Comprehensive Bioinformatics Analysis of Human Matrix Metalloproteinase-9 (MMP9): Sequence Analysis, Structural Characterization, and Functional Annotation

Comprehensive Bioinformatics Analysis of Human Matrix Metalloproteinase-9 (MMP9): Sequence Analysis, Structural Characterization, and Functional Annotation | 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 Research Article Comprehensive Bioinformatics Analysis of Human Matrix Metalloproteinase-9 (MMP9): Sequence Analysis, Structural Characterization, and Functional Annotation Satish Prajapati This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9224356/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Matrix metalloproteinase-9 (MMP9) is a zinc-dependent endopeptidase that plays a crucial role in extracellular matrix remodeling, inflammation, and cancer metastasis. This study presents a comprehensive bioinformatics analysis of the human MMP9 protein (UniProt ID: P14780), encompassing sequence analysis, physicochemical characterization, domain architecture, posttranslational modifications, genetic variants, and functional annotations. The 707-amino acid protein has a calculated molecular weight of 78,458 Da and an isoelectric point of 7.02, indicating near-neutral charge at physiological pH. Domain architecture analysis revealed a conserved structural organization comprising a signal peptide (residues 1-19), propeptide (20-93), three fibronectin type-II repeats (225-390), and four hemopexin-like domains (518-704). The catalytic domain contains the canonical zinc-binding motif HEXXHXXGXXH with Glu-402 as the catalytic residue. Post-translational modification analysis identified three N-glycosylation sites and seven disulfide bonds crucial for structural stability. Genetic variant analysis revealed nine known single nucleotide polymorphisms, including the clinically significant Q279R variant (rs17576) associated with intervertebral disc disease. Secondary structure prediction indicates 15 α-helices, 48 β-strands, and 6 turns, with structured regions comprising 68.3% of the protein. Protein-protein interaction network analysis identified 16 binding partners, including tissue inhibitors of metalloproteinases (TIMPs) and extracellular matrix components. This comprehensive analysis provides a foundation for understanding MMP9 structure-function relationships and its role in human diseases Bioinformatics Structural Biology Biochemical Research Methods Developmental Biology Cancer Biology Computational Biology Molecular Biology MMP9 matrix metalloproteinase bioinformatics protein structure post-translational modifications genetic variants protein-protein interactions Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted 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-9224356","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":612088918,"identity":"98db08d2-a7df-416a-b8a0-046df85f5395","order_by":0,"name":"Satish Prajapati","email":"data:image/png;base64,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","orcid":"https://orcid.org/0009-0006-3801-1137","institution":"Government College of Engineering And Ceramic Technology","correspondingAuthor":true,"prefix":"","firstName":"Satish","middleName":"","lastName":"Prajapati","suffix":""}],"badges":[],"createdAt":"2026-03-25 14:24:48","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":true,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":true},"doi":"10.21203/rs.3.rs-9224356/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9224356/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":105444898,"identity":"47d2fcc9-c247-496a-a11d-aa8cec2694b8","added_by":"auto","created_at":"2026-03-26 06:58:03","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1472044,"visible":true,"origin":"","legend":"","description":"","filename":"ComprehensiveBioinformaticsAnalysisofHumanMatrixMetalloproteinase9MMP9.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9224356/v1_covered_66a4a22c-78b1-4380-a738-b47e87d2ec85.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eComprehensive Bioinformatics Analysis of Human Matrix Metalloproteinase-9 (MMP9): Sequence Analysis, Structural Characterization, and Functional Annotation\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Government College of Engineering And Ceramic Technology","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"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":"MMP9, matrix metalloproteinase, bioinformatics, protein structure, post-translational modifications, genetic variants, protein-protein interactions","lastPublishedDoi":"10.21203/rs.3.rs-9224356/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9224356/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eMatrix metalloproteinase-9 (MMP9) is a zinc-dependent endopeptidase that plays a crucial role in \u0026nbsp;extracellular matrix remodeling, inflammation, and cancer metastasis. This study presents a \u0026nbsp;comprehensive bioinformatics analysis of the human MMP9 protein (UniProt ID: P14780), \u0026nbsp;encompassing sequence analysis, physicochemical characterization, domain architecture, post\u0002translational modifications, genetic variants, and functional annotations. The 707-amino acid \u0026nbsp;protein has a calculated molecular weight of 78,458 Da and an isoelectric point of 7.02, indicating \u0026nbsp;near-neutral charge at physiological pH. Domain architecture analysis revealed a conserved \u0026nbsp;structural organization comprising a signal peptide (residues 1-19), propeptide (20-93), three \u0026nbsp;fibronectin type-II repeats (225-390), and four hemopexin-like domains (518-704). The catalytic \u0026nbsp;domain contains the canonical zinc-binding motif HEXXHXXGXXH with Glu-402 as the \u0026nbsp;catalytic residue. Post-translational modification analysis identified three N-glycosylation sites \u0026nbsp;and seven disulfide bonds crucial for structural stability. Genetic variant analysis revealed nine \u0026nbsp;known single nucleotide polymorphisms, including the clinically significant Q279R variant \u0026nbsp;(rs17576) associated with intervertebral disc disease. Secondary structure prediction indicates 15 \u0026nbsp;α-helices, 48 β-strands, and 6 turns, with structured regions comprising 68.3% of the protein. \u0026nbsp;Protein-protein interaction network analysis identified 16 binding partners, including tissue \u0026nbsp;inhibitors of metalloproteinases (TIMPs) and extracellular matrix components. 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