How Colorful Ribbon Diagrams Became the Face of Proteins

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Article</title><path fill="currentColor" d="M2.1 0h45.8v50L25.5 37.5 2.1 50V0z"></path></svg> <div class='h6t uppercase kern ml1 mv0 theme__text'> Read Later </div> </button> <div class='q-tooltip hidden force-mobile-placement w-32 ml-n16 -top-10'> <div class='q-tooltip-content'> <div class='q-tooltip-arrow -bottom-3'></div> <div class='q-tooltip-inner py-1 pl-1' role='tooltip'> <div class='h6t relative z1 uppercase kern--w mx025'> <span class='small no-wrap'>Read Later</span> </div> </div> </div> </div> </div> </li> </ul> <div class='nav__local__progress absolute fit-b fit-l fit-r z1 theme__accent'> <span class='block' style='transform: translateX(-100%);' data-role='content-progress-bar'></span> </div> </div> </div> <div id='postBody' class='theme__background-background theme__text'> <section class='post__title__wrapper relative '> <section class='outer fill-h relative outer--content '> <div class='mha container--s'> <div class='header-spacer'></div> <div class='post__title pv1 scale1 mha'> <div class='scale0'> <div class='mb1 pb025 mt0 h6t post__title__kicker '> <a class="kicker theme__accent theme__text-hover uppercase" href="/tag/molecular-biology/">molecular biology</a> </div> <h1 class='post__title__title mv025 noe theme__text' >How Colorful Ribbon Diagrams Became the Face of Proteins</h1> <div class='post__title__author-date h5 mt1'> <div class='byline relative flex flex-items-start merriweather mv025 mr1 gray3 h6t theme__text-hover'> <em class='byline__by gray4 mr075'>By </em> <a href='https://www.quantamagazine.org/authors/yasemin-saplakoglu/'> <span class='byline__author uppercase kern light small'>Yasemin Saplakoglu</span> </a> </div> <p class="h6 mv1 pv025 o6"><em>August 23, 2024</em></p> </div> <div class='post__title__meta flex flex-wrap flex-items-start'> <div class='post__title__excerpt wysiwyg p italic mb1 mt025 pr2 o4 theme__text ' > Proteins are often visualized as cascades of curled ribbons and twisted strings, which both reveal and conceal the mess of atoms that make up these impossibly complex molecules. </div> <div class='post__title__actions h5 mt025 flex-auto flex flex-items-center'> <div class='comments-button mr05 flex flex-items-center theme__accent-hover h5 theme__accent' data-name='comment-bubble' > <a href='#comments' class='flex flex-items-center pangram'> <svg viewbox='0 0 50 50' enable-background='new 0 0 50 50' xmlns='http://www.w3.org/2000/svg' class=''><title>Comment</title><path fill='currentColor' d='M9.4 4.2h31.2c8.6 0 9.4 7 9.4 15.6s-.7 15.6-9.4 15.6h-2.2l-.9 9.4-18.8-9.4H9.4c-8.6 0-9.4-7-9.4-15.6S.7 4.2 9.4 4.2z'></path></svg> <div> <span class='comments-button__count ml075 small mbold disqus-comment-count' data-disqus-identifier='140004 https://www.quantamagazine.org/?p=140004'></span> </div> </a> </div> <span class='o-divider mh075 relative'></span> <div class='relative'> <button class='bookmark-button mh05 flex flex-items-center theme__accent-hover ' data-toggle-hover='tooltip' data-id='140004' 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src="https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-scaled.webp" class="mb-6 w-full s:mb-4" alt="Hand-drawn curls of ribbon and pointed arrows represent a protein’s structure." decoding="async" fetchpriority="high" srcset="https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-scaled.webp 2560w, https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-1720x968.webp 1720w, https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-520x293.webp 520w, https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-768x432.webp 768w, https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-1536x864.webp 1536w, https://www.quantamagazine.org/wp-content/uploads/2024/08/RibbonModel-crJaneRichardson-Lede-2048x1152.webp 2048w" sizes="(max-width: 2560px) 100vw, 2560px" /> </div> </div> <figcaption class='block my-0 mx-auto w-full'> <section class='py-0 px-12 s:p-0 m:px-16'> <div class='w-full my-0 mx-auto flex flex-col s:mx-5 s:w-full-minus-25 s:max-w-mod-inline m:max-w-mod-inline l:flex-row l:max-w-mod-large justify-end s:mb-4'> <div class='caption wysiwyg h5 theme__anchors--solid fill-h w-auto l:w-140'> <p>Jane Richardson’s ribbon diagrams abstract proteins’ atomic structures into beautiful, clear illustrations. In this pencil drawing of triose phosphate isomerase, alpha helices and beta strands are represented by blue spirals and green arrows, respectively.</p> </div> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h text-left w-auto before:block l:before:hidden l:w-half-minus-17 l:text-right l:pl-24'> <p>Jane Richardson</p> </div> </div> </section> </figcaption> </figure> <div class='acf-content scale1 mt2'> <h2 class='screen-reader-text'>Introduction</h2> <div class='post__wrapper scale0 show-dropcap'> <div class='mha container--m'> <div class='post__content relative flex flex-items-start flex-justify-between'> <aside class='post__sidebar hide flex flex-justify-center '> <div class='post__sidebar__content'> <div class='post__sidebar__content__inner'> <div class='align-c mb075'> <div class='sidebar__author'> <a class='theme__accent-hover transition--color ' href='https://www.quantamagazine.org/authors/yasemin-saplakoglu/'> <div class='sidebar__author__avatar mha mb1'> <div class='image mx0 relative image--circle '> <div class='image__inner absolute fit-x is-loaded'> <img width="1500" height="1500" src="https://www.quantamagazine.org/wp-content/uploads/2022/02/YSaplakoglu_1.jpg" class="absolute fit-x fill-h fill-v mxa" alt="Yasemin Saplakoglu" decoding="async" srcset="https://www.quantamagazine.org/wp-content/uploads/2022/02/YSaplakoglu_1.jpg 1500w, https://www.quantamagazine.org/wp-content/uploads/2022/02/YSaplakoglu_1-520x520.jpg 520w, https://www.quantamagazine.org/wp-content/uploads/2022/02/YSaplakoglu_1-768x768.jpg 768w, https://www.quantamagazine.org/wp-content/uploads/2022/02/YSaplakoglu_1-160x160.jpg 160w" sizes="(max-width: 1500px) 100vw, 1500px" /> </div> </div> </div> <div class='h3t mv05'> <span class='screen-reader-text'>By </span>Yasemin Saplakoglu </div> <p class="o8 theme__text h5 mt05 mb1"><em>Staff Writer</em></p> </a> </div> <hr class='mb075 o1'> <p class="h6 mv1 pv025 o6"><em>August 23, 2024</em></p> </div> <form 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class='post__content wysiwyg p theme__anchors--underline '> <p><a href="https://www.biochem.duke.edu/profile/jane-shelby-richardson">Jane Richardson</a> never considered herself an artist. Then, in the late 1970s, the structural biologist found herself in need of some colored pencils, pastels and sketching paper.</p> <p>Richardson, a professor of biochemistry at Duke University, studied proteins, the biomolecules that underpin all the workings of life. At the time, structural biologists were getting better at creating 3D models of proteins’ minuscule atomic structures; she and her husband Dave, with whom she shared a lab, had determined two of the field’s first 20 known protein structures. But the scientists struggled to convey the information to one another. The field had no standardized way to compare protein shapes. In scientific papers, the complex molecules were portrayed without uniformity, as if each researcher had invented their own way of illustrating them.</p> <p>So Richardson took up the challenge of designing a new kind of scientific illustration — just for proteins. She studied how to represent three-dimensional shapes in two dimensions, including the artwork of <a href="https://www.escherinhetpaleis.nl/escher-today/rind/?lang=en">M.C. Escher</a>. She spoke with artists. She thought back to a class she had taken on illusions. She examined a belt as she twisted it left and right.</p> <p>Then she picked up her pencils and began sketching. “I’m not an artist; I can’t draw anything else,” she said in a recent interview with <em>Quanta</em>. It was “a lot of draw and erase, draw and erase, draw and erase.” After a year of trial and error, she homed in on elegant sheets and looping ribbons to represent atomic structures. These drawings, which first appeared in the journal <a href="https://doi.org/10.1016/S0065-3233(08)60520-3"><em>Advances in Protein Chemistry</em></a> in 1981, became known as ribbon diagrams.</p> <p>Richardson’s drawing style was quickly adopted. Structural biologists appreciated how well the diagrams conveyed the folds of a protein’s molecular backbone and how they allowed researchers to compare different proteins using the same visual language.</p> </div> </div> </div> </section> <aside class='post__sidebar hide flex flex-justify-center theme__anchors--solid '> <div class='post__sidebar__content'> <div class='post__sidebar__content__inner'> <div class='h3t mt0'> Share this article </div> <div data-id='social-links'> <div class='social-links social-links--share flex flex-justify-between'> <a href='http://www.facebook.com/sharer.php?u=https://www.quantamagazine.org/how-colorful-ribbon-diagrams-became-the-face-of-proteins-20240823/' class='social-links__link flex flex-items-center relative' target="_blank" > <div class='icon-button inline-block relative pointer theme__accent-hover-child'> <div class='absolute fit-x mxa o2 hover--opaque theme__text'> </div> <svg class="absolute fit-x mxa theme__text" viewbox="0 0 50 50" 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items-center justify-center flex-col max-w-img-regular py-0 px-0 l:px-0 '> <div class='w-full flex justify-center max-w-mod-regular m:max-w-unset image--module s:flex-col s:m-auto'> <div class='w-auto mr-2 last:mr-0 s:m-0 s:flex s:flex-col flex-1'> <img width="2560" height="1588" src="https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-scaled.webp" class="mb-6 w-full s:mb-4" alt="Jane Richardson poses with a model protein and one of her sketches." decoding="async" srcset="https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-scaled.webp 2560w, https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-1720x1067.webp 1720w, https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-520x323.webp 520w, https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-768x476.webp 768w, https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-1536x953.webp 1536w, https://www.quantamagazine.org/wp-content/uploads/2024/08/JaneRichardson-crJaredLazarus_DukeUniversity-2048x1270.webp 2048w" sizes="(max-width: 2560px) 100vw, 2560px" /> </div> </div> <figcaption class='block my-0 mx-auto w-full l:max-w-mod-inline'> <section class='p-0 m:py-0 m:px-16'> <div class='w-full my-0 mx-auto flex flex-col s:mx-5 s:w-full-minus-25 s:max-w-mod-inline m:max-w-mod-inline l:m-0 l:p-0 max-w-mod-inline s:mb-4'> <div class='caption wysiwyg h5 theme__anchors--solid fill-h '> <p>Jane Richardson, a structural biologist at Duke University, spent the early 1980s studying art. Her ribbon diagrams, which represent protein molecules, show proteins’ elegance and complexity without being overwhelming, she said.</p> </div> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h '> <p>Jared Lazarus/Duke University</p> </div> </div> </section> </figcaption> </figure> <div class='acf-content scale1 mt2'> <section class='outer mha js-router-anchors outer--content'> <div class='flex-auto mha container--xs '> <div class='post__content__section wysiwyg p theme__anchors--underline' data-role='selectable'> <div class='post__content wysiwyg p theme__anchors--underline '> <p>“The ribbon-diagram representation was invaluable,” said <a href="https://www.nki.nl/research/research-groups/anastassis-tassos-perrakis/">Anastassis Perrakis</a>, a structural biologist at the Netherlands Cancer Institute and Utrecht University. It helped scientists communicate, teach and classify protein structure, and it captured the imaginations of scientists and nonscientists alike. It was able to “convince people how elegant [proteins] are and to see the complexity, without it being overwhelming,” Richardson said.</p> <p>Today, ribbon diagrams are the ubiquitous face of proteins in scientific articles, textbooks and magazines, known for their particular combination of clarity and beauty. “It’s hard to imagine a scientific representation of data that is more meaningful,” said <a href="https://engineering.virginia.edu/faculty/philip-e-bourne">Philip Bourne</a>, dean of the University of Virginia School of Data Science.</p> <p>The diagrams have been so successful that it can be hard to remember that our cells are not, in fact, filled with colorful ribbons and broad arrows.</p> <h2><strong>The Face of Proteins</strong></h2> <aside class="post__aside mb2 relative post__aside--right"><figure class='mb2 mt1 image--shortcode s:mt-0'> <div class='relative image mx0'> <img width="2560" height="2319" src="https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-scaled.webp" class="block fit-x fill-h fill-v is-loaded mxa" alt="A sketch of a protein is smudged with graphite and sketched lines." decoding="async" srcset="https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-scaled.webp 2560w, https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-1720x1558.webp 1720w, https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-520x471.webp 520w, https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-768x696.webp 768w, https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-1536x1391.webp 1536w, https://www.quantamagazine.org/wp-content/uploads/2024/08/StaphnucleaseRibbonPencilSketch-coJaneRichardson-2048x1855.webp 2048w" sizes="(max-width: 2560px) 100vw, 2560px" /> </div> <figcaption class='image__meta mt1'> <div class='caption wysiwyg h5 theme__anchors--solid fill-h post__aside__caption post__aside__caption--shortcode'> <p>The pencil smudges on Richardson’s original sketch of staphylococcal nuclease reveal her process: “A lot of draw and erase, draw and erase, draw and erase,” she said.</p> </div> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h post__aside__attribution'> <p>Courtesy of Jane Richardson</p> </div> </figcaption> </figure> </aside> <p>Day in and day out, our cells are hard at work constructing different kinds of proteins. Proteins are made of strings of molecules called amino acids, and each amino acid has one or more side chains made up of several atoms “coming off it like a lollipop,” said <a href="https://www.ebi.ac.uk/people/person/janet-thornton/">Janet Thornton</a>, a computational biologist who retired from the European Molecular Biology Laboratory last year. The amino acid backbone innately folds into a three-dimensional shape, known as a protein structure, which determines which other molecules the protein can bind to and, therefore, its function in a cell.</p> <p>Once a structural biologist completed what used to be a years-long process of reconstructing a protein’s 3D structure, they faced a new problem: how to communicate that structure to other scientists. In truth, it’s impossibly difficult to represent a protein’s realistic structure. Proteins are minuscule, on the order of nanometers, and can contain hundreds of thousands of atoms. “If those atoms are all drawn and then joined together, it becomes very difficult to see,” Thornton said.</p> <p>Richardson’s innovation was a reproducible method of representing the folds of a protein’s amino acid backbone without getting bogged down in the details of specific atomic arrangements. She relied on proteins’ tendency to fold into two energetically favorable shapes: coils called alpha helices and flat shapes called beta strands, which can line up into so-called beta sheets. Then there are loops, which connect alpha helices to beta strands like corner pieces in a puzzle.</p> <p>There are other folding structures, and “people have come up with lots of names” for them, Perrakis said. “But at the end of the day, the ones that matter are the helices and the sheets.”</p> </div> </div> </div> </section> </div> <figure class='leading-0 w-full my-0 mx-auto flex items-center justify-center flex-col max-w-img-inline py-0 px-16 s:px-0 l:px-16 '> <div class='w-full flex justify-center max-w-mod-inline image--module s:flex-col s:m-auto'> <div class='w-auto mr-2 last:mr-0 s:m-0 s:flex s:flex-col flex-1 s:px-5'> <img src="https://www.quantamagazine.org/wp-content/uploads/2024/08/Protein_Ribbons-Fig1-crMarkBelan-Mobile-v2-02.svg" class="w-full m:hidden l:hidden mb-6 w-full s:mb-4" alt="" decoding="async" /><img src="https://www.quantamagazine.org/wp-content/uploads/2024/08/Protein_Ribbons-Fig1-crMarkBelan-Desktop-v2-01.svg" class="mb-6 w-full s:mb-4 s:hidden" alt="" decoding="async" /> </div> </div> <figcaption class='block my-0 mx-auto w-full'> <section class='s:pt-0 s:px-5 s:pb-6 s:w-full-minus-25'> <div class='w-full my-0 mx-auto max-w-mod-inline s:mt-4 s:mb-4'> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h '> <p>Mark Belan for <em>Quanta Magazine</em></p> </div> </div> </section> </figcaption> </figure> <div class='acf-content scale1 mt2'> <section class='outer mha js-router-anchors outer--content'> <div class='flex-auto mha container--xs '> <div class='post__content__section wysiwyg p theme__anchors--underline' data-role='selectable'> <div class='post__content wysiwyg p theme__anchors--underline '> <p>In her year of sketching, Richardson came up with simple ways to illustrate these basic shapes. Alpha helices are coils that look like the tails of decorative ribbons, curled with the edge of a pair of scissors. Beta strands are arrows that point in the direction in which the amino acid chain was built. And thin wires represent the loops and turns that connect the structures. “That allowed us to follow the chain round and to see these folds and visualize them in three dimensions,” Thornton said.</p> <p>Richardson’s drawings quickly caught on among biologists for the way they blend beauty with scientific accuracy. “They’re almost miraculous to me. I couldn’t begin to do it,” Thornton said. “People would write to Jane and say, ‘Will you do a drawing of my structure?’ … It was obvious that nobody else could draw such beautiful diagrams.”</p> <p>But Richardson couldn’t spend all her time drawing proteins. So biologists turned to computers for artistic help. About a decade after the diagrams’ 1981 debut, researchers developed algorithms to generate ribbon diagrams on computers. Richardson often collaborates with computer scientists working to bring new features to the diagrams. And they’re still used today: As <a href="https://www.quantamagazine.org/how-ai-revolutionized-protein-science-but-didnt-end-it-20240626/">artificial intelligence</a> has seeped into the field of protein science, ribbon diagrams are outputs from algorithms such as Google’s AlphaFold2.</p> </div> </div> </div> </section> </div> <figure class='leading-0 w-full my-0 mx-auto flex items-center justify-center flex-col max-w-img-large py-0 px-0 l:px-0 '> <div class='w-full flex justify-center max-w-mod-large m:max-w-unset image--module s:flex-col s:m-auto'> <div class='w-auto mr-2 last:mr-0 s:m-0 s:flex s:flex-col flex-1'> <img width="2560" height="702" src="https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-scaled.webp" class="mb-6 w-full s:mb-4" alt="A triptych of drawings of proteins, all drawn by hand with colored pencil and showing ribbons and arrows in Richardson’s style" decoding="async" srcset="https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-scaled.webp 2560w, https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-1720x471.webp 1720w, https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-520x143.webp 520w, https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-768x210.webp 768w, https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-1536x421.webp 1536w, https://www.quantamagazine.org/wp-content/uploads/2024/08/ProteinRibbonDrawings-crJaneRichardson-Triptych-2048x561.webp 2048w" sizes="(max-width: 2560px) 100vw, 2560px" /> </div> </div> <figcaption class='block my-0 mx-auto w-full'> <section class='py-0 px-12 s:p-0 m:px-16'> <div class='w-full my-0 mx-auto flex flex-col s:mx-5 s:w-full-minus-25 s:max-w-mod-inline m:max-w-mod-inline l:flex-row l:max-w-mod-large justify-end s:mb-4'> <div class='caption wysiwyg h5 theme__anchors--solid fill-h w-auto l:w-140'> <p>Jane Richardson’s hand-drawn ribbon diagrams communicate protein structure consistently and elegantly. From left: para-hydroxybenzoate hydroxylase, catabolite activator protein, glycogen phosphorylase.</p> </div> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h text-left w-auto before:block l:before:hidden l:w-half-minus-17 l:text-right l:pl-24'> <p>Jane Richardson</p> </div> </div> </section> </figcaption> </figure> <div class='acf-content scale1 mt2'> <section class='outer mha js-router-anchors outer--content'> <div class='flex-auto mha container--xs '> <div class='post__content__section wysiwyg p theme__anchors--underline' data-role='selectable'> <div class='post__content wysiwyg p theme__anchors--underline '> <p>Richardson is glad she doesn’t have to personally draw the many protein structures that have now been decoded. “I don’t have the eyes for it anymore, or the time,” she said.</p> <h2><strong>Beyond Ribbons</strong></h2> <p>Richardson’s ribbon diagram has become so ubiquitous, it can be difficult to imagine proteins looking any other way. Bourne often reminds his students that proteins don’t actually look like that.</p> <p>“A protein is nothing like a ribbon,” he said. It’s much more dynamic, he added. Sure, proteins’ backbones fold up into structures like the coils and sheets that the ribbon diagrams represent. But researchers can’t actually see those structures when they image proteins.</p> </div> </div> </div> </section> </div> <figure class='leading-0 w-full my-0 mx-auto flex items-center justify-center flex-col max-w-img-regular py-0 px-0 l:px-0 '> <div class='w-full flex justify-center max-w-mod-regular m:max-w-unset image--module s:flex-col s:m-auto'> <div class='w-auto mr-2 last:mr-0 s:m-0 s:flex s:flex-col flex-1'> <img width="2560" height="855" src="https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-scaled.webp" class="mb-6 w-full s:mb-4" alt="Three protein model types. From left: Ribbon diagram, ball-and-stick, space-filling." decoding="async" srcset="https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-scaled.webp 2560w, https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-1720x574.webp 1720w, https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-520x174.webp 520w, https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-768x256.webp 768w, https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-1536x513.webp 1536w, https://www.quantamagazine.org/wp-content/uploads/2024/08/Ribbon_BallAndStick_SpaceFill-crProteinDataBank-Triptych-1-2048x684.webp 2048w" sizes="(max-width: 2560px) 100vw, 2560px" /> </div> </div> <figcaption class='block my-0 mx-auto w-full l:max-w-mod-inline'> <section class='p-0 m:py-0 m:px-16'> <div class='w-full my-0 mx-auto flex flex-col s:mx-5 s:w-full-minus-25 s:max-w-mod-inline m:max-w-mod-inline l:m-0 l:p-0 max-w-mod-inline s:mb-4'> <div class='caption wysiwyg h5 theme__anchors--solid fill-h '> <p>Different ways of modeling proteins convey different kinds of structural information. From left: Ribbon diagrams show the amino acid backbone. Ball-and-stick models place every atom exactly. Space-filling models reveal binding sites for other molecules.</p> </div> <div class='attribution theme__anchors--solid wysiwyg pangram h6 mb1 fill-h '> <p>Protein Data Bank</p> </div> </div> </section> </figcaption> </figure> <div class='acf-content scale1 mt2'> <section class='outer mha js-router-anchors outer--content'> <div class='flex-auto mha container--xs '> <div class='post__content__section wysiwyg p theme__anchors--underline' data-role='selectable'> <div class='post__content wysiwyg p theme__anchors--underline '> <p>“I like to think of them as soft silicone models,” Perrakis said. “You can squeeze them a bit or bend them.”</p> <p>As simplifications, ribbon diagrams have their limitations, of course. They can’t convey some structural elements, such as tunnels or pockets where other molecules might bind — information critical for understanding how proteins work and designing drugs to target them. They also don’t communicate structure well for larger proteins or complexes of multiple proteins.</p> <aside class="post__aside mb2 relative post__aside--right post__aside--medium hide-on-print"> <div class='card clearfix mv05 pv1 theme__anchors--none is-grid-variant is-shortcode border-grey-o25'> <div class='card__image mr1 mb1' data-toggle-hover='card'> <a href='https://www.quantamagazine.org/how-ai-revolutionized-protein-science-but-didnt-end-it-20240626/' class='relative'> <span class='screen-reader-text'>How AI Revolutionized Protein Science, but Didn’t End It</span> <div class='image mx0 relative image--standard'> <div class='image__inner absolute fit-x is-loaded'> <img width="521" height="293" src="https://www.quantamagazine.org/wp-content/uploads/2024/06/ProteinFolding-crFranPulido-Default.webp" class="absolute fit-x fill-h fill-v mxa" alt="" decoding="async" /> </div> </div> </a> </div> <div class='card__content '> <div class='mb1 pb025 mt0 h6t card__kicker'> <a class="kicker theme__accent theme__text-hover uppercase" href="/tag/molecular-biology/">molecular biology</a> </div> <a href='https://www.quantamagazine.org/how-ai-revolutionized-protein-science-but-didnt-end-it-20240626/' data-toggle-hover='card'> <h3 class='card__title noe mv0 theme__accent-hover transition--color h2t'> How AI Revolutionized Protein Science, but Didn’t End It </h3> </a> <div class='card__meta mb0 mt025 flex flex-items-center flex-wrap'> <div class='card-date h6 flex flex-items-center mv05'> <div class='uppercase mr1 kern small gray3'>June 26, 2024</div> <span class='o-divider o-divider--vertical mr1 relative'></span> </div> <div class='card__actions h6 flex flex-items-center mv05'> <div class='comments-button mr05 flex flex-items-center theme__accent-hover ' data-name='comment-bubble' > <a href='https://www.quantamagazine.org/how-ai-revolutionized-protein-science-but-didnt-end-it-20240626/#comments' class='flex flex-items-center pangram'> <svg viewbox='0 0 50 50' enable-background='new 0 0 50 50' xmlns='http://www.w3.org/2000/svg' class='o2'><title>Comment</title><path fill='currentColor' d='M9.4 4.2h31.2c8.6 0 9.4 7 9.4 15.6s-.7 15.6-9.4 15.6h-2.2l-.9 9.4-18.8-9.4H9.4c-8.6 0-9.4-7-9.4-15.6S.7 4.2 9.4 4.2z'></path></svg> </a> </div> <span class='o-divider mh075 relative'></span> <div class='relative'> <button class='bookmark-button mh05 flex flex-items-center theme__accent-hover ' data-toggle-hover='tooltip' data-id='138623' data-active-class='' aria-expanded='false'> <svg class="icon" viewbox="0 0 50 50" enable-background="new 0 0 50 50" xmlns="http://www.w3.org/2000/svg"><title>Save Article</title><path fill="currentColor" d="M2.1 0h45.8v50L25.5 37.5 2.1 50V0z"></path></svg> </button> <div class='q-tooltip hidden force-mobile-placement w-32 ml-n16 -top-10'> <div class='q-tooltip-content'> <div class='q-tooltip-arrow -bottom-3'></div> <div class='q-tooltip-inner py-1 pl-1' role='tooltip'> <div class='h6t relative z1 uppercase kern--w mx025'> <span class='small no-wrap'>Read Later</span> </div> </div> </div> </div> </div> </div> </div> <div class='card__excerpt h5 pangram o6 mb4 mt025'> </div> </div> </div> </aside> <p>“It gives you a three-dimensional view of the shape, but it also hides a lot of the features that we know to be true about proteins,” Bourne said. “So that then can narrow one’s thinking.” He called this “<a href="https://doi.org/10.1371/journal.pbio.3001901">the curse of the protein ribbon diagram</a>” in a 2022 essay.</p> <p>Another popular representation is the space-filling model, which shows how much room atoms take up and looks more like an actual protein. It can show proteins’ pockets and tunnels — but it can’t represent the protein architecture, such as helices and sheets. “It depends what you want to show,” Perrakis said. Many researchers look at different types together to glean all the important structural information. What a protein looks like, Richardson said, is how you choose to represent it.</p> <p>“That’s one of the freeing things about drawing proteins … It’s also scary,” she said. “It’s a little weird to me that everybody sees proteins the way I see them, or the way I saw them in 1980.”</p> <p>Her diagrams are a pretty good way to see them, she added. “But it’s not the only way, that’s for sure.”</p> <p><em><strong>Update:</strong> August 26, 2024</em><br /> <i>A figure of a protein loop in the graphic was removed while we investigate a potential correction.</i></p> </div> </div> </div> </section> </div> <div class='pv2'></div> <div class='post__footer'> <div class='mha container--m'> <div class='flex flex-wrap flex-items-stretch'> <div class='post__footer__col fill-h pv2 flex flex-items-center flex-justify-center'> <section class='outer'> <aside class='post__sidebar hide flex flex-justify-center post__sidebar--footer'> <div class='post__sidebar__content'> <div 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How Colorful Ribbon Diagrams Became the Face of Proteins | Quanta Magazine