Vibrational Contribution to the Sub-Terahertz Dielectric Response of Kinesin and Its Hydration Shell

Vibrational Contribution to the Sub-Terahertz Dielectric Response of Kinesin and Its Hydration Shell | 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 Vibrational Contribution to the Sub-Terahertz Dielectric Response of Kinesin and Its Hydration Shell Saurabh K. Pandey, Michal Cifra This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8135880/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Mar, 2026 Read the published version in Scientific Reports → Version 1 posted 10 You are reading this latest preprint version Abstract The ability of proteins to change conformation underlies both their biological function and their use in bio-nanoelectromechanical systems as molecular machines and transducers. These conformational transitions are suggested to be facilitated by global physical vibrational modes in the sub-THz frequency range. However, direct experimental detection of these modes is difficult to achieve due to their weak spectroscopic signatures and strong water background. Thus, computational approaches fill knowledge gaps, help steer and interpret experiments. In this study, we used molecular dynamics simulations combined with normal mode analysis to explore the vibrational modes of an all-atom model of the globular motor domain of protein kinesin. We explored the coupling of these modes, via the corresponding modal dipole variation, to the electromagnetic field and predicted the resulting dielectric properties and absorption spectra in absolute units. We found that the inclusion of a water layer in the system leads to a blue-shift and reduced amplitude in the absorption spectra in the low-frequency (0-400 GHz) region. Further decomposition of absorption spectra into protein and water components showed non-additive behavior, arising from partially antiparallel dipole variation vectors of the protein and water fractions, which reduced the overall absorption. Comparison showed that the tubulin heterodimer has stronger absolute sub-THz absorption, consistent with its larger molecular weight and, hence, higher number of atoms and degrees of freedom than kinesin. Together, these results provide a mechanistic understanding of hydration effects on vibrational modes and dielectric properties of proteins. In a greater context, the results have implications for methods in bio-nanoelectromechanical systems for protein dynamics and conformation sensing and in biomedicine and bioelectromagnetics for electromagnetic field-mediated functional modification of proteins. Biological sciences/Biophysics Physical sciences/Physics Full Text Additional Declarations No competing interests reported. Supplementary Files A2304S1.pdf A2304S2.pdf Cite Share Download PDF Status: Published Journal Publication published 01 Mar, 2026 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 01 Jan, 2026 Reviews received at journal 31 Dec, 2025 Reviewers agreed at journal 22 Dec, 2025 Reviews received at journal 29 Nov, 2025 Reviewers agreed at journal 28 Nov, 2025 Reviewers agreed at journal 28 Nov, 2025 Reviewers invited by journal 28 Nov, 2025 Editor assigned by journal 19 Nov, 2025 Submission checks completed at journal 19 Nov, 2025 First submitted to journal 17 Nov, 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. 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-8135880","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":548606599,"identity":"c06ca691-98ff-45de-81ff-aa88253957ca","order_by":0,"name":"Saurabh K. 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These conformational transitions are suggested to be facilitated by global physical vibrational modes in the sub-THz frequency range. However, direct experimental detection of these modes is difficult to achieve due to their weak spectroscopic signatures and strong water background. Thus, computational approaches fill knowledge gaps, help steer and interpret experiments.\nIn this study, we used molecular dynamics simulations combined with normal mode analysis to explore the vibrational modes of an all-atom model of the globular motor domain of protein kinesin. We explored the coupling of these modes, via the corresponding modal dipole variation, to the electromagnetic field and predicted the resulting dielectric properties and absorption spectra in absolute units. We found that the inclusion of a water layer in the system leads to a blue-shift and reduced amplitude in the absorption spectra in the low-frequency (0-400 GHz) region. Further decomposition of absorption spectra into protein and water components showed non-additive behavior, arising from partially antiparallel dipole variation vectors of the protein and water fractions, which reduced the overall absorption. Comparison showed that the tubulin heterodimer has stronger absolute sub-THz absorption, consistent with its larger molecular weight and, hence, higher number of atoms and degrees of freedom than kinesin.\nTogether, these results provide a mechanistic understanding of hydration effects on vibrational modes and dielectric properties of proteins. In a greater context, the results have implications for methods in bio-nanoelectromechanical systems for protein dynamics and conformation sensing and in biomedicine and bioelectromagnetics for electromagnetic field-mediated functional modification of proteins.","manuscriptTitle":"Vibrational Contribution to the Sub-Terahertz Dielectric Response of Kinesin and Its Hydration Shell","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-25 02:57:33","doi":"10.21203/rs.3.rs-8135880/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-01-01T05:40:18+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-31T09:57:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"289376238904268123588315024329521668136","date":"2025-12-22T12:05:12+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-29T17:29:58+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"48807919076841265788968323430686863705","date":"2025-11-28T14:15:08+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"217317929767909363156778391925200808230","date":"2025-11-28T12:17:46+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-11-28T10:21:51+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-19T11:16:14+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-11-19T11:15:53+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-11-17T13:12:10+00:00","index":"","fulltext":""}],"status":"published","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}}],"origin":"","ownerIdentity":"942c2993-0fc7-41ca-9821-0c6475c90217","owner":[],"postedDate":"November 25th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":58372592,"name":"Biological sciences/Biophysics"},{"id":58372593,"name":"Physical sciences/Physics"}],"tags":[],"updatedAt":"2026-03-02T16:12:48+00:00","versionOfRecord":{"articleIdentity":"rs-8135880","link":"https://doi.org/10.1038/s41598-026-40625-0","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2026-03-01 15:58:40","publishedOnDateReadable":"March 1st, 2026"},"versionCreatedAt":"2025-11-25 02:57:33","video":"","vorDoi":"10.1038/s41598-026-40625-0","vorDoiUrl":"https://doi.org/10.1038/s41598-026-40625-0","workflowStages":[]},"version":"v1","identity":"rs-8135880","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8135880","identity":"rs-8135880","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}