind of ALS, which is important to Science, Medicine, and the lives of people who have been diagnosed or effected by this disease. The protein is seemingly the same on both sides but is flipped, so it’s like the mirror image, which is very interesting and cool to look at. The SOD 1 protein produces SOD, which uses copper and zinc to break down charged oxygen molecules in the body. The misformation of this protein causes these toxic charged molecules to not break down.

Reference: Robbins, R. (2023, April 25). F.D.A. approves drug for rare form of A.L.S. The New York Times. https://www.nytimes.com/2023/04/25/business/biogen-fda-als-drug.html

10. Reporter: Keegan Oakes

Sonic the Hedgehog: The Protein

Headline: Better Ovarian Cancer treatment: Thank the Sonic Hedgehog gene?

I wasn’t originally planning on doing the Sonic protein. I was looking to do something surrounding lab  grown meat, when I got frustrated trying to find a specific protein, I just googled “proteins in animals” and on that list was the Sonic protein. As soon as I read the name I knew this was the protein I needed to do.  After preliminary research, I found that the SHH protein was a signaling protein with a silly name. So I looked online trying to find a news article about this protein, until I found one covering its correlation to cancer treatment. A basic rundown is that mesenchymal cells are blocking or “hedgehogging” around cancer cells, effectively blocking anything good from reaching the cancer cells. Scientists have been using the SHH protein to attempt and create an inhibitor to the “hedgehog” signal so that T-cells can go fight the cancer.

 

 

 

 

 

 

 

Reference: McGrath, C.,et al. (2022, May 20). Better Ovarian Cancer treatment: Thank the Sonic Hedgehog gene? WAFB 9. Retrieved April 23, 2023.

 

11. Reporter: Andrea Perez

Headline: Preparing Rubisco for a tune up

 

Reference: Conlan, B., Whitney, S. Preparing Rubisco for a tune up. Nature Plants 4, 12–13 (2018). https://doi.org/10.1038/s41477-017-0089-2

12. Reporter: Kylie Rocha

MOUNJARO SET TO OVERSHADOW OZEMPIC AS MAINSTREAM WEIGHT LOSS DRUG

Headline: Watch out, Ozempic? Another diabetes drug leads to impressive weight loss in studies

Over the past year, the injectable diabetes medication Ozempic dominated the media. People bragged about their ability to get off-label versions of the medication to use for their weight loss. A new diabetes medication, Mounjaro, is now gaining media attention for having even more powerful weight loss properties. A name-brand medication for Tirzepatide acts as an agonist for glucagon-like peptide 1 (GLP-1) AND Gastric inhibitory polypeptide (GIP).

As an agonist for both peptides, Mounjaro enhances the effect of suppressing appetite – like GLP-1 – AND breaking down sugars and fats – like GIP. Mounjaro is currently awaiting FDA approval as a weight-loss medication.

To promote this news, I have depicted the new upcoming drug in the PDBID 7FIM structure, bound as an agonist to the GLP-1 receptor. To show Mounjaro’s role in weight loss and “cutting inches” around the user’s waste, I used measuring tapes glued to wire to create 7FIM’s tertiary structure. Mounjaro was created using a purple measuring tape to make it stand out against the pink receptor. These colors were chosen because they are Mounjaro’s brand colors. The background was created using 6×12 plywood and weight loss magazine clippings, which were used to depict more iconography of weight loss and a “healthy lifestyle” propaganda presented in the media.Overall, I wanted to show Mounjaro’s ability to improve one’s health, while simultaneously showing its possibility to be used for more surface-level reasons, such as becoming skinny, rather than healthy.

 

Reference: Pawlowski, A. (2023, May 3). Watch out, Ozempic? Another diabetes drug leads to impressive weight loss in studies. TODAY.Com

13. Reporter: Alexandra Swisher 

Tasting Stars

Headline: Octopuses Hunt by ‘Tasting’ With Their Suckers

I have always loved octopuses and thought they were very interesting creatures. When I saw this headline, I thought it was interesting because it was just another strange and cool adaptation that octopuses have. When looking at the primary article, the CRT-1 protein looked like a sucker itself.

That inspired me to incorporate the protein shape with the sucker. As I looked up the protein in the database when I looked at the top-down view it looked like a star. The star motif I wanted to continue into how the “star eye” of the octopus was looking at the star-like protein.

The octopus has a lot of unique qualities, and I wanted the more traditional-looking octopus to contrast with the abstract and bright CRT-1 protein. I wanted to change the way it looked while still getting the shape. The filled-in rectangles signify the alpha helices, and the five “O” shapes are the beta sheets. Since this protein is a pentamer I used different bright colors to signify each peptide chain. Where the octopus is a muted red the protein is bright and vibrant like a star.

 

 

 

 

 

 

 

 

 

References:

Thompson, Benjamin, and Nick Petrić Howe. “Octopuses Hunt by ‘Tasting’ with Their Suckers.” Nature, April 12, 2023.https://doi.org/10.1038/d41586-023-01262-z.

Bank, RCSB Protein Data. “RCSB PDB – 8EIS: Cryo-EM Structure of Octopus Sensory Receptor CRT1.” Accessed May 3, 2023.https://www.rcsb.org/structure/8EIS.

14. Reporter: Aidan Tucker-Calkins

Myelin-associated glycoprotein defends against dairy’s sneaky shenanigans

Headline: Immune Reaction to Milk Protein May Explain Dairy’s Link to MS

This article stood out to me because it involved casein (which I am allergic to), and how it could be making symptoms of MS worse. The article talked about how when someone with MS drinks milk or consumes casein it triggers antibodies like Myelin-associated glycoprotein (MAG) to attack it. These antibodies may be able to be measured, which would allow people to self-test for having MS early on.

I painted my piece using watercolor with milk to show how the MAG is activated when it detects the presence of casein, and to give it a whitish color. I wanted my portrait to highlight the heroic nature of the MAG, so I painted the MAG in bright red to make it stand out, and I focused on only one domain so that more of the details could be seen. I also made the background a light green to reflect its healing, and protective properties.

Marisa Wexler, M. (2022, March 8). Ms link to dairy may lie in immune reaction to casein, a milk protein. Multiple Sclerosis News Today.