Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2

Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2 | 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 Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2 Joost Holthuis, Sebastian Bieker, Michael Timme, Nils Woge, Dina Hassan, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4797057/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Feb, 2025 Read the published version in Communications Biology → Version 1 posted You are reading this latest preprint version Abstract Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) has far-reaching physiological implications. However, the structural basis of this interaction is unclear. Combining computer simulations with experiments in cells, we here show that complex assembly relies on intimate contacts between the N-terminal alpha-helix of HKI and a charged membrane-buried glutamate on the outer wall of VDAC1 and VDAC2. Protonation of this residue blocks complex formation in silico while acidification of the cytosol causes a reversable release of HKI from mitochondria. Membrane insertion of HKI occurs adjacent to the bilayer-facing glutamate where a pair of polar channel residues mediates a marked thinning of the cytoplasmic leaflet. Disrupting the membrane thinning capacity of VDAC1 dramatically impairs its ability to bind HKI in silico and in cells. Our data reveal key topological and mechanistic insights into HKI-VDAC complex assembly that may benefit the development of therapeutics to counter pathogenic imbalances in this process. Biological sciences/Biophysics/Computational biophysics Biological sciences/Biochemistry/Ion channels/Porins Biological sciences/Computational biology and bioinformatics/Computational models Full Text Additional Declarations There is NO Competing Interest. Supplementary Files VDAC1HKIinteractionmoviefinal.mp4 Movie S1 | MD simulation of complex formation between HKI-N and VDAC1 VDAC2HKIinteractionmoviefinal.mp4 Movie S2 | MD simulation of complex formation between HKI-N and VDAC2 BiekerTimmeSupplInfo220724.pdf Cite Share Download PDF Status: Published Journal Publication published 10 Feb, 2025 Read the published version in Communications Biology → Version 1 posted 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. 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-4797057","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":336342184,"identity":"f061d270-a7aa-427e-a6ea-c8a1c06c1699","order_by":0,"name":"Joost Holthuis","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAs0lEQVRIiWNgGAWjYBACAwbmBmYGBgkGfjCXjSgtjI3NIC2SDSRqATIOEKvFnL2x/XFhm4W98Y3kwx8YymwIa7HsOdjYPLNNInHbjbQ0CYZzaUQ47EZiYzNvm0SC2Y0cMwbGtsPEa7E3npFj/IGx7T/xWhg3SOQYSDC2HSBCy5mDjbN5zkkkzjjzLE0i4VwyEVqONx/4zFNWZ8/fDgyxD2V2hLWgggRSNYyCUTAKRsEowA4AW185U9339a4AAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0001-8912-1586","institution":"University of Osnabrueck","correspondingAuthor":true,"prefix":"","firstName":"Joost","middleName":"","lastName":"Holthuis","suffix":""},{"id":336342185,"identity":"787bad41-ee66-4a84-b0f8-3b1ba503f88b","order_by":1,"name":"Sebastian Bieker","email":"","orcid":"","institution":"University of Osnabrueck","correspondingAuthor":false,"prefix":"","firstName":"Sebastian","middleName":"","lastName":"Bieker","suffix":""},{"id":336342186,"identity":"9cbc041e-ea20-4b69-814d-44234907dda1","order_by":2,"name":"Michael Timme","email":"","orcid":"","institution":"University of Osnabrueck","correspondingAuthor":false,"prefix":"","firstName":"Michael","middleName":"","lastName":"Timme","suffix":""},{"id":336342187,"identity":"ed5f755a-2022-40cf-bd27-d6b6cd5fe8fa","order_by":3,"name":"Nils Woge","email":"","orcid":"","institution":"University of Osnabrueck","correspondingAuthor":false,"prefix":"","firstName":"Nils","middleName":"","lastName":"Woge","suffix":""},{"id":336342188,"identity":"0077680b-720d-4638-8fdc-ee85d6192828","order_by":4,"name":"Dina Hassan","email":"","orcid":"","institution":"Ain Shams University","correspondingAuthor":false,"prefix":"","firstName":"Dina","middleName":"","lastName":"Hassan","suffix":""},{"id":336342189,"identity":"52df370c-6a44-4056-ba24-ae14af46b53f","order_by":5,"name":"Chelsea Brown","email":"","orcid":"https://orcid.org/0000-0003-2006-5015","institution":"University of Groningen","correspondingAuthor":false,"prefix":"","firstName":"Chelsea","middleName":"","lastName":"Brown","suffix":""},{"id":336342190,"identity":"61993b53-4833-40b5-baff-701d19db010b","order_by":6,"name":"Siewert Marrink","email":"","orcid":"https://orcid.org/0000-0001-8423-5277","institution":"University of Groningen","correspondingAuthor":false,"prefix":"","firstName":"Siewert","middleName":"","lastName":"Marrink","suffix":""},{"id":336342191,"identity":"86941225-eb24-42e1-89e5-5a1a877e1c1a","order_by":7,"name":"Manuel Melo","email":"","orcid":"https://orcid.org/0000-0001-6567-0513","institution":"Universidade Nova de Lisboa","correspondingAuthor":false,"prefix":"","firstName":"Manuel","middleName":"","lastName":"Melo","suffix":""}],"badges":[],"createdAt":"2024-07-24 17:10:18","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4797057/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4797057/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s42003-025-07551-9","type":"published","date":"2025-02-10T05:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":75984552,"identity":"525c6a16-bd33-4a7c-ad0c-611d6ffcb5b3","added_by":"auto","created_at":"2025-02-11 08:09:10","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":8830505,"visible":true,"origin":"","legend":"","description":"","filename":"BiekerTimmeMS220724.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4797057/v1_covered_dfcf8a32-37a4-49eb-9fa2-e34e5c8aaf4a.pdf"},{"id":64880317,"identity":"4f2fd563-b199-409d-89e5-e7c4dfeba608","added_by":"auto","created_at":"2024-09-20 03:07:20","extension":"mp4","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":11922459,"visible":true,"origin":"","legend":"Movie S1 | MD simulation of complex formation between HKI-N and VDAC1","description":"","filename":"VDAC1HKIinteractionmoviefinal.mp4","url":"https://assets-eu.researchsquare.com/files/rs-4797057/v1/d9aebb24b74aa862af055580.mp4"},{"id":64880318,"identity":"6cf47d97-1774-4852-991b-0656c5d40a25","added_by":"auto","created_at":"2024-09-20 03:07:20","extension":"mp4","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":26580863,"visible":true,"origin":"","legend":"\u003cp\u003eMovie S2 | MD simulation of complex formation between HKI-N and VDAC2\u003c/p\u003e","description":"","filename":"VDAC2HKIinteractionmoviefinal.mp4","url":"https://assets-eu.researchsquare.com/files/rs-4797057/v1/85233beaedecfc146ea2f50e.mp4"},{"id":64880316,"identity":"3c44a409-016f-4e24-8efa-511e98e99cbd","added_by":"auto","created_at":"2024-09-20 03:07:20","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":10279377,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cbr\u003e\u003c/p\u003e","description":"","filename":"BiekerTimmeSupplInfo220724.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4797057/v1/572825f97087e0d8d9409900.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2","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":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-4797057/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4797057/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) has far-reaching physiological implications. However, the structural basis of this interaction is unclear. Combining computer simulations with experiments in cells, we here show that complex assembly relies on intimate contacts between the N-terminal alpha-helix of HKI and a charged membrane-buried glutamate on the outer wall of VDAC1 and VDAC2. Protonation of this residue blocks complex formation in silico while acidification of the cytosol causes a reversable release of HKI from mitochondria. Membrane insertion of HKI occurs adjacent to the bilayer-facing glutamate where a pair of polar channel residues mediates a marked thinning of the cytoplasmic leaflet. Disrupting the membrane thinning capacity of VDAC1 dramatically impairs its ability to bind HKI in silico and in cells. Our data reveal key topological and mechanistic insights into HKI-VDAC complex assembly that may benefit the development of therapeutics to counter pathogenic imbalances in this process.","manuscriptTitle":"Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-09-20 03:07:15","doi":"10.21203/rs.3.rs-4797057/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"communications-biology","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"commsbio","sideBox":"Learn more about [Communications Biology](http://www.nature.com/commsbio/)","snPcode":"","submissionUrl":"","title":"Communications Biology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Communications Series","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"8292d7f5-a97f-463e-9f79-e34402592ad6","owner":[],"postedDate":"September 20th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":35624740,"name":"Biological sciences/Biophysics/Computational biophysics"},{"id":35624741,"name":"Biological sciences/Biochemistry/Ion channels/Porins"},{"id":35624742,"name":"Biological sciences/Computational biology and bioinformatics/Computational models"}],"tags":[],"updatedAt":"2025-02-11T08:08:57+00:00","versionOfRecord":{"articleIdentity":"rs-4797057","link":"https://doi.org/10.1038/s42003-025-07551-9","journal":{"identity":"communications-biology","isVorOnly":false,"title":"Communications Biology"},"publishedOn":"2025-02-10 05:00:00","publishedOnDateReadable":"February 10th, 2025"},"versionCreatedAt":"2024-09-20 03:07:15","video":"","vorDoi":"10.1038/s42003-025-07551-9","vorDoiUrl":"https://doi.org/10.1038/s42003-025-07551-9","workflowStages":[]},"version":"v1","identity":"rs-4797057","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4797057","identity":"rs-4797057","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}