JEFS Proteinber 2024 - November : simplebooklet.com

Day 1 HEMOGLOBIN, THE PAINTER Hemoglobin is a special protein found in red blood cells that helps your body by carrying oxygen from your lungs to the rest of your body, like your muscles and organs. It also takes carbon dioxide, a waste gas, from your body back to your lungs so you can breathe it out. Hemoglobin has four parts, each with a tiny iron atom inside. The iron grabs onto oxygen in places where there’s a lot of it, like in your lungs.Then, when the red blood cells reach places that need oxygen, like your muscles, hemoglobin lets go of the oxygen so the cells can use it. What’s cool about hemoglobin is that it works more efﬁciently depending on what your body needs. When your body needs more oxygen, hemoglobin is good at picking up or releasing oxygen based on environmental conditions when it is needed. Day 2 I studied G protein-coupled receptors (GPCRs) in my past and even tried to get them to fold in a cell-free E. coli extract. Let me tell you, GPCR alpha helices are much easier to fold using paper! (I customized my folded protein, shown in the photo collage, from this resource: https://lnkd.in/gfRDMY5j) GPCRs are membrane proteins that transmit signals from outside to inside the cell. They have seven alpha helices that change shape when a molecule, called a ligand, binds to them. This binding activates bound G proteins, which split into two parts, each triggering different signaling pathways. GPCRS, THE UX/UI DESIGNERS GPCRs function like switches, controlling cell processes like sensory perception and immune responses. Their shape-shifting ability is essential for cell function making them important drug targets because regulating their activity can affect many biological processes. In the creative world, I see a connection between GPCRs and UX/UI designers. Here are some reasons: Interface Design - A GPCR acts as an interface between the extracellular environment and the cell’s interior. An UX/UI Designer creates interfaces between users and digital products. Signal Interpretation - A GPCR interprets external signals (ligands) and translates them into cellular responses. A UX/UI Designer interprets user needs and translates them into intuitive designs. Responsiveness - A GPCR changes conformation in response to stimuli. A UX/UI Designer creates responsive designs that adapt to different devices and user interactions. Information Flow - A GPCR facilitates the ﬂow of information from outside to inside the cell. A UX/UI Designer facilitates the ﬂow of information between users and digital systems. Adaptability - A GPCR can adapt to different cellular contexts. A UX/UI Designer creates adaptive designs that work in different contexts. In thinking about a graphic artist to highlight, I thought of the work of M.C. Escher. Not your typical UX/UI designer, but both Escher’s artworks and UX/UI designs use intricate, interlocking elements to create engaging experiences that challenge and guide the viewer or user. To honor both Escher and GPCRs, I added an Escher-like pattern to my GPCR alpha helices pattern, printed, cut, folded, and taped together my GPCR. I put my paper GPCR in the center of a digitally generated Midjourney image collaged with the help of Photoshop. Do you see the connection between GPCR proteins and interactive, graphic design? Henri Monet’s paintings often capture the natural environment, such as gardens, water lilies, and changing light. Monet adjusted his brushstrokes and colors to reﬂect how light and atmosphere changed over time, showing a deep understanding of the environment around him. In both cases, Monet and hemoglobin adapt and respond to the environment. I hope I captured both the science and the art in this video design cover image! 7 6

Page 7

Page 8

Page 9

Page 10

Day 3 ELASTIN, THE SURREALIST Alright, this is a weird one (but not really), isn’t that the way many people think about something that behaves outside of what we expect. Elastin is a key protein in the extracellular matrix, responsible for providing tissues with elasticity and resilience. Elastin allows structures like skin, blood vessels, and lungs to stretch and recoil without losing their shape, making it essential for maintaining the functional integrity of these organs. The ﬁbers of elastin are highly ﬂexible, enabling them to extend up to 1,000 times their original length before returning to their resting state. This remarkable property of elastin is due to its unique molecular structure. Day 4 COLLAGEN, THE WEAVER Our younger selves never worry about our faces becoming less springy or our joints becoming more rigid. As we get older, we all start worrying about our diminishing collagen. Our older selves love collagen. Collagen is the body’s natural “glue” that helps hold everything together. Think of collagen as the scaffolding in a building—it provides the structure that holds everything up, whether it’s your skin, bones, or muscles. Collagen ﬁbers also connect different parts of the body, like how tendons connect muscles to bones, and ligaments link bones to each other. Five facts about collagen proteins: • Collagen has a triple-helix structure with repeating XaaYaaGly sequence. • Collagen is the most abundant protein in mammals (25-35% of body’s protein). • Collagen comes in multiple types with various functions in connective tissues. • Collagen has a complex synthesis process requiring vitamin C. • Collagen is a stable yet ﬂexible structure important for tissue function. Are you starting to see how collagen acts as a weaver? Weavers understand how threads come together to form something beautiful and substantial. I chose Anni Albers as a weaver artist highlight.; she is a pioneering textile artist who elevated weaving to the realm of ﬁne art. Trained at the Bauhaus, Anni Albers combines modernist aesthetics with ancient techniques, innovating with unconventional materials and geometric patterns. Look her up! My collagen design practice was a time-lapse video of me drawing the image below. Elastin consists of hydrophobic segments that form a disordered network when stretched, allowing it to accommodate mechanical stress. When the tension is released, the hydrophobic segments drive the recoil process, restoring the tissue to its original form. This elastic behavior is what makes elastin so crucial in tissues that undergo repeated deformation, such as arteries and lungs. How is this all connected to surrealism? The artist I highlight is Salvador Dali; his art is characterized by its ﬂuid, malleable forms that seem to defy rigid structures. His famous “melting clocks” in “The Persistence of Memory” exemplify this quality, mirroring elastin’s ability to stretch and return to its original shape. Elastin mimics surrealism because it doesn’t conform. Elastin exhibits ﬂexibility, complexity, and persistence, all surreal qualities. Five unique qualities of elastin: —Elastin is 1,000 times stretchier than collagen. —Elastin’s exceptional elasticity is crucial for heart function. —Elastin is synthesized mainly during fetal development and adolescence. —Elastin has a remarkably long half-life of about 70 years. —Elastin becomes more stableas temperature rises. The still above is part of an elastin video I designed using multiple AI models to get the heart image. I animated the ﬁnal image using Immensity AI. Are you working on science projects that don’t quite ﬁt? 11 10

Page 11

Page 12

Day 5 GFP, THE LIGHT ARTIST GFP is an important protein when used as a reporter to help scientists study living things. Five key facts about GFP: 1. GFP comes from jellyﬁsh and was foriginally isolated in 1962 by Osamu Shimomura. Scientists now use it in many different organisms for research. 2. GFP glows bright green when exposed to blue or ultraviolet light. It absorbs light with a peak at 395 nm and emits green light with a peak at 509 nm. 3. GFP has a unique barrel-like shape with a chromophore at its center, formed by three speciﬁc amino acids that allows it to glow without needing any extra chemicals. 4. Scientists use GFP to: • See proteins inside living cells • Study how genes work • Observe how proteins interact • Measure things like acidity in cells 5. Scientists have created new types of GFP that glow in different colors, like yellow and blue. Day 6 MYOSIN V, THE DANCER I showed my husband this cartoon I made, and he said, “What is that?” Out of context, this cartoon is so speciﬁc that only a protein biologist who studies myosin V and is a dancer might get it. I created it anyway. First, I love the New Yorker cartoons. Second, I love proteins. I don’t care if no one gets it but let me share the connection between myosin V and Martha Graham. Myosin V is a motor protein that moves along actin ﬁlaments in a hand-over-hand fashion to transport cargo within cells (https://www.ibiology. org/cell-biology/motor-proteins/). Five facts about Myosin V protein: • Myosin V – Dances along actin ﬁlaments for long distances without detaching. • Myosin V – Transports various intracellular cargo, including organelles and mRNA. • Myosin V – Has multiple functions in vesicle tethering and interacts with SNARE proteins for exocytosis. • Myosin V - Features two motor domains and a high duty ratio for efﬁcient movement. • Myosin V – Is in involved in synaptic functions, including receptor recycling and endoplasmic reticulum tethering. Martha Graham invented modern dance (check out this video https://www.youtube.com/ watch?v=G9LGVsKY1iQ ) both she and myosin V, embody discipline and precision, with Graham’s dance techniques showcasing emotional adaptability, and myosin V’s structure enabling efﬁcient cellular cargo transport. I see the connection because Myosin V moves to convey the message of organelles, vesicles, and other cellular components to speciﬁc locations within the cell. Martha Graham choreography emphasized powerful, controlled movements to tell stories and explore the human condition. Proteins can move just like people can dance. Where have you seen the connection between the function of proteins and creative artists? I was lucky enough to work with GFP variants in my previous work to make E.coli turn purple to show when a recombinant protein was expressed. How do you use GFP in your research? 13 12

Page 13

Page 14

Day 7 TUBULIN, THE ARCHITECT Day 8 ACETYLCHOLINESTERASE, THE POINTILLIST Have you ever wondered how nerve gas works? Nerve gas contains chemicals called nerve agents that stop an enzyme in your body, acetylcho-linesterase (AChE), from doing its job. Normally, AChE breaks down acetylcholine (ACh), a neurotransmitter that sends signals between nerve cells. AChE has multiple active sites, each acting as a ‘point’ of activity that independently breaks down ACh molecules, all contributing to the overall result. When AChE is blocked, ACh builds up in synapses, causing continuous stimulation of nerve cells. This overload leads to overstimulation of both the central and peripheral nervous systems, resulting in symptoms like uncontrolled muscle contractions, excessive secretions, and more. I see a connection between AChE’s function and the painting technique of French post-impressionist Georges Seurat: Seurat’s paintings consist of thousands of tiny dots that, when combined, create a complete image (a technique called pointillism). Similarly, AChE rapidly breaks down many acetyl-choline molecules through the collective action of its small, individual active sites, producing a systemic result. Both Seurat’s painting technique and AChE’s function achieve their effects through the coordinated action of many small, discrete units. What I used to make the cover design: • Hand-drawn synapse junction • Adobe Fireﬂy • Midjourney • Runway • Luma • Canva • Suno I hope the resulting video relays a pointillistic-styled impression of AChE in action. I started my early life in Milwaukee, Wisconsin, but I have yet to visit the Milwaukee Art Museum (MAM), which opened the Santiago Calatrava designed Quadracci Pavilion in 2001. The MAM is beautiful and ties into an analogy I see with tubulin, a protein that builds. Calatrava’s designs often mimic natural forms and structures, a practice known as biomimicry. His work is more accurately described as biomorphic, evoking living forms through abstract expressions. I see tubulin structures in his work. Here are ﬁve things to know about tubulin: — Tubulin is a protein that’s like a building block in cells. It comes in different types, but the main ones are called α-tubulin and β-tubulin. — Tubulin proteins join to form long, hollow tubes called microtubules. These are super important for giving cells their shape and helping things move around inside them. — When cells divide, tubulin helps by forming a structure called the mitotic spindle. This structure pulls chromosomes apart, so each new cell gets the right amount. — There are six main types of tubulins. The most common are ɑ and ꞵ, but there are also γ, δ, ε, and ζ types. —Some cancer drugs work by disrupting tubulin. This stops cancer cells from dividing properly. Scientists are studying tubulin to make better cancer treatments. While tubulin serves crucial cellular functions, it also creates visually striking patterns. This takes me back to Calatrava, who likewise blends functionality with aesthetic appeal in his designs. The image I created is a collage of multiple images I prompted using both Adobe Fireﬂy and Midjourney inspired by tubulin. I layered multiple images together in Adobe Photoshop and sculpted the ﬁnal image in this post. Does protein biology or nature inspire you to create? I would love to know. 14 15

Page 15

Page 16

Page 17

Page 18

Day 9 MYC, THE CONDUCTOR Imagine a single protein with the power to control the fate of thousands of genes, driving cell growth and division. Yet, when pushed too far, it can unleash chaos, fueling cancer’s relentless spread. This is the story of Myc, a molecular maestro that can conduct with both life-sustaining and life-threatening potential. The Myc protein is like a master conductor, guiding the activity of thousands of genes and orchestrating critical processes that keep our cells functioning. By amplifying gene expression, Myc ensures that cells grow, divide, and make proteins when needed. Day 10 TOP7, THE AI ARTIST My imagining of Top 7 protein accepting the prize for being a signiﬁcant contribution to science at the Nobel Prize award ceremony. Seems right to use generative AI to spotlight a protein synthesized with the help of computational protein design. Top7 is not just any protein; it is a demonstration of the immense potential of artiﬁcial intelligence in reshaping the future of biology. AI has found its way into every aspect of our lives. This year’s 2024 Nobel Prize in Chemistry celebrates that speciﬁc shift. Demis Hassabis and John M. Jumper are honored for their work on the AlphaFold algorithm, while David Baker receives recognition for designing Top7 using the Rosetta software. Together these individuals demonstrate how AI is changing scientiﬁc research into something more exponential. Five key facts to spotlight Top 7: Top7 is a de novo (newly designed) protein, meaning it was created from scratch rather than being derived from any naturally occurring protein. Top 7 was designed using computational protein design software called Rosetta, which predicts how sequences of amino acids will fold into three-dimensional structures. Top 7 has a unique ฀/฀-fold, which combines both alpha-helices and beta-sheets in its structure. Top7 does not have a speciﬁc biological function; it was created to demonstrate that computational tools can predict protein folding accurately and design stable proteins. Top 7 serves as a proof-of-concept for engineering proteins with novel structures. It opened new possibilities for designing proteins for speciﬁc applications, such as therapeutics, enzyme design, or industrial biotechnology. For the photo design, I used a mix of generative AI features from Midjourney, Illustrator, and Photoshop to place the Top 7 protein structure on center stage. How are you using AI to amplify your research? It also plays a pivotal role in stem cell renewal and DNA replication both key components in healthy development and tissue repair. However, Myc’s power comes with a downside. When overactive, it transforms into a driver of cancer, fueling uncontrolled cell growth by disrupting the normal checks and balances in DNA replication. The tale of two conductors On one hand Myc conducts like John Williams, who often directs with an exactness, ensuring genes are expressed in harmony to regulate cell growth, division, and protein production, much like the familiar, resonant themes in Williams’ compositions. On the other hand, Myc can also mirror the experimental unpredictability of conductor John Cage. When overactive, Myc disrupts this order, driving uncontrolled cell growth and abnormal replication, much like Cage’s dissonant, chance-based compositions. This change from careful control to chaotic actions illustrates Myc’s two-sided role, showing how it can greatly affect both the health of cells and the development of diseases. The design I share is all my own. I created it in Adobe Illustrator. I was inspired by the idea of a maestro conducting between two paths with the common thread of a nucleic acid in between one regulated and deregulated by Myc expression. 19 18

Page 19

Page 20

Day 11 GLUK2, THE SENSORY ARTIST Day 12 TITIN, THE KINETIC ARTIST Titin is a giant protein. With a length ranging from ~27,000 to ~35,000 amino acids, titin is the largest known protein in the human body. It acts as an elastic spring in our muscles, allowing them to move, stretch, and recoil with precision and grace. Researchers study titin to understand how its various forms contribute to neuromuscular the 1930s with his large mobiles, is art engineered to move naturally or mechanically to create a temporal and immersive experience for the viewer. I am not a kinetic artist, but if I could be, I would recreate the sculpture I share in this video I generated with the help of Midjourney and Runway Gen-3 Alpha. If this sculpture were real, I would engineer it to Not many of us like to hold a handful of ice cubes for too long. We start feeling sharp pain and are happy to toss the ice in our water glass or on the ground. The reason for the pain we feel is because of a transmembrane receptor protein called GluK2, short for Glutamate ionotropic receptor kainate type subunit 2. GluK2 was recently identiﬁed by University of Michigan researchers when they found mice without the GluK2 gene showed no response to cold, but still reacted to other temperature ranges. https://lnkd.in/g49rBp-E While GluK2 is best known for helping neurons in the brain communicate, this new research shows it also acts as a sensor for cold temperatures in the peripheral nervous system. This discovery suggests that GluK2’s role as a cold sensor may be linked to its original evolutionary function of detecting environmental changes that is conserved back to single-cell bacteria. Understanding this separate role for GluK2, could lead to new treatments for cold-related pain, such as those experienced by chemotherapy patients. An artist known for tapping into sensory experiences with cold is Icelandic-Danish artist, Olafur Eliasson. Eliasson has a permanent sculptural installation in the Italian Alps called “Our glacial perspectives” https://lnkd.in/gTiF6NXj Visitors must hike up to the summit of mount Grawand to ﬁnd a series of arches punctuated by an oversized armillary sphere. The arches represent the different ice ages in earth’s history spaced by the length of each period. I imagine seeing this artwork would make me more aware of my body’s GluK2 expression and how its cold sensor function has needed to evolve over time. Do you have a painful reaction to cold? disorders, given its critical role in muscle function. As I learned more about titin, I began to imagine how it could inspire a kinetic artist to create a dynamic, moving sculpture. Kinetic art, pioneered by Alexander Calder in gently sway to mimic how titin coordinates muscle elements to insure the seamless interaction between actin and myosin ﬁlaments. Generative AI helped me get close, what do you think? How would you design a piece that captures the essence of this giant protein? 21 20

Page 21

Page 22

Day 13 INSULIN, THE SUGAR ARTIST Although insulin is only 51 amino acids long, its small size doesn’t reﬂect the critical role it plays in regulating glucose levels in our bloodstream. There is a lot to this tiny hormone. Here is how insulin works: —Insulin moves glucose into muscle and fat cells by triggering GLUT4 transporters. —Insulin is released when blood sugar rises and continues at low levels between meals to maintain balance. — Insulin stops the liver from making more glucose and breaking down glycogen. —It stores excess glucose as glycogen in your liver and muscles. — Insulin stops the liver from making more glucose and breaking down glycogen. — It prevents glucagon from releasing more glucose from the liver. —Insulin converts extra glucose into fatty acids for storage in fat tissue. You can imagine that without insulin, the body cannot regulate blood sugar, leading to dangerously high levels (hyperglycemia) as glucose builds up in the bloodstream. —In type 1 diabetes, your body doesn’t Day 14 TOPOISOMERASE, THE REMIX ARTIST You wouldn’t think an enzyme has much in common with a DJ, but topoisomerases manipulate DNA like a skilled remixer works the turntables. Topoisomerases are proteins that manage DNA structure during essential cellular processes like replication, transcription, and mitosis. These enzymes unwind or rewind the double helix, preventing DNA from twisting and tangling during critical processes like replication and transcription to keep everything running smoothly kind of like a DJ who controls the dance ﬂoor. How about ﬁve fun functional similarities between topoisomerases and musical remixers? 1. Similar to a DJ equalizing sound levels to keep the beat ﬂowing, topoisomerases relieve supercoiling tension by untangling overwound DNA. 2. Like a DJ transitioning between tracks, topoisomerases ensure a smooth ﬂow for DNA replication. 3. As a DJ prevents their vinyl from scratching, topoisomerases protect DNA from excessive stress, preventing damage during transcription. 4. Like a DJ making the rave with a ﬂawless remix, topoisomerases help RNA polymerase slide smoothly along DNA without obstructions. 5. Similar to a DJ layering beats, topoisomerases compact DNA during mitosis, expertly controlling DNA supercoiling. Topoisomerases ensure every aspect of DNA interaction runs smoothly and stays synced like the best DJs who map their beats. I admire both topoisomerases and DJs for their skills since the directional changes of winding and rewinding are too challenging for me. One DJ who is a master at fusing digital and analog elements is Bonobo (A.K.A Simon Green). Bonobo is known for his ability to blend downtempo, trip-hop, jazz, and world music inﬂuences into richly textured soundscapes. Bonobo’s music is marked by intricate layers, organic instrumentation, and deep, atmospheric beat that creates a soulful, immersive experience that resonates both on the dance ﬂoor and in more intimate settings. Topoisomerases and Bonobo are remix artists. As a music lover and protein enthusiast, I had fun making the video design for this post. — I made a good reference photo in Midjourney that I put into Adobe Fireﬂy to create different styles. —I took my favorite image and prompted Luma.ai to animate. — I put it altogether using Canva. produce insulin. —In type 2 diabetes, your body doesn’t produce enough insulin or doesn’t use it effectively (insulin resistance). Cells become starved of energy because they can’t absorb glucose. The body starts to break down fat and muscle for fuel instead. Additionally, the liver continues to produce glucose unchecked, worsening hyperglycemia. Over time, these disruptions can lead to serious complications, including nerve damage and organ failure. Insulin is important, which is why we should do our best to maintain a healthy lifestyle. However, when you do make indulgences, they should be beautiful pulled sugar dragons. In researching for this post, I found out about an amazing sugar artist from Hong Kong named Louis To. To, or the “Sugarman” as he is commonly known, pulls sugar using a traditional sugar technique to make mythical Chinese ﬁgurines on sticks. Click this link to read more about To: https://lnkd.in/gafbYFVv A side beneﬁt to To’s creations is that he uses isomalt instead of maltose, which not only makes his ﬁgurines last longer they are safe for people to eat who have diabetes. To’s sugar work inspired the cover design I made using Midjourney, ChimeraX, and Photoshop. (The Chinese characters say “Sugarman”) 23 22

Page 23

Page 24

Page 25

Page 26

Day 15 SONIC HEDGEHOG (SHH), THE CREATIVE ARTIST Day 16 HEAT SHOCK PROTEINS (HSPS), THE QUILT ARTISTS I made this science sweatshirt for my husband who is a middle school science teacher (Yes, I should have taken a picture of him wearing it, but he already left for school.) If you look through the picture carousel, you can see I sewed it together using scraps of different materials. I like sewing together scraps of material to make appliques, pictures, or quilts. There is something about repurposing and reorganizing things into something new that speaks to me. If I were a protein, I would probably be a heat shock protein (HSP). HSPs are a family of specialized molecular chaperones that help protect cells from stress by stabilizing, refolding, or repairing damaged proteins. They are activated when cells are exposed to environmental stressors like heat, toxins, or UV light. When things are chaotic at the molecular level, HSPs take misfolded or denatured proteins and help fold them back into their correct, ordered three-dimensional structures, making them functional again in the cell. The connection I see with HSPs and quilters, like me, is that we adapt our designs based on the materials we have at hand. HSPs are similarly activated in response to environmental stress (such as heat or toxins) and adapt by helping a variety of different proteins refold or prevent further aggregation. Patchwork quilting is preserving the memory of the original fabric by helping it live on with a new function. Likewise, HSPs preserve the “functionality” of proteins. Without HSPs, proteins might clump together or degrade, causing the cell to malfunction. HSPs ensure that proteins maintain their functionality even after being stressed. Quilters and HSPs both act to repair, organize, and stabilize, components in their respective worlds (whether fabric or proteins) to create a more harmoniously structured outcome. I identify with an HSP, because I enjoy the challenge of creating order from chaos. Now, that I halfway through PROTeinBER, have you found a protein function you can identify with? We are surprised by the unexpected. I remember the ﬁrst time I saw one of Anne Geddes photos of a tiny baby nestled in a whimsical dreamlike nature-inspired scene. My thought was how creative (and patient) Geddes is to imagine and intricately curate babies into photo shoots that symbolize the beauty and wonder of new life. Another creative artist that works with babies is the Sonic Hedgehog (Shh) protein. Shh is a protein that functions behind the scenes to make sure we are formed correctly as embryos. Just like Geddes carefully arranges her baby photo shoots, Shh coordinates the formation of essential body parts, like the brain, spinal cord, and limbs. Shh is a fundamental cellular blueprint designer, ensuring everything grows in the right place, at the right time. You may wonder how Shh got its name. The original hedgehog gene (hh) was discovered in fruit ﬂies. The mutation of the gene caused ﬂies to develop spiky, bristle-like structures, which resembled the spikes of a hedgehog. When researchers later discovered the vertebrate version, Shh protein, in the 1990s, they named it after the Sonic the Hedgehog video game character. Why? Because one of the discovering researchers, Dr. Robert Riddle, was inspired by the spiky blue hair of video game character, Sonic the Hedgehog. That playful nod to pop culture stuck, and now Sonic Hedgehog has an ofﬁcial place in biology textbooks! Want some cool facts about Shh? Here are ﬁve: —Shh is the master planner of early embryonic development and organizes body structures. —It helps form the neural tube, which becomes your brain and spinal cord. —Shh is the reason your ﬁngers and toes show up in all the right spots! —SHH helps establish the line that separates the right and left sides of the forebrain. —Problems with Shh signaling are linked to developmental disorders and some cancers. Like Geddes creates beautiful, nurturing portraits, Sonic Hedgehog is the unseen creative protein artist, shaping your body’s blueprint for an intact, symmetrical future. For my design, I used Midjourney to generate the image of a hedgehog holding a baby, I used photoshop for retouching in the blue (for Sonic effect), and Illustrator to ﬁnish with text and formatting. 26 27

Page 27

Page 28

Day 17 UBIQUITIN, THE PICASSO OF PROTEINS Ubiquitin is like the Picasso of proteins, a master of cellular artistry that is found all over the place. Playing a vital role in various cellular processes, this small regulatory protein is most notable for tagging other proteins for degradation, a process known as ubiquitination. Versatility Ubiquitin participates in protein degradation, DNA repair, and cell cycle regulation. Ubiquitin can form chains by attaching to itself (polyubiquitin), leading to different biological outcomes. Ubiquitin constantly redeﬁnes protein function just like Picasso’s art adapted across styles from realism to cubism and surrealism. Complexity The linking of different ubiquitin chains (through lysine 48 or lysine 63) inﬂuence what happens to a protein. Day 18 LEAF BRANCH COMPOST CUTINASE, THE BIOARTIST This enzyme is a mouthful, Leaf Branch Compost Cutinase (LCC), but it performs a function we greatly need, the breakdown of plastic. Normally, cutinases allow fungi and bacteria to digest away plant skin, but researchers found some species of these organisms adapted their cutinases to use plastic as a food source too. Plastic-eating enzymes like LCC work by hydrolyzing polyethylene terephthalate (PET) into its monomeric units. PET is a plastic used in numerous consumer products, but ﬁnding a good recycling loop has been challenging. Leveraging LCC is helping pave the way for new options. French company, Carbios, has engineered LCC to create an enzymatic recycling process that recycles all types of PET waste to produce 100% recycled/recyclable PET products. Some PET containers are already in use by major French cosmetic companies. Check out this article to ﬁnd out more: https://lnkd.in/gmwkXGMN The clunky video I made for this post is to provide a visual touchpoint for you, but there are bioartists who create cool art with organisms, like Anna Dumitriu and Candice Lin. I found this interesting article about bioartists if you want to learn more: https://lnkd.in/gccY-iPk. Isn’t nice to know that there is an enzyme that can help us clean up our waste? This attachment process adds multilayered control to cellular systems, from degradation to signaling. Ubiquitin introduces multiple “angles” to protein regulation much like varied angles of Picasso’s cubism. Universal impact Ubiquitin is present in every eukaryotic cell. It’s essential for life, just as Picasso’s inﬂuence touches every corner of the art world. Ubiquitin is to cells what Picasso is to creativity, widely recognized and indispensable. The result of ubiquitin’s presence? → Transformation. Ubiquitin alters protein function, stability, and localization, much like Picasso’s work transformed art perspectives. Both ubiquitin and Picasso’s art are ubiquitous! 29 28

Page 29

Page 30

Day 19 URICASE, THE EXPERIMENTAL ARTIST Day 20 NOBODY MICROPROTEIN, THE CONTEMPORARY ARTIST Have you ever been to a Yayoi Kusama mirror room exhibit? If you have, you will know that the experience is all enveloping and a touch transcendental. I tried to do a little recreation of the Kusama effect with this post. Why not take the function of the NoBody protein and tie it back to renown contemporary artist like Yayoi Kusama. I won’t go on about the NoBody protein (short for Non-Oligomeric Decapping Body) and say that it is too special, but for a small protein, it does a lot. The NoBody protein is involved in the regulation of RNA decay, particularly in a process known as mRNA decapping. NoBody plays a role in the “cleanup” processes that prevent the accumulation of non-functional or potentially harmful RNA in the cell. This process is crucial for the degradation of messenger RNA (mRNA) molecules, which is a key step in controlling gene expression and maintaining proper cellular function. For a protein named NoBody, this protein does a lot. Are you small, yet mighty? What ways do you ﬁnd to do more with less? Humans don’t have a functional uricase enzyme. In most animals, uricase breaks down uric acid in urine into a more water-soluble compound called allantoin. However, in humans, uric acid is removed primarily through urine because we don’t have uricase. The artist Andy Warhol, best known for his Campbell Soup cans and celebrity portraits, turned this biological quirk into a creative opportunity by incorporating human urine (and its uric acid) into his art. In the late 70s, Warhol had his assistants and visitors urinate on canvases covered in metallic paints to create his Oxidation series of paintings. The uric acid in the urine oxidized the copper alloys in the paint to create unique abstract designs https://lnkd.in/gVqcqwdU. Warhol’s experimental works highlight how destruction or breakdown can result in something new. Did the use of urine as medium in Warhol’s art diminish its value? Judging by the ~$35M sale price of Warhol’s oxidized Jean-Michel Basquiat portrait in 2021, the answer is clearly no. Interestingly, our lack of uricase offers some beneﬁts besides making urine an art medium, as uric acid acts as a potent antioxidant in our bloodstream. However, excess uric acid can lead to gout, a painful condition caused by the formation of uric acid crystals in and around the joints. For the cover art, I made a collage of Warhol-inspired images using Illustrator, no urine involved. Would you buy a painting made using bodily ﬂuids? 30 31

Page 31

Page 32

Page 33

Page 34

Day 21 CLOCK/BMAL1, THE CONCEPTUAL ARTIST If you thought of your body as a large, complex building with many systems like lights, heating, air conditioning, and security, the CLOCK/ BMAL1 protein complex would be the master control board that manages all these systems on a 24-hour schedule. CLOCK and BMAL1 are two proteins that bind together to control the body’s internal clock. Here are a few examples of what the CLOCK/ BMAL1 complex does: — Core Circadian Regulators: Maintains our body’s internal 24-hour rhythms. — Transcriptional Feedback Loop: Operates in a self-regulating feedback loop. — Wide-Ranging Inﬂuence: Controls the circadian expression of numerous genes involved in key metabolic processes. —Dysregulation: Can contribute to cancer development. CLOCK/BMAL1 helps shape our internal sense of time. Time is a signiﬁcant theme in our Day 22 A long time ago, I was lucky enough to visit the Louvre Museum in Paris and see Michelangelo’s sculptures, The Slaves. What struck me about the sculptures was the amazing movement that Michelangelo captured carving from a hard stone like marble. Our cells contain a protein called actin that provides both structure and movement. As a key structural protein, actin is a major component of the cytoskeleton, which gives cells their shape and internal organization. If we were missing actin: —Cells would lose their structure, causing tissue and organ breakdown. —Muscles wouldn’t contract, leading to paralysis and heart failure. —Wounds wouldn’t heal due to impaired cell migration. —Cells couldn’t divide, halting growth and regeneration. —Intracellular transport would fail, disrupting vital cellular functions. Actin gives us form and function, much like the great sculptor Michelangelo carved form to evoke emotion. In both art and biology, the ability to shape and move brings life to the form. For my design, I used Illustrator to rework and reform a sculptural image I generated in Midjourney. Do you have a favorite sculptor or sculpture? lives, inspiring many artists to explore it in their work. One such artist is Christian Marclay. Marclay spent three years creating a 24-hour video montage called “The Clock,” which assembles thousands of movie and TV clips featuring clocks, watches, and references to time. Each clip is synchronized to the actual time, creating a real-time experience where the displayed time matches the viewer’s local time. “The Clock” is held in the collections of several major museums, but you can watch a snippet I found on YouTube: https://lnkd.in/ gJdX4ZbN For my short video montage, I decided to highlight the CLOCK/BMAL1 heterodimer in a kiosk-like display. Does the concept of time overwhelm you? CLOCK and BMAL1 are two proteins that are trying to keep you in sync. 34 ACTIN, THE SCULPTOR 35

Page 35

Page 36

Day 23 RAG RECOMBINASE, THE OPTICAL ARTIST Day 24 P53, THE MURALIST/GRAFFITI ARTIST Public art, whether a commissioned mural or grafﬁti tag, reﬂects the state of a community. Some well-known examples come from street artist Banksy, who uses simple yet impactful imagery to make satirical commentary on various social issues. Similarly, the p53 protein could be considered the muralist or grafﬁti artist of the cell, responding to the cellular environment and leaving its “mark” depending on the condition. p53 plays a crucial role as a tumor suppressor, regulating several vital cellular functions: • DNA Damage Response and Repair • Cell Cycle Regulation • Apoptosis Induction • Autophagy Regulation • Metabolic Regulation • Stem Cell Regulation • Tumor Suppression Its central role in maintaining the integrity of the cell is so vital that, when mutated, p53 can switch from a guardian to a cellular foe, actively driving cancer progression through various oncogenic pathways. In fact, the TP53 gene is the most frequently mutated gene in human cancer. This transformation of p53 mirrors the dual nature of public art; it can inspire or disturb as it reﬂects both the potential for healing and the possibility of harm. I took a crack at a Banksy-inspired mural to highlight the balancing act p53 plays in our cells. The resulting collage was made using both Photoshop and Illustrator. Tell me about your thoughts on public art. Do you love it or hate it? Spider webs, protein, and Optical art (Op art) just the right combination for October. The protein structure you see the spider spinning is RAG (Recombination Activating Gene) recom-binase complex (RAG1/2), which is known for its ability to cut and rearrange DNA. Here are some interesting things to know about the RAG —The RAG complex is an immune diversity creator helping generate a huge variety of antibodies and T-cell receptors to ﬁght infections. —It acts like DNA “Scissors” to cut speciﬁc DNA segments shufﬂing immune genes and creating new combinations. —RAG begins the process of mixing V, D, and J gene segments to form unique immune receptors. —After RAG cuts DNA, it works with DNA repair systems to rejoin the broken DNA. —RAG requires strict control, as mistakes can lead to harmful DNA changes or cancer. RAG recombinase’s ability to generate diversity through meticulous DNA rearrangements reminds me of Op artist Bridget Riley, known for her precise, repetitive, and optical-effect-driven art. Riley’s paintings often involve repeated patterns and transformations that seem to shift and move before the viewer’s eyes, mimicking the continuous, evolving process of recombination in the immune system. For my video, I used Illustrator to make a trippy spider web background inspired by Riley’s 1963 work, Disﬁgured circle. I layered in the structure video downloaded using Chimera X. Do you think it’s possible to be both precise and diverse in your work, whether in science, art, or any other ﬁeld? 36 37

Page 37

Page 38

Day 25 FERRITIN, THE MAGICAL REALIST Ferritin can hold thousands of iron atoms within a microscopic protein shell by converting individual iron atoms into stable iron oxide clusters. This conversion of reactive iron into stable crystals allows ferritin to safely store and release iron ions as needed, preventing iron toxicity in the body. Without enough iron, the body can’t effectively transport oxygen, produce energy, or support immune and cognitive functions. Ferritin reorganizes iron into a reservoir essential for life-preserving cellular functions Day 26 BDNF, THE NEURO ARTIST During his scientiﬁc career, Spanish scientist Santiago Ramón y Cajal created nearly 3,000 detailed sketches of neurons to support his groundbreaking theory of the individuality of nerve cells. https://lnkd.in/g9cfWVzn His dedication and artistic precision helped him earn the Nobel Prize in 1906, which he shared with Camillo Golgi, who developed the staining technique Cajal used to visualize neurons. Cajal’s artistic skills and discoveries ultimately garnered him the title of “father of modern neuroscience.” One protein that mirrors Cajal’s legacy of neuro artistry is BDNF (Brain-Derived Neurotrophic Factor), a neurotrophin vital to the brain’s growth and resilience. Here are ﬁve ways BDNF shapes and reﬁnes the brain, much like Cajal’s artistic inﬂuence: • Promotes Synaptic Growth by strengthening neuron connections, making communication more effective. • Enables neuroplasticity helping the brain adapt and recover. • Supports emotional well-being. Higher BDNF levels reduce risks of mood disorders. • Enhances memory by strengthening circuits in the hippocampus, aiding long-term memory storage. • Physical activity and mental engagement increase BDNF production. I made a “neuro art” video to highlight the neuron using modern tools. I hope it captures the spirit of both Cajal and BDNF! Has art helped you make discoveries in your own work? performing wonders with a simple mineral. For Frida Kahlo, painting was a life-preserving function that helped her deal with the strangeness and pain in her everyday life. Kahlo survived polio and a terrible bus accident as a teenager, which left her in constant pain and unable to have children. Kahlo’s paintings reveal her deep connection to her Mexican heritage, blending realistic depictions with magical elements that embody the style of magical realism. “They thought I was a surrealist, but I wasn’t. I never painted dreams. I painted my own reality.” – Frida Kahlo I see a connection between the function of ferritin and Frida Kahlo’s art, as both work to transform and preserve in their unique ways. I created my Frida-inspired cover design in Illustrator. The ﬂowers are made of human transferrin receptor 1 (greens)- H-Ferritin complexes (pinks/purples). Iron is a key component of what other protein? 38 39

Page 39

Page 40

Page 41

Page 42

Day 27 ALBUMIN, THE MODERN ARTIST Day 28 RHODOPSIN, THE LIGHT PHOTOGRAPHER Ever write your name in the night sky using a sparkler? It’s captivating to see the letters appear then slowly fade away. Rhodopsin, a light-sensitive protein in the rod cells of our eyes, plays a vital role in allowing us to see this effect, especially in low light conditions. When our eyes capture the intense bursts of light the sparkler emits, rod cells, which are highly sensitive to dim light, rely on rhodopsin to detect even slight changes in light intensity. As the sparkler moves, our eyes continuously refresh the image of its path, forming an impression of each light ﬂash. Rhodopsin molecules in the rods absorb photons from the sparkler’s glow and initiate a signal cascade that tells your brain there’s light there. The trail effect or “persistence of vision” is a result of both biological and cognitive processing. Thanks to rhodopsin, our eyes capture rapid ﬂashes even in low light, while our brain stitches these images into a continuous line creating a trace that looks like a name written in the air. Light photographer, Eric Staller, uses long-exposure photography with extended shutter times to capture an entire sequence of light movements in one shot. https://lnkd.in/gbFvcQPH Staller’s photos essentially let us see this persistence of light in a single, lasting image. His art preserves what our eyes can only perceive momentarily, showing paths of light in ways that are usually only visible within the mind. Is there anything ﬂeeting in your life that you wish you could make last longer? One of my ﬁrst art purchases was a print of “Red Poppy” by Georgia O’Keefe. The undulating poppy petals in shades of red and coral transported me into nature every time I looked at it. Georgia O’Keeffe was a pioneering ﬁgure in 20thcentury art, known for breaking from traditional realism to embrace abstraction, minimalism, and bold perspectives. O’Keeffe’s unique modernist approach captured the essence of nature, translating it into powerful, simpliﬁed forms. One protein that also transports the essence of nature is albumin. Here are ﬁve of its important functions: • Albumin is the most abundant plasma protein; it transports hormones, vitamins, drugs, and waste throughout the bloodstream. • It maintains osmotic pressure and helps to regulate blood pressure. • Albumin binds waste products and carries them to the liver or kidneys for removal. • With a half-life of about 20 days, albumin reliably performs its functions without frequent replacement. • It is used in medical treatments to restore ﬂuid balance and in laboratories as a stabilizing agent for other proteins. Like O’Keefe distilled the beauty of the natural world into her art, albumin plays a crucial role in capturing and transporting essential elements within the body. My design is collage of the structure of albumin nestled among an animal skull inspired by O’Keefe’s 1936 “Blue Morning Glories.” Who was the ﬁrst artist who transported you? 42 43

Page 43

Page 44

Day 29 TOLL-LIKE RECEPTORS, THE GOTHIC ARTISTS Not afraid of a threat, the toll-like receptors (TLRs) are proteins that help make up the body’s primary defense mechanisms. Located on immune cells such as macrophages and dendritic cells, TLRs detect pathogen-associated molecular patterns (PAMPs) from bacteria, viruses, and fungi. When activated, TLRs stimulate immune cells to release cytokines and other signaling molecules, promoting a more targeted immune response that involves T-cells and B-cells. Different TLRs are specialized to recognize distinct components of pathogens. — LR4 detects lipopolysaccharides (LPS) from bacterial cell walls — TLR3 detects double-stranded RNA from viruses — LR9 senses unmethylated CpG DNA commonly found in bacterial and viral genomes Day 30 APOLIPOPROTEIN E, THE RENAISSANCE ARTIST Both scientists and artists are appreciative of the Renaissance genius, Leonardo da Vinci. Aside from his amazing skills as a painter, da Vinci was a polymath who moved seamlessly between disciplines like engineering, physics, and anatomy. In thinking about a protein whose function could be multifaceted enough to echo da Vinci, I landed on Apolipoprotein E (ApoE). ApoE’s primary role is in the transport and metabolism of lipids, such as cholesterol and triglycerides, within the body. In addition to its role in lipid transport, ApoE is also known for its diverse functions in other physiological processes, such as: —Brain health - ApoE supports neuroplasticity and repair by transporting cholesterol to neurons, which is crucial for brain function. —Immune modulation - ApoE inﬂuences immune responses and can modulate inﬂammation. —Tissue repair - ApoE plays a role in the recovery and regeneration of damaged tissues. Variations in the ApoE gene, particularly in its three major alleles (ε2, ε3, and ε4), can inﬂuence a person’s risk for conditions like cardiovascular disease and Alzheimer’s disease. ApoE has multi-faceted roles and far-reaching biological impact, which channels the spirit of da Vinci, who sought to understand and optimize human potential across many domains. My ApoE design is a collage of images I made using Photoshop and Illustrator, some generated, some vector. What multiple disciplines does your job require you to master? I imagine TLRs to be similar to modern Gothic artists, who often explore themes of mortality, decay, protection, and the thin line between life and death. One such Gothic artist is Banks Violette whose minimalist black and white art installations are part of larger evocative exhibits that explore the touchpoints of death and violence. My cover video may be a stretch, but I wanted to use a video I just took of a creepy balloon swirling around my local grocery store parking lot. The TLR4-MD-2 complex watches ready to respond. How do you respond to threats? Do you retreat or face problems head-on like TLRs? 45 44

Page 45

Page 46

Page 47

Page 48

Page 49

Page 50

Bonus Quiz! Discover your “Protein-Artist” style! Uncover your unique approach to science and creativity, and see which protein type best matches your scientiﬁc personality! Instructions: - Choose the answer that best ﬁts you. At the end, add up your points to ﬁnd out your type. 1. How do you tackle a new project? A. Develop a structured plan before starting (2 points) B. Begin with brainstorming to generate ideas (4 points) C. Ask for team input to get various viewpoints (3 points) D. Start experimenting right away (5 points) 2. When brainstorming with your team, you usually… A. Keep everyone organized and on task (2 points) B. Encourage thinking beyond the usual ideas (4 points)C. Make sure everyone’s ideas are heard (3 points) D. Push for concrete steps to implement ideas (5 points) 3. How do you prefer to learn new techniques in the lab? A. Practice repeatedly to master it (2 points) B. Test various approaches for improvement (4 points)C. Collaborate with others to learn together (3 points) D. Jump in and adjust as you go (5 points) 4. What’s your approach to troubleshooting? A. Carefully analyze to ﬁnd the root cause (2 points) B. Try unconventional methods to solve it (4 points)C. Gather team feedback for insights (3 points) D. Experiment quickly to ﬁnd what works (5 points) 5. What type of project do you enjoy most? A. Projects that require precision and order (2 points) B. Open-ended projects that allow creative freedom (4 points)C. Team projects with collaborative problem-solving (3 points)D. Fast-paced tasks with real-time results (5 points) Add your points to ﬁnd your Protein/Artist Type: 10-11 points: “Analytical Builder” You provide a stable, structured approach, akin to a structural protein. 12-14 points: “Innovative Catalyst” Like an enzyme, you bring creativity and drive new ideas forward. 15-18 points: “Bridge Builder” You connect ideas and people, similar to transport proteins. 19-25 points: “Rapid Responder” Adaptive and quick, you’re like a signaling protein, responding to changes efﬁciently. Need help making an interactive book of your own technical content? Yes! I want to connect with JEFS! 50 51

Page 51

JEFS Proteinber 2024 - November

Page 1

Page 2

Page 3

Page 4

Page 5

Page 6