Directional Proton Conductance in Bacteriorhodopsin Is Driven by 2 Concentration Gradient, Not Affinity Gradient

Directional Proton Conductance in Bacteriorhodopsin Is Driven by 2 Concentration Gradient, Not Affinity Gradient | 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 Biological Sciences - Article Directional Proton Conductance in Bacteriorhodopsin Is Driven by 2 Concentration Gradient, Not Affinity Gradient Zhong Ren This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-944138/v3 This work is licensed under a CC BY 4.0 License Status: Posted Version 3 posted You are reading this latest preprint version Show more versions Abstract It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable. General Biochemistry proton pump retinal serial crystallography singular value decomposition X-ray free electron laser Full Text Additional Declarations Yes there is potential Competing Interest. ZR is the founder of Renz Research, Inc. that currently holds the copyright of the computer software dynamiX. Supplementary Files SupplementaryFile.docx Cite Share Download PDF Status: Posted Version 3 posted You are reading this latest preprint version Show more versions 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. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-944138","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":56778681,"identity":"b0b2a450-a528-464a-b99a-501d5c443c2a","order_by":0,"name":"Zhong Ren","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAmElEQVRIiWNgGAWjYLCCDwwSIMqAeB2MM0jWwswDoYnUIj/78LHHtm0W8gzszdskiHNUX1q6cW6bhGEDz7Ey4rQw8/CYSQO1JDBI5JgRp4WNh/+btCVIi/wbIrXw8PCwSTOCbeEhUosED5uZZM85CcM2nrRiC6K0yPcwP5P4UVYnz89+eOMNorTAARtpykfBKBgFo2AU4AUAx68emyZy+b8AAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0001-7098-3127","institution":"University of Illinois at Chicago","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Zhong","middleName":"","lastName":"Ren","suffix":""}],"badges":[],"createdAt":"2021-09-27 18:55:39","currentVersionCode":3,"declarations":"","doi":"10.21203/rs.3.rs-944138/v3","doiUrl":"https://doi.org/10.21203/rs.3.rs-944138/v3","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":15159836,"identity":"d1b51cc6-219e-4feb-9c7b-018049fb4fc2","added_by":"auto","created_at":"2021-11-02 19:08:59","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":11191781,"visible":true,"origin":"","legend":"","description":"","filename":"protonPump.pdf","url":"https://assets-eu.researchsquare.com/files/rs-944138/v3_covered.pdf"},{"id":15159835,"identity":"e56f08eb-533f-417d-8a9f-3e1259181661","added_by":"auto","created_at":"2021-11-02 19:08:40","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":68188340,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFile.docx","url":"https://assets-eu.researchsquare.com/files/rs-944138/v3/727c88f6c56082f7668fd7f2.docx"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nZR is the founder of Renz Research, Inc. that currently holds the copyright of the computer software dynamiX.","formattedTitle":"\u003cp\u003eDirectional Proton Conductance in Bacteriorhodopsin Is Driven by 2 Concentration Gradient, Not Affinity Gradient\u003c/p\u003e","fulltext":[{"header":"Full Text","content":"This preprint is available for \u003ca href='/article/rs-944138/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e."}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"proton pump, retinal, serial crystallography, singular value decomposition, X-ray free electron laser","lastPublishedDoi":"10.21203/rs.3.rs-944138/v3","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-944138/v3","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"It is widely spread that microorganisms can harvest energy from sun light to establish electrochemical potential across cell membrane by pumping protons outward. Light driven proton pumping against a transmembrane gradient entails exquisite electronic and conformational reconfiguration at fs to ms time scales. However, transient molecular events along the photocycle of bacteriorhodopsin are difficult to comprehend from noisy electron density maps obtained from multiple experiments when the intermediate populations coexist and evolve as a function of 13 decades of time. Here I report an in-depth meta-analysis of the recent time-resolved datasets collected by several consortiums. This analysis deconvolutes the observed mixtures, thus substantially improves the quality of the electron density maps, and provides a clear visualization of the isolated intermediates from I to M. The primary photoproducts revealed here suggest a proton transfer uphill against 15 pH units is accomplished by the same physics that governs the tablecloth trick. While the Schiff base is displaced at the beginning of the photoisomerization within ~30 fs, the proton stays due to its inertia. This affinity-independent early deprotonation builds up a steep proton concentration gradient that drives the directional proton conductance toward the extracellular medium. This mechanism fundamentally deviates from the widely adopted assumption based on equilibrium processes driven by light-induced changes of proton affinities. 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