2024
Mapping the influence of hydrocarbons mixture on molecular mechanisms, involved in breast and lung neoplasms: in silico toxicogenomic data-mining
Abu-Bakar A, Ismail M, Zulkifli M, Zaini N, Shukor N, Harun S, Inayat-Hussain S. Mapping the influence of hydrocarbons mixture on molecular mechanisms, involved in breast and lung neoplasms: in silico toxicogenomic data-mining. Genes And Environment 2024, 46: 15. PMID: 38982523, PMCID: PMC11232146, DOI: 10.1186/s41021-024-00310-y.Peer-Reviewed Original ResearchNon-apoptotic programmed cell deathSignaling pathwayMolecular mechanismsResponse to oxidative stressInterleukin-17 signaling pathwayMolecular pathwaysSurvival signaling pathwaysAdaptive response to oxidative stressOxidative stress responseBreast cancer invasionGenetic interactionsModulate IL-8Protein domainsCytoscape softwareAir pollutionCritical genesCell deathCo-expressionGenesRisk of breastStress responseToxicogenomic analysisToxicogenomics toolsDevelopment of breastInvestigated hydrocarbons
2023
Induced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations
Cale J, Ham K, Li D, McIntosh C, Watts G, Wilton S, Aung-Htut M. Induced alternative splicing an opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations. Scientific Reports 2023, 13: 19725. PMID: 37957262, PMCID: PMC10643364, DOI: 10.1038/s41598-023-47005-y.Peer-Reviewed Original ResearchConceptsProtein isoformsAntisense oligomersModulate RNA processingLDL receptorInduce alternative splicingLevels of LDL receptorPhysiologically relevant concentrationsHuh-7 cellsLow-density lipoprotein (LDL) receptorProtein domainsRNA processingAlternative splicingExon 2Exon 8Target exonsHinge regionExonHuh-7LDL receptor activityIsoformsPhysiologically relevant levelsLDL uptakeSplicingIsoform expressionProtein overexpressionDrebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons
Dorskind J, Sudarsanam S, Hand R, Ziak J, Amoah-Dankwah M, Guzman-Clavel L, Soto-Vargas J, Kolodkin A. Drebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons. Journal Of Neuroscience 2023, 43: 7745-7765. PMID: 37798130, PMCID: PMC10648559, DOI: 10.1523/jneurosci.0553-23.2023.Peer-Reviewed Original ResearchConceptsLoss-of-functionCollateral axonal branchingMolecular mechanismsF-actin bundlesStructure-function analysisCircuit formationAxon collateral branchesCortical circuit formationAxonal branchesPyramidal excitatory neuronsLoss-of-function experimentsFemale mouse modelProtein domainsF-actinCortical neuronal morphologyLaminar-specific mannerBranch initiationGene expressionSynaptic partnersSingle-cell labelingAxonal protrusionsDrebrinExcitatory neuronsSomatosensory neuronsDBN12A peptide from ERBV-1 efficiently separates endogenous protein domains in the fission yeast Schizosaccharomyces pombe
Ren Y, Lin Q, Berro J. 2A peptide from ERBV-1 efficiently separates endogenous protein domains in the fission yeast Schizosaccharomyces pombe. MicroPublication Biology 2023, 2023: 10.17912/micropub.biology.000941. PMID: 37767365, PMCID: PMC10520729, DOI: 10.17912/micropub.biology.000941.Peer-Reviewed Original ResearchChemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides
Chen Y, Cao X, Loh K, Slavoff S. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochemical Society Transactions 2023, 51: 1071-1082. PMID: 37171061, PMCID: PMC10317152, DOI: 10.1042/bst20221074.Peer-Reviewed Original ResearchConceptsChemical labelingAlternative open reading framesOpen reading frameLimited sequence homologyMammalian genomesGene classesProtein domainsQuantitative proteomicsReading frameSequence homologyBiological roleProteomic discoveryMolecular levelSmORFsCell proliferationProteomicsInteractomeGenomeSpecific propertiesExperimental techniquesLabelingHomologyPolypeptideProteinFunctionalization
2022
Revealing the human mucinome
Malaker SA, Riley NM, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. Revealing the human mucinome. Nature Communications 2022, 13: 3542. PMID: 35725833, PMCID: PMC9209528, DOI: 10.1038/s41467-022-31062-4.Peer-Reviewed Original ResearchConceptsModular protein domainsKey molecular signaturesProtein domainsTransmembrane proteinDetection of hundredsMucin domainGlycoprotein identificationHuman diseasesMolecular signaturesCell lysatesEnrichment strategyGlycoproteinVivo sourceOverlapping populationsImportant roleDomainStcEProteinLysatesOvarian cancer patientsComplex samples
2021
Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function
Feke A, Vanderwall M, Liu W, Gendron JM. Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function. PLOS ONE 2021, 16: e0235938. PMID: 33730063, PMCID: PMC7968664, DOI: 10.1371/journal.pone.0235938.Peer-Reviewed Original ResearchConceptsLOV KELCH PROTEIN 2Kelch repeat domainRepeat domainLOV domainsF-BOX PROTEIN 1Protein-protein interaction domainsPlant circadian clockFLAVIN-BINDING KELCHProtein domain architecturePotential interacting partnerE3 ubiquitin ligasesInteracting partnerDomain architectureProtein complexesUbiquitin ligasesKelch proteinProtein familyTransgenic linesFlowering timeKelch familyProtein domainsZEITLUPEInteraction domainClock functionUnique photoreceptor
2019
Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays
Zigáčková D, Rájecká V, Vaňáčová Š. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays. Methods In Molecular Biology 2019, 2062: 237-253. PMID: 31768980, DOI: 10.1007/978-1-4939-9822-7_12.Peer-Reviewed Original ResearchConceptsActivity of exosomesTRAMP complexExosome complexPolyadenylation complexRNA maturationRNA processingProtein complexesProtein domainsAuxiliary proteinsRNA substratesIndividual subunitsHigh processivityYeastParticular mutationAberrant formsActivation assaysRNAExosomesComplexesTRAMPWeak activityProcessivityPurificationSubunitsComplete degradationA programmable DNA-origami platform for studying lipid transfer between bilayers
Bian X, Zhang Z, Xiong Q, De Camilli P, Lin C. A programmable DNA-origami platform for studying lipid transfer between bilayers. Nature Chemical Biology 2019, 15: 830-837. PMID: 31320758, PMCID: PMC6650167, DOI: 10.1038/s41589-019-0325-3.Peer-Reviewed Original ResearchConceptsLipid transferNon-vesicular lipid transportSynaptotagmin-like mitochondrial lipid-binding protein (SMP) domainLipid transportMembrane contact sitesLipid transport proteinsSMP domainImportant physiological roleDNA origami platformProtein domainsUnstructured linkerContact sitesSynaptotagmin-1Förster resonance energy transferPhysiological roleResonance energy transferMechanistic insightsDNA origami nanostructuresAcceptor liposomesThe mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins
Malaker SA, Pedram K, Ferracane MJ, Bensing BA, Krishnan V, Pett C, Yu J, Woods EC, Kramer JR, Westerlind U, Dorigo O, Bertozzi CR. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 7278-7287. PMID: 30910957, PMCID: PMC6462054, DOI: 10.1073/pnas.1813020116.Peer-Reviewed Original ResearchConceptsModular protein domainsProtein domainsSecreted proteinsMucin domainFunctional analysisHuman diseasesMucin biologyGlycosylation patternsCultured cellsMolecular levelCell surfaceSequence coverageKey playersBacterial proteasesCancer-associated mucinsDiscrete peptidesBiological ligandsProteaseHuman mucinsGlycoform analysisStcESiglec-9Domain structureMass spectrometryDomain
2018
Model Colibactins Exhibit Human Cell Genotoxicity in the Absence of Host Bacteria
Shine EE, Xue M, Patel JR, Healy AR, Surovtseva YV, Herzon SB, Crawford JM. Model Colibactins Exhibit Human Cell Genotoxicity in the Absence of Host Bacteria. ACS Chemical Biology 2018, 13: 3286-3293. PMID: 30403848, PMCID: PMC7001666, DOI: 10.1021/acschembio.8b00714.Peer-Reviewed Original ResearchConceptsHost bacteriaGenotoxic secondary metabolitesDNA double-strand breaksDNA interstrandSpecific protein domainsWild-type pathwayDouble-strand breaksFull molecular mechanismsCell culturesFamily of metabolitesHuman cell linesProtein domainsPresence of membranesModule skippingCellular phenotypesExtracellular supplementationNative pathwaysHuman cell culturesMolecular mechanismsSecondary metabolitesHuman cellsColibactinEfficient DNA interstrandObserved modulesPhenotype
2017
Domain-Targeted Metabolomics Delineates the Heterocycle Assembly Steps of Colibactin Biosynthesis
Trautman EP, Healy AR, Shine EE, Herzon SB, Crawford JM. Domain-Targeted Metabolomics Delineates the Heterocycle Assembly Steps of Colibactin Biosynthesis. Journal Of The American Chemical Society 2017, 139: 4195-4201. PMID: 28240912, PMCID: PMC5831107, DOI: 10.1021/jacs.7b00659.Peer-Reviewed Original ResearchConceptsNonribosomal peptide synthetasesPolyketide synthasesModular polyketide synthasesSite-directed mutagenesisCombination of genesCellular metabolic levelsColibactin biosynthesisMultidomain proteinsProtein domainsPeptide synthetasesCatalytic domainControl pathwaysProtein biochemicalPathway analysisCertain Escherichia coliComplete deletionHybrid pathwayEscherichia coliFunctional readoutBiosynthesisCatalytic mechanismCellular levelMetabolic levelPathwayGenes
2016
Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea
Lakshmanan V, Bansal D, Kulkarni J, Poduval D, Krishna S, Sasidharan V, Anand P, Seshasayee A, Palakodeti D. Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. G3: Genes, Genomes, Genetics 2016, 6: 3035-3048. PMID: 27489207, PMCID: PMC5068929, DOI: 10.1534/g3.116.031120.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsComputational BiologyGenome-Wide Association StudyGenome, HelminthHigh-Throughput Nucleotide SequencingMicroRNAsMolecular Sequence AnnotationPlatyhelminthsPoly APolyadenylationReproducibility of ResultsRNA InterferenceRNA Processing, Post-TranscriptionalRNA, MessengerConceptsSchmidtea mediterraneaAdvent of next-generation sequencing technologiesNext-generation sequencing technologiesGene expressionTissue-specific expression patternsMiRNA mediated gene regulationGenome-wide scaleGenome-wide analysisPoly(A) sitePosttranscriptional gene expressionRegulate posttranscriptional gene expressionGene annotationInternal exonsPolyadenylated transcriptsTranscript isoformsPolyadenylation eventsDegradome sequencingProtein domainsSequencing technologiesPre-mRNAGene regulationCoding sequenceIdeal model systemStem cell functionFreshwater planariansExtended‐Synaptotagmins as Lipid Transporters at ER‐PM Contact Sites
Reinisch K, Schauder C, Wu X, Saheki Y, Narayanaswamy P, Torta F, Wenk M, De Camilli P. Extended‐Synaptotagmins as Lipid Transporters at ER‐PM Contact Sites. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.115.2.Peer-Reviewed Original ResearchMembrane contact sitesSMP domainContact sitesExtended synaptotagminsEndoplasmic reticulumPlasma membraneER-PM contact sitesLipid transportLipid transferLipid-binding modulesER-PM tethersΒ-barrel structureExchange of lipidsERMES complexE-SytsProtein modulesProtein domainsVesicular transportC2 domainÅ resolutionLipid transportersHydrophobic residuesUehara Memorial FoundationSynaptotagmin 2Direct role
2014
Membrane adhesion dictates Golgi stacking and cisternal morphology
Lee I, Tiwari N, Dunlop MH, Graham M, Liu X, Rothman JE. Membrane adhesion dictates Golgi stacking and cisternal morphology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 1849-1854. PMID: 24449908, PMCID: PMC3918774, DOI: 10.1073/pnas.1323895111.Peer-Reviewed Original ResearchConceptsFK506-binding protein (FKBP) domainsGolgi cisternaeGolgi matrix proteinsClass of proteinsCisternal morphologyCisternal maturationProtein domainsGolgi membranesGolgi stacksRegulatory proteinsGolgiMatrix proteinsMembrane adhesionMembrane transportProtein 55Adhesive processHeLa cellsAdhesive proteinsProteinGolginsCargo transportAncient formCisternaeQuantitative electron microscopyMitochondria
2013
In silico investigation of the ATP7B gene: insights from functional prediction of non-synonymous substitution to protein structure
Squitti R, Siotto M, Bucossi S, Polimanti R. In silico investigation of the ATP7B gene: insights from functional prediction of non-synonymous substitution to protein structure. BioMetals 2013, 27: 53-64. PMID: 24253677, DOI: 10.1007/s10534-013-9686-3.Peer-Reviewed Original ResearchConceptsNon-synonymous substitutionsDisease-causing mutationsWilson disease-causing mutationsDisease-causing variantsUnknown gene variantsGenetic variantsProtein X-ray structuresSequence-based approachesCopper-transporting ATPaseNovel genetic variantsAmino acid changesUncharacterized proteinsProtein functionNovel ATP7B mutationsProtein domainsFunctional predictionCopper homeostasisBioinformatics methodsAmino acidic changeATP7B geneProtein structureAcid changesATP7B proteinGenesX-ray structureStructural Insights into the Intrinsic Self-Assembly of Par-3 N-Terminal Domain
Zhang Y, Wang W, Chen J, Zhang K, Gao F, Gao B, Zhang S, Dong M, Besenbacher F, Gong W, Zhang M, Sun F, Feng W. Structural Insights into the Intrinsic Self-Assembly of Par-3 N-Terminal Domain. Structure 2013, 21: 997-1006. PMID: 23643951, DOI: 10.1016/j.str.2013.04.004.Peer-Reviewed Original ResearchConceptsN-terminal domainPAR-3PAR-3/PARCell polarity establishmentPolarity establishmentEpithelial polarizationScaffold proteinProtein domainsLongitudinal packingStructural basisStructural insightsCryoelectron microscopyCentral organizerFilament-like structuresC complexFilament structureSelf-association capacitySelf-associationUnderlying mechanismDomainElectrostatic interactionsInteraction modesProteinCrystal structure
2012
SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins.
de Souza J, Galante P, de Almeida R, da Cunha J, Ohara D, Ohno-Machado L, Old L, de Souza S. SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins. Cancer Immunology Research 2012, 12: 15. PMID: 23390370, PMCID: PMC3554024.Peer-Reviewed Original ResearchConceptsCell surface proteinsSurface proteinsProtein-protein interactionsUCSC Genome BrowserImportant data repositoryUser-friendly web interfaceGene annotationProtein domainsGenome browserHuman genesGene expressionGene namesGenesSomatic mutationsProteinExcellent targetAnnotationTherapeutic reagentsWeb interfaceNCBIMutationsExpressionDomainTargetRNA–protein interactions in vivo: global gets specific
Änkö M, Neugebauer KM. RNA–protein interactions in vivo: global gets specific. Trends In Biochemical Sciences 2012, 37: 255-262. PMID: 22425269, DOI: 10.1016/j.tibs.2012.02.005.Peer-Reviewed Original ResearchConceptsNumerous protein domainsRNA-binding specificityRNA-protein interactionsEndogenous RNA moleculesShort RNA sequencesProperties of proteinsProtein domainsPolyadenylation factorsRNA moleculesRNA sequencesRNALimited repertoireProteinStructural determinationChaperonesCellsRecent advancesSplicingVivoSpecificitySequenceCrucial contributionDestabilizerRepertoireLocalization factor
2011
Regulated Intramembrane Proteolysis: Signaling Pathways and Biological Functions
Lal M, Caplan M. Regulated Intramembrane Proteolysis: Signaling Pathways and Biological Functions. Physiology 2011, 26: 34-44. PMID: 21357901, DOI: 10.1152/physiol.00028.2010.Peer-Reviewed Original ResearchConceptsFundamental cellular processesIntegral membrane proteinsFunctional protein domainsCellular processesProtein domainsElicit biological responsesMembrane proteinsTransmembrane proteinIntramembrane cleavageBiological functionsPhysiological processesProteolytic cleavageBiological responsesProteinCleavageDomainMessengerEnzymePathwayMembrane
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