2022
The mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions
Ogbunugafor C. The mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution 2022, 76: 37-48. PMID: 34989399, DOI: 10.1111/evo.14428.Peer-Reviewed Original ResearchConceptsReaction normsFitness effects of mutationsPhenotypic consequences of mutationsEvolution of antimicrobial resistanceEffects of mutationsConsequences of mutationsGenetic interactionsPopulation geneticsEpistatic interactionsPhenotypic consequencesGenetic informationMutational effectsFunction of environmental contextUnpredictability of evolutionFitness effectsMutationsAntimicrobial resistanceLayer of complexityEnvironmental contextModern SynthesisPerformance of genotypesReverse evolutionEpistasisGeneticsPublic health
2019
Computational algorithms for in silico profiling of activating mutations in cancer
Jordan EJ, Patil K, Suresh K, Park JH, Mosse YP, Lemmon MA, Radhakrishnan R. Computational algorithms for in silico profiling of activating mutations in cancer. Cellular And Molecular Life Sciences 2019, 76: 2663-2679. PMID: 30982079, PMCID: PMC6589134, DOI: 10.1007/s00018-019-03097-2.Peer-Reviewed Original ResearchConceptsTarget proteinsSingle nucleotide polymorphismsB-RafSerine/threonine-protein kinase B-RafDifferent target proteinsEffects of mutationsStructure-based computational approachKinase domainStructure-based methodsStructure-based modelProtein structureProtein activationSilico profilingAnaplastic lymphoma kinaseInteraction of inhibitorsMutational landscapeHuman cancersPoint mutationsProteinMutationsMutational patternsDifferent mutationsActivation statusComputational approachLymphoma kinaseAPOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma
Cannataro VL, Gaffney SG, Sasaki T, Issaeva N, Grewal NKS, Grandis JR, Yarbrough WG, Burtness B, Anderson KS, Townsend JP. APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Oncogene 2019, 38: 3475-3487. PMID: 30647454, PMCID: PMC6499643, DOI: 10.1038/s41388-018-0657-6.Peer-Reviewed Original ResearchConceptsPositive selectionCancer phenotypeStrong positive selectionIntensity of selectionEffects of mutationsBasis of mutationsSomatic genetic variantsSomatic evolutionNeutral driftMutational processesAPOBEC mutagenesisBiochemical experimentsSelection intensityMolecular understandingCytosine basesIndividual substitutionsAPOBEC3B proteinMutant stateMutational signaturesGenetic variantsNeck squamous cell carcinomaMutationsE545KGene variantsPhenotype
2018
cis‐Proline mutants of quiescin sulfhydryl oxidase 1 with altered redox properties undermine extracellular matrix integrity and cell adhesion in fibroblast cultures
Javitt G, Grossman‐Haham I, Alon A, Resnick E, Mutsafi Y, Ilani T, Fass D. cis‐Proline mutants of quiescin sulfhydryl oxidase 1 with altered redox properties undermine extracellular matrix integrity and cell adhesion in fibroblast cultures. Protein Science 2018, 28: 228-238. PMID: 30367560, PMCID: PMC6295897, DOI: 10.1002/pro.3537.Peer-Reviewed Original ResearchConceptsQuiescin sulfhydryl oxidase 1Protein disulfide isomeraseSulfhydryl oxidase 1Thioredoxin superfamilyCatalyst of disulfide bond formationDisulfide isomeraseCis-prolineProtein disulfide isomerase familyEffects of such mutationsThioredoxin-fold proteinsCell adhesionAmino acidsEffects of mutationsExtracellular matrix assemblyCanonical amino acidsActive-site regionDisulfide bond formationRedox-active enzymesSuperfamily enzymesSequence homologyFibroblast culturesBacterial enzymesMutated residuesMutantsDistant memberProgrammable sequential mutagenesis by inducible Cpf1 crRNA array inversion
Chow RD, Kim HR, Chen S. Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. Nature Communications 2018, 9: 1903. PMID: 29765043, PMCID: PMC5954137, DOI: 10.1038/s41467-018-04158-z.Peer-Reviewed Original Research
2015
Yeast Fex1p Is a Constitutively Expressed Fluoride Channel with Functional Asymmetry of Its Two Homologous Domains*
Smith KD, Gordon PB, Rivetta A, Allen KE, Berbasova T, Slayman C, Strobel SA. Yeast Fex1p Is a Constitutively Expressed Fluoride Channel with Functional Asymmetry of Its Two Homologous Domains*. Journal Of Biological Chemistry 2015, 290: 19874-19887. PMID: 26055717, PMCID: PMC4528147, DOI: 10.1074/jbc.m115.651976.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCell MembraneConserved SequenceDrug Resistance, FungalEscherichia coliFluoridesGene ExpressionGene Expression Regulation, FungalGenome, FungalIon TransportMembrane ProteinsMolecular Sequence DataMutationPatch-Clamp TechniquesPhosphorylationPhylogenyProtein FoldingProtein MultimerizationProtein Structure, SecondaryProtein Structure, TertiaryRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentStatic ElectricityConceptsC-terminal domainSaccharomyces cerevisiae functionsYeast plasma membraneN-terminal domainEffects of mutationsDuplicate proteinsYeast genomeCerevisiae functionsSequence conservationHelix domainLinker helixUbiquitous environmental toxinHomologous domainsImportant residuesFluoride channelsPlasma membraneParticular residuesBiological speciesSimilar mutationsIon channelsContinuous expressionProteinAntiparallel dimerMutationsResiduesGenome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis
Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis. Cell 2015, 160: 1246-1260. PMID: 25748654, PMCID: PMC4380877, DOI: 10.1016/j.cell.2015.02.038.Peer-Reviewed Original ResearchConceptsSingle guide RNAsGenome-wide CRISPR screenGenome-scale libraryCRISPR/Cas9-mediated lossLate-stage primary tumorsEffects of mutationsGenetic screenTumor growthCRISPR screensFunction screenMouse cancer cell linesCancer evolutionGene phenotypeDiverse phenotypesFunction mutationsCancer cell linesGenesCell linesPrimary screenCell poolSpecific lossPrimary tumor growthSmall poolMutationsPhenotype
2009
Regulation of the epidermal growth factor receptor intracellular domain
Choi S, Lemmon M. Regulation of the epidermal growth factor receptor intracellular domain. The FASEB Journal 2009, 23: 883.2-883.2. DOI: 10.1096/fasebj.23.1_supplement.883.2.Peer-Reviewed Original ResearchC-terminal tailTyrosine kinase domainIntracellular domainJuxtamembrane regionJM regionEGFR intracellular domainEpidermal growth factor receptorC-tailEGFR extracellular regionC-tail regionReceptor intracellular domainEffects of mutationsReceptor tyrosine kinasesReceptor-receptor interactionsSmall-angle X-ray scatteringKinase assaysKinase domainGrowth factor receptorExtracellular regionReceptor dimerizationEGFR activationBaculovirus systemIntracellular dimerTyrosine kinaseDeletion mutations
2004
cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model
Kluger HM, Kluger Y, Gilmore-Hebert M, DiVito K, Chang JT, Rodov S, Mironenko O, Kacinski BM, Perkins AS, Sapi E. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Laboratory Investigation 2004, 84: 320-331. PMID: 14767486, DOI: 10.1038/labinvest.3700044.Peer-Reviewed Original ResearchConceptsAutophosphorylation sitesHC11 mammary epithelial cellsMAP kinase phosphatase-1SNARE protein Ykt6Macrophage colony-stimulating factor receptorK cDNA microarrayColony-stimulating factor receptorCDNA microarray analysisKinase phosphatase-1Effects of mutationsMammary epithelial cellsTransmembrane tyrosine kinase receptorTyrosine kinase receptorsPhosphatase 1HC11 cellsCDNA microarrayTumorigenic phenotypeChaperonin 10Gene expressionFms oncogeneMicroarray analysisInvasive phenotypeMetastatic competenceKinase receptorsVivo tumorigenesis
2000
The Flagellar Sigma Factor FliA (ς28) Regulates the Expression of Salmonella Genes Associated with the Centisome 63 Type III Secretion System
Eichelberg K, Galán J. The Flagellar Sigma Factor FliA (ς28) Regulates the Expression of Salmonella Genes Associated with the Centisome 63 Type III Secretion System. Infection And Immunity 2000, 68: 2735-2743. PMID: 10768967, PMCID: PMC97482, DOI: 10.1128/iai.68.5.2735-2743.2000.Peer-Reviewed Original ResearchConceptsType III secretion systemSecretion systemExpression of componentsRegulatory proteinsType III protein secretion systemRegulatory mechanismsSerovar TyphimuriumFlagellar sigma factor FliASigma factor FliAProtein secretion systemTranscriptional regulatory proteinsSalmonella pathogenicity island 1Complex regulatory mechanismsFlagellar regulatory genesPathogenicity island 1Macrophage cell deathEffects of mutationsType III systemCultured epithelial cellsFlagellar genesEnterica serovar TyphimuriumMild centrifugal forceRegulatory genesSalmonella genesS. enterica serovar TyphimuriumThe Two Faces of Mutation: Extinction and Adaptation in RNA Viruses
Elena S, Miralles R, Cuevas J, Turner P, Moya A. The Two Faces of Mutation: Extinction and Adaptation in RNA Viruses. IUBMB Life 2000, 49: 5-9. PMID: 10772334, DOI: 10.1080/713803585.Peer-Reviewed Original ResearchConceptsRNA virusesPopulation sizeGenetic variabilityDrastic fitness lossFace of mutationCellular DNA replicationHigh genetic variabilityEffects of mutationsLarge population sizesViral population sizeBottleneck eventsGenetic driftFitness lossDNA replicationFitness gainsSegment exchangeDifferent tissuesViral extinctionReplicative intermediatesInfected hostExtinctionMutationsPopulation standpointHostReplication
1993
Effects of mutations of Torpedo acetylcholine receptor alpha 1 subunit residues 184-200 on alpha-bungarotoxin binding in a recombinant fusion protein.
Chaturvedi V, Donnelly-Roberts D, Lentz T. Effects of mutations of Torpedo acetylcholine receptor alpha 1 subunit residues 184-200 on alpha-bungarotoxin binding in a recombinant fusion protein. Biochemistry 1993, 32: 9570-6. PMID: 8373764, DOI: 10.1021/bi00088a008.Peer-Reviewed Original ResearchConceptsAlpha 1 subunitFusion proteinAlpha-bungarotoxin bindingFusion protein containingOligonucleotide-directed mutagenesisEffects of mutationsPossible structure-function relationshipsStructure-function relationshipsTyr-189Dissimilar residuesPro-194Recombinant fusion proteinHigher apparent affinityAlpha subunitTyr-198Asp-195Cys-192Cys-193Protein containingFunctional interactionAmino acidsSubunitsResiduesMutationsPosition 184Folding and Assembly of Viral Membrane Proteins
Doms R, Lamb R, Rose J, Helenius A. Folding and Assembly of Viral Membrane Proteins. Virology 1993, 193: 545-562. PMID: 8460475, DOI: 10.1006/viro.1993.1164.Peer-Reviewed Original ResearchConceptsViral membrane proteinsQuality control mechanismsMolecular chaperonesGRP78-BiPMembrane proteinsER molecular chaperonesEffects of mutationsMisfolded proteinsProtein transportConformational maturationMisfolded moleculesProtein foldingEnergy-driven processChaperonesProtein structureMolecular mechanismsER environmentGRP78 synthesisExogenous proteinsNascent moleculesProteinDirect roleStructural variabilityControl mechanismsExperimental strategies
1992
Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants
Sherman J, Rogers K, Rogers M, Söll D. Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants. Journal Of Molecular Biology 1992, 228: 1055-1062. PMID: 1474577, DOI: 10.1016/0022-2836(92)90314-a.Peer-Reviewed Original ResearchConceptsAmber suppressorTyrosine tRNAN-terminal protein sequencingGlutamyl-tRNA synthetaseE. coli dihydrofolate reductaseAminoacyl-tRNA synthetasesEffects of mutationsEfficiency of aminoacylationColi dihydrofolate reductaseSite of aminoacylationTyrosine specificityTRNAs exhibitGlutamine tRNAMutagenic analysisProtein sequencingGlutamate tRNAImportant identity elementVivo identityTRNANucleotide substitutionsTRNA identityDiscriminator baseDihydrofolate reductaseMultiple mutationsSynthetasesExpression of functional parvoviral NS1 from recombinant vaccinia virus: Effects of mutations in the nucleotide-binding motif
Noesch J, Cotmore S, Tattersall P. Expression of functional parvoviral NS1 from recombinant vaccinia virus: Effects of mutations in the nucleotide-binding motif. Virology 1992, 191: 406-416. PMID: 1413512, DOI: 10.1016/0042-6822(92)90202-z.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBiological TransportBlotting, WesternCell LineCell NucleusCloning, MolecularDNA ReplicationDNA, ViralGenes, ViralHumansMiceMinute virus of miceMolecular Sequence DataPlasmidsPolymerase Chain ReactionRecombinant ProteinsTranscriptional ActivationVaccinia virusViral Nonstructural ProteinsConceptsWild-type NS1Mutant formsEfficient cap-independent translationVaccinia thymidine kinase geneNucleotide-binding motifCap-independent translationBacteriophage T7 promoterT7 RNA polymeraseEffects of mutationsThymidine kinase geneExpression of NS1Recombinant vaccinia virusP38 promoterRNA polymeraseReplicative proteinsChromosomal sitesLysine codonPurine triphosphatesKinase geneT7 promoterUntranslated regionMouse cellsNuclear extractsVaccinia virusVTF7-3
1991
Translation initiation of IS50R read-through transcripts
Schulz V, Reznikoff W. Translation initiation of IS50R read-through transcripts. Journal Of Molecular Biology 1991, 221: 65-80. PMID: 1717696, DOI: 10.1016/0022-2836(91)80205-9.Peer-Reviewed Original ResearchConceptsRNA secondary structureTranslation initiationSecondary structureRibosome binding siteRNA secondary structure analysisPotential RNA secondary structureSecondary structure analysisEffects of mutationsTransposase proteinTransposase geneIS50RNormal transcriptTransposase expressionTranscriptsInsertion sequenceBinding sitesMutationsGenesTransposaseReadsStructure analysisProteinOuter endLow levelsSequence
1990
Differences in the extent of activation of Epstein-Barr virus replicative gene expression among four nonproducer cell lines stably transformed by OriP/BZLF1 plasmids
Gradoville L, Grogan E, Taylor N, Miller G. Differences in the extent of activation of Epstein-Barr virus replicative gene expression among four nonproducer cell lines stably transformed by OriP/BZLF1 plasmids. Virology 1990, 178: 345-354. PMID: 2171186, DOI: 10.1016/0042-6822(90)90331-k.Peer-Reviewed Original ResearchConceptsCell linesEffects of mutationsStable cell linesExtent of activationProtein functionCellular genesGene productsExtrachromosomal plasmidsGene expressionNonproducer cell linesExpression vectorEarly antigenEarly genesGenesLymphoid cell linesCellular subclonesEBV early genesReplicative gene expressionX50-7 cellsZEBRA proteinPlasmidZebraBZLF1 gene productLatent EBVEBV genes
1987
Effects of mutations in three domains of the vesicular stomatitis viral glycoprotein on its lateral diffusion in the plasma membrane.
Scullion B, Hou Y, Puddington L, Rose J, Jacobson K. Effects of mutations in three domains of the vesicular stomatitis viral glycoprotein on its lateral diffusion in the plasma membrane. Journal Of Cell Biology 1987, 105: 69-75. PMID: 3038931, PMCID: PMC2114925, DOI: 10.1083/jcb.105.1.69.Peer-Reviewed Original ResearchConceptsCytoplasmic domainTransmembrane domainMutant proteinsMembrane proteinsExtracellular domainWild-type G proteinG proteinsMutant G proteinsVesicular stomatitis viral glycoproteinIntegral membrane proteinsEntire cytoplasmic domainLateral mobilitySite-directed mutagenesisEffects of mutationsCOS-1 cellsSlow mutantsFastest mutantPlasma membraneChimeric proteinType G proteinsG cDNAVirus spike glycoproteinPalmitate additionFluorescence recoveryArtificial bilayers
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