2024
O-Glycoproteomics: Methods, Challenges, and New Opportunities
Riley N, Malaker S. O-Glycoproteomics: Methods, Challenges, and New Opportunities. 2024, 118-162. DOI: 10.1039/9781839166433-00118.Peer-Reviewed Original ResearchElectron transfer dissociationMass spectrometryBeam-type collision-induced dissociationSupplemental collisional activationCollision-induced dissociationSolid-phase extractionCollisional activationTransfer dissociationGlycopeptide analysisTandem MSO-glycoproteomeDissociationO-glycoproteinsSite-specific localizationGlycopeptidesEThcDO-glycansSpectrometryGlycoproteomicsSpectraElectronExpanding the repertoire of GalNAc analogues for cell-specific bioorthogonal tagging of glycoproteins
Zafar A, Sridhar S, Bineva-Todd G, Cioce A, Abdulla N, Chang V, Malaker S, Hewings D, Schumann B. Expanding the repertoire of GalNAc analogues for cell-specific bioorthogonal tagging of glycoproteins. RSC Chemical Biology 2024, 5: 1002-1009. PMID: 39238612, PMCID: PMC11369666, DOI: 10.1039/d4cb00093e.Peer-Reviewed Original ResearchAnalysis of Mucin‐Domain Glycoproteins Using Mass Spectrometry
Mahoney K, Malaker S. Analysis of Mucin‐Domain Glycoproteins Using Mass Spectrometry. Current Protocols 2024, 4: e1100. PMID: 38984456, PMCID: PMC11239139, DOI: 10.1002/cpz1.1100.Peer-Reviewed Original ResearchGlycoproteomics: Charting new territory in mass spectrometry and glycobiology
Malaker S. Glycoproteomics: Charting new territory in mass spectrometry and glycobiology. Journal Of Mass Spectrometry 2024, 59: e5034. PMID: 38726698, DOI: 10.1002/jms.5034.Peer-Reviewed Original ResearchStress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors
Rivet-Noor C, Merchak A, Render C, Gay N, Beiter R, Brown R, Keeler A, Moreau G, Li S, Olgun D, Steigmeyer A, Ofer R, Phan T, Vemuri K, Chen L, Mahoney K, Shin J, Malaker S, Deppmann C, Verzi M, Gaultier A. Stress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors. Brain Behavior And Immunity 2024, 119: 665-680. PMID: 38579936, PMCID: PMC11187485, DOI: 10.1016/j.bbi.2024.03.028.Peer-Reviewed Original ResearchMicrobiome shiftsDespair behaviorTranscription factor familyChronic stressRegulation of mucinsState of dysbiosisMicrobiome composition changesAssociated with disease pathologyDepressive-like symptomsModel of chronic stressLimited treatment optionsContext of stressHuman microbiomeMicrobiome compositionPsychological stress exposureMicrobial compositionFactor familyMicrobial dysbiosisMicrobial changesMicrobiome dysbiosisMicrobiomeTreatment optionsUpstream mediatorDepressive symptomsStress exposureMass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome
Mahoney K, Chang V, Lucas T, Maruszko K, Malaker S. Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome. Analytical Chemistry 2024, 96: 5242-5250. PMID: 38512228, DOI: 10.1021/acs.analchem.3c05762.Peer-Reviewed Original ResearchMucin-domain glycoproteinsO-glycopeptidesGlycopeptide signalsIn-gel digestionMass spectrometryElution conditionsSolid supportBinding moietyElution stepDownstream analysisO-glycosylationIn-gelBiological functionsElutionHuman serumEnrichment strategyCell linesMoietyEffective isolationSpectrometryCatalyticallyGlycoproteinSampling requirementsGlycopeptidesStcEGlycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SME and molecular dynamics simulations
Rosenfeld M, Kearns F, Chongsaritsinsuk J, Steigmeyer A, Mahoney K, Lucas T, Ince D, Battison A, Hollenhorst M, Shon D, Bertozzi C, Farracane M, Lemmon M, Malaker S, Amaro R. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SME and molecular dynamics simulations. Biophysical Journal 2024, 123: 14a. DOI: 10.1016/j.bpj.2023.11.205.Peer-Reviewed Original Research
2023
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
Chongsaritsinsuk J, Steigmeyer A, Mahoney K, Rosenfeld M, Lucas T, Smith C, Li A, Ince D, Kearns F, Battison A, Hollenhorst M, Judy Shon D, Tiemeyer K, Attah V, Kwon C, Bertozzi C, Ferracane M, Lemmon M, Amaro R, Malaker S. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature Communications 2023, 14: 6169. PMID: 37794035, PMCID: PMC10550946, DOI: 10.1038/s41467-023-41756-y.Peer-Reviewed Original ResearchConceptsFamily of proteinsMucin domainO-glycosylationBiological functionsKey regulatorComplex glycansMass spectrometric analysisFunctional relevanceTIM familyDetailed molecular structureCritical roleGlycosylationProteinSpectrometric analysisStructural featuresUnique abilityStructural dynamicsMolecular dynamics simulationsTim-3 functionFamilyPowerful workflowRegulatorImmune cellsCheckpointGlycansFalse-Positive Glycopeptide Identification via In-FAIMS Fragmentation
Rangel-Angarita V, Mahoney K, Kwon C, Sarker R, Lucas T, Malaker S. False-Positive Glycopeptide Identification via In-FAIMS Fragmentation. JACS Au 2023, 3: 2498-2509. PMID: 37772174, PMCID: PMC10523363, DOI: 10.1021/jacsau.3c00264.Peer-Reviewed Original ResearchDesign of a mucin-selective protease for targeted degradation of cancer-associated mucins
Pedram K, Shon D, Tender G, Mantuano N, Northey J, Metcalf K, Wisnovsky S, Riley N, Forcina G, Malaker S, Kuo A, George B, Miller C, Casey K, Vilches-Moure J, Ferracane M, Weaver V, Läubli H, Bertozzi C. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nature Biotechnology 2023, 42: 597-607. PMID: 37537499, PMCID: PMC11018308, DOI: 10.1038/s41587-023-01840-6.Peer-Reviewed Original ResearchCancer progressionSpecific protein glycoformsUndruggable proteinsTargeted degradationProtein degradationBreast cancer progressionCell surface bindingSubstrate selectivityCell-type selectivityCell deathGlycan motifsProtein glycoformsDiscrete peptidesCancer cellsProteinCulture modelProteaseTarget cellsTumor growthCancer-associated mucinsCellsMouse modelDegradersGrowthMotifMutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity
Hollander M, Malaker S, Riley N, Perez I, Abney N, Gray M, Maxson J, Cochran J, Bertozzi C. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. Journal Of Biological Chemistry 2023, 299: 104755. PMID: 37116708, PMCID: PMC10245049, DOI: 10.1016/j.jbc.2023.104755.Peer-Reviewed Original ResearchConceptsProtein domain mappingSingle amino acid mutationLigand-independent activityChronic neutrophilic leukemiaCell surface receptorsAmino acid mutationsColony-stimulating factor 3 receptorSerine residuesPresence of GalNAcHotspot residuesNeutrophilic leukemiaHuman diseasesAcid mutationsReceptor signalingAmino acidsCell growthSurface receptorsReceptor alpha chainMutationsAbundant typeDomain mappingDisease mechanismsUncontrolled activityAlpha chainWhite blood cellsVibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization
Huang X, Nero T, Weerasekera R, Matej K, Hinbest A, Jiang Z, Lee R, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng W, Malaker S, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nature Communications 2023, 14: 2104. PMID: 37055389, PMCID: PMC10102183, DOI: 10.1038/s41467-023-37660-0.Peer-Reviewed Original ResearchConceptsBiofilm matrix exopolysaccharideFacilitate host colonizationVibrio cholerae biofilmsΒ-propeller domainMatrix exopolysaccharideModular domainsHost colonizationRedundant rolesDistinct functionsAbiotic surfacesAdhesive proteinsHost surfaceHuman pathogensVibrio choleraeAdhesinsBacterial biofilmsHost tissuesColonization modelColonizationBAP1BiofilmsPathogensAntibiotic resistanceRBMCDomainThe 2022 Nobel Prize in Chemistry—sweet!
Boyce M, Malaker S, Riley N, Kohler J. The 2022 Nobel Prize in Chemistry—sweet! Glycobiology 2023, 33: 178-181. PMID: 36892406, DOI: 10.1093/glycob/cwad016.Peer-Reviewed Original ResearchO‑Linked Sialoglycans Modulate the Proteolysis of SARS-CoV‑2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern
Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney K, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel A, Benton D, Nawrath P, Flitsch S, Joshi D, González-Ramírez A, Wilkinson K, Wilkinson R, Wall E, Hurtado-Guerrero R, Malaker S, Schumann B. O‑Linked Sialoglycans Modulate the Proteolysis of SARS-CoV‑2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS Central Science 2023, 9: 393-404. PMID: 36968546, PMCID: PMC10037455, DOI: 10.1021/acscentsci.2c01349.Peer-Reviewed Original ResearchComprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation
Hollenhorst M, Tiemeyer K, Mahoney K, Aoki K, Ishihara M, Lowery S, Rangel-Angarita V, Bertozzi C, Malaker S. Comprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation. Journal Of Thrombosis And Haemostasis 2023, 21: 995-1009. PMID: 36740532, PMCID: PMC10065957, DOI: 10.1016/j.jtha.2023.01.009.Peer-Reviewed Original ResearchConceptsO-glycositesGPIb-IX-V complexMajor ligand-binding subunitAmino acid sitesLigand-binding subunitVon Willebrand factor bindingPlatelet glycoprotein IbαMechanosensory domainFactor bindingEndogenous proteinsRecombinant proteinsN-glycositesStructural rolePlatelet biologyGlycan structuresGlycoprotein IbαO-glycansT antigenGlycosylation profileDiverse repertoireGlycosylationGlycansComprehensive analysisGlycositesVon Willebrand factorBump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells
Calle B, Gonzalez-Rodriguez E, Mahoney K, Cioce A, Bineva-Todd G, Tastan O, Roustan C, Flynn H, Malaker S, Schumann B. Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells. STAR Protocols 2023, 4: 101974. PMID: 36633947, PMCID: PMC9843269, DOI: 10.1016/j.xpro.2022.101974.Peer-Reviewed Original ResearchConceptsProtein substratesGlycosylation sitesGalNAc-T familyTransfection of cellsIndividual glycosyltransferasesBioorthogonal reportersN-acetylgalactosamine transferaseSubstrate specificityBiological functionsGalNAc-TsDisease relevanceMolecular biologyComplete detailsGlycosyltransferasesTransferaseCellsBiosynthesisBiologyReporterTransfectionGlycansSubstrateEnzymeHole engineeringSites
2022
Cell-specific bioorthogonal tagging of glycoproteins
Cioce A, Calle B, Rizou T, Lowery SC, Bridgeman VL, Mahoney KE, Marchesi A, Bineva-Todd G, Flynn H, Li Z, Tastan OY, Roustan C, Soro-Barrio P, Rafiee MR, Garza-Garcia A, Antonopoulos A, Wood TM, Keenan T, Both P, Huang K, Parmeggian F, Snijders AP, Skehel M, Kjær S, Fascione MA, Bertozzi CR, Haslam SM, Flitsch SL, Malaker SA, Malanchi I, Schumann B. Cell-specific bioorthogonal tagging of glycoproteins. Nature Communications 2022, 13: 6237. PMID: 36284108, PMCID: PMC9596482, DOI: 10.1038/s41467-022-33854-0.Peer-Reviewed Original ResearchConceptsMass spectrometry glycoproteomicsArtificial biosynthetic pathwayTumor-derived cell linesCellular model systemNon-transfected cellsCellular functionsProtein glycosylationBiosynthetic pathwayProteome analysisGlycosylation sitesBioorthogonal tagsCancer developmentCell linesModel systemImportant modulatorIntricate interactionsCo-culture modelGlycoproteinCellsGlycoprotein expressionMouse modelGlycoproteomeGlycosylationTaggingMonocultureA previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond
Medley BJ, Leclaire L, Thompson N, Mahoney KE, Pluvinage B, Parson MAH, Burke JE, Malaker S, Wakarchuk W, Boraston AB. A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond. Journal Of Biological Chemistry 2022, 298: 102439. PMID: 36049519, PMCID: PMC9513282, DOI: 10.1016/j.jbc.2022.102439.Peer-Reviewed Original ResearchConceptsUncharacterized proteinsCarbohydrate-binding moduleHuman gut microbiotaHost adaptationSubstrate recognitionCatalytic motifN-terminalHost healthGut environmentPeptidase activityHost mucinsNutrient sourceAkkermansia muciniphilaEnzymeKey membersPeptide bondProteinBacteriumActive siteGut microbiotaTn antigenPeptide backboneGenesMicrobesGlycoproteomics
Bagdonaite I, Malaker S, Polasky D, Riley N, Schjoldager K, Vakhrushev S, Halim A, Aoki-Kinoshita K, Nesvizhskii A, Bertozzi C, Wandall H, Parker B, Thaysen-Andersen M, Scott N. Glycoproteomics. Nature Reviews Methods Primers 2022, 2: 48. DOI: 10.1038/s43586-022-00128-4.Peer-Reviewed Original ResearchGlycan structuresMass spectrometryPost-translational additionIntact glycopeptide analysisSite of modificationProtein glycosylationProtein modificationBioinformatics platformBiological processesGlycopeptide analysisMS fragmentationGlycoproteomic methodsGlycoproteomicsGlycosylationProtein isolationProteolytic digestionPeptide sequencesSystem-wide contextStudy of glycopeptidesPrimersRecent advancesExciting fieldProteinGlycansSpectrometryCurrent strategies for characterization of mucin-domain glycoproteins
Ince D, Lucas TM, Malaker SA. Current strategies for characterization of mucin-domain glycoproteins. Current Opinion In Chemical Biology 2022, 69: 102174. PMID: 35752002, DOI: 10.1016/j.cbpa.2022.102174.Peer-Reviewed Original ResearchConceptsGlycopeptide mimeticsPost-translational modificationsCurrent characterization techniquesCellular glycosylation pathwaysSynthetic methodCharacterization techniquesGlycosylation pathwayMucin domainO-glycosylationBiological functionsGlycoproteomic workflowGlycosylationGlycoproteinExciting avenuesRecent breakthroughsMucin glycoproteinsRecent developments