Partial Orientation Retrieval of Proteins From X-ray Free-Electron-Laser induced Explosions for Single Particle Imaging

Partial Orientation Retrieval of Proteins From X-ray Free-Electron-Laser induced Explosions for Single Particle Imaging | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Partial Orientation Retrieval of Proteins From X-ray Free-Electron-Laser induced Explosions for Single Particle Imaging Tomas André, Alfredo Bellisario, Emilano Santis, Nicusor Timneanu, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7259620/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 23 Oct, 2025 Read the published version in Scientific Reports → Version 1 posted 11 You are reading this latest preprint version Abstract Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel approach to partially retrieve the relative orientation of proteins exposed to ultrafast X-ray pulses by analyzing the fragmentation patterns resulting from Coulomb explosions. We simulate these explosions for 85 proteins in the size range 100 – 4000 atoms using a hybrid Monte Carlo/Molecular Dynamics approach and capture the resulting ion ejection patterns on two virtual detectors. We exploit information from the explosion to infer orientations of proteins at the time of X-ray exposure. Our results demonstrate that partial orientation information can be extracted, particularly for larger proteins. We conclude that knowledge on ion data from X-ray laser induced explosions can directly provide the sample’s relative orientation, complementary to traditional orientation-retrieval algorithms based on diffraction patterns. Physical sciences/Optics and photonics Physical sciences/Physics Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 23 Oct, 2025 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 12 Sep, 2025 Reviews received at journal 08 Sep, 2025 Reviews received at journal 08 Sep, 2025 Reviewers agreed at journal 23 Aug, 2025 Reviewers agreed at journal 19 Aug, 2025 Reviewers agreed at journal 19 Aug, 2025 Reviewers invited by journal 19 Aug, 2025 Editor invited by journal 13 Aug, 2025 Editor assigned by journal 13 Aug, 2025 Submission checks completed at journal 12 Aug, 2025 First submitted to journal 31 Jul, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7259620","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":504589687,"identity":"41ff33f9-2424-4711-a129-d1b38dd57a1d","order_by":0,"name":"Tomas André","email":"","orcid":"","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Tomas","middleName":"","lastName":"André","suffix":""},{"id":504589688,"identity":"eeaa9e26-12ab-4043-a06b-af05d5ec5a78","order_by":1,"name":"Alfredo Bellisario","email":"","orcid":"","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Alfredo","middleName":"","lastName":"Bellisario","suffix":""},{"id":504589689,"identity":"bc8db8cd-9626-4fac-8475-e49d2c02d936","order_by":2,"name":"Emilano Santis","email":"","orcid":"","institution":"University of Rome Tor Vergata \u0026 INFN","correspondingAuthor":false,"prefix":"","firstName":"Emilano","middleName":"","lastName":"Santis","suffix":""},{"id":504589690,"identity":"7bb11f87-9a3b-4013-aad0-119071b8cc35","order_by":3,"name":"Nicusor Timneanu","email":"","orcid":"","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Nicusor","middleName":"","lastName":"Timneanu","suffix":""},{"id":504589691,"identity":"07e790ae-c38b-4694-9a03-278b8c8fa3e2","order_by":4,"name":"Carl Caleman","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFElEQVRIiWNgGAWjYHACxgNAQgbM/MAAZDMToQekhQeseQbJWph5wGwCgL/97IMDDDV2PPxih589tt1xJ3F+O/PjD4xthxnk2xuwapE4k25wgOFYMo/k7DRz49wzzxI3HGYzkwBpMTiD3UoDhjSGA4wNzDwGtxPMpHPbDiduYOZhYwBrkUjAroX/GUhLPY/97fRv0pZALfObeZghDpv/ALsWCbAth3kMpHPMpIEqE4FsBrDDGG5g977EDaAtCceO80jczimT7D1z2Bjsl4Rz6TwGZ7A7jL8/jfHBh5pqOf7Z6dskfu44LDu///DjDx/KrOXk27F7HwzgpjE2MDg2QEV4cKtHBkAt9sSpHAWjYBSMgpEEAFP0XifjcdOpAAAAAElFTkSuQmCC","orcid":"","institution":"Uppsala University","correspondingAuthor":true,"prefix":"","firstName":"Carl","middleName":"","lastName":"Caleman","suffix":""}],"badges":[],"createdAt":"2025-07-31 08:08:32","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7259620/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7259620/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41598-025-23827-w","type":"published","date":"2025-10-23T16:16:51+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":94489955,"identity":"b213e2be-69d1-4e6e-828c-d51b1c904191","added_by":"auto","created_at":"2025-10-27 17:06:40","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":811295,"visible":true,"origin":"","legend":"","description":"","filename":"andre2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7259620/v1_covered_8a660985-493a-45ba-849a-942ed831ed24.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Partial Orientation Retrieval of Proteins From X-ray Free-Electron-Laser induced Explosions for Single Particle Imaging","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7259620/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7259620/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. 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