2024
Non-mutational neoantigens in disease
Stern L, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nature Immunology 2024, 25: 29-40. PMID: 38168954, PMCID: PMC11075006, DOI: 10.1038/s41590-023-01664-1.Peer-Reviewed Original ResearchConceptsNon-canonical initiation codonsPost-translational protein modificationMature T cellsRibosomal RNA processingAlternative RNA splicingProtein-coding regionsNon-mutational mechanismsAbility of mammalsRNA processingRNA splicingInitiation codonProtein modificationHuman diseasesMature T cell repertoireAntigenic peptidesImmune recognitionAdaptive immune responsesT cellsAntigenic determinantsMHC class ICellsSplicingNovel antigenic determinantsMammalsCodon
2019
Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs
Baclaocos J, Santesmasses D, Mariotti M, Bierła K, Vetick MB, Lynch S, McAllen R, Mackrill JJ, Loughran G, Guigó R, Szpunar J, Copeland PR, Gladyshev VN, Atkins JF. Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs. Journal Of Molecular Biology 2019, 431: 4381-4407. PMID: 31442478, PMCID: PMC6885538, DOI: 10.1016/j.jmb.2019.08.007.Peer-Reviewed Original ResearchConceptsSELENOP geneEvolution of selenoproteinsPacific oyster Magallana gigasC-terminal domainN-terminal domainOyster Magallana gigasGene evolutionRibosome profilingMammalian counterpartsRibosome progressionMagallana gigasCertain insectsDynamic evolutionary processInitiation codonSECIS elementsGenetic elementsRNA structureCommon spiderEvolutionary processesSelenoprotein expressionSELENOP mRNAUGAAquatic organismsBivalve molluscsSelenocysteine
2013
The initiation of mammalian protein synthesis and mRNA scanning mechanism
Lomakin IB, Steitz TA. The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature 2013, 500: 307-311. PMID: 23873042, PMCID: PMC3748252, DOI: 10.1038/nature12355.Peer-Reviewed Original ResearchConceptsSmall ribosomal subunitTranslation initiationRibosomal subunitMammalian translation initiationProtein synthesisInitiator transfer RNAMammalian protein synthesisMultiple initiation factorsMRNA scanningTransfer RNAInitiation factorsInitiation codonConformational changesMessenger RNAFunctional implicationsEukaryotesDistinct stepsP siteSubunitsRNAFunctional stateEIF1ARibosomesEIF1Codon
2005
The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH
Lomakin IB, Shirokikh NE, Yusupov MM, Hellen C, Pestova TV. The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH. The EMBO Journal 2005, 25: 196-210. PMID: 16362046, PMCID: PMC1356347, DOI: 10.1038/sj.emboj.7600904.Peer-Reviewed Original ResearchConceptsInitiator tRNA selectionRibosomal subunitTRNA selectionEukaryotic initiation factors eIF1Common evolutionary originSmall ribosomal subunitInitiation factor eIF1Initiation factor IF3Initiation codon selectionCodon-anticodon mismatchesEIF2-bound GTPRelated conformational changesIF3 functionEvolutionary originSmall ribosomalTranslation initiationInitiation complexInitiation factorsFactor bindingInitiation codonTerminal domainHeterologous systemsCodon selectionInitiator tRNAHeterologous subunits
2003
Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site
Kolupaeva VG, Lomakin IB, Pestova TV, Hellen CU. Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site. Molecular And Cellular Biology 2003, 23: 687-698. PMID: 12509466, PMCID: PMC151537, DOI: 10.1128/mcb.23.2.687-698.2003.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBase SequenceBinding SitesCodon, InitiatorEncephalomyocarditis virusEscherichia coliEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GGene DeletionModels, BiologicalModels, MolecularMolecular Sequence DataPlasmidsProtein BindingProtein BiosynthesisProtein ConformationProtein Structure, SecondaryProtein Structure, TertiaryRibosomesRNASequence Homology, Nucleic AcidConceptsInternal ribosome entry siteEukaryotic initiation factor 2EIF4GCentral domainEukaryotic initiation factor 4GConformational changesInitiation factor 2K domainRibosome binding siteInitiation of translationInternal ribosomal entry siteEntry siteExtensive conformational rearrangementsThree-way helical junctionInitiation codon AUGRibosome entry siteEncephalomyocarditis virus internal ribosomal entry siteEncephalomyocarditis virus (EMCV) mRNAInitiation codonRibosomal complexesC-terminusIRES functionProductive bindingCodon AUGN-terminus
2000
The joining of ribosomal subunits in eukaryotes requires eIF5B
Pestova T, Lomakin I, Lee J, Choi S, Dever T, Hellen C. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 2000, 403: 332-335. PMID: 10659855, DOI: 10.1038/35002118.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCatalysisCodon, InitiatorEukaryotic Initiation Factor-1Eukaryotic Initiation Factor-2Eukaryotic Initiation Factor-3Eukaryotic Initiation Factor-5GTP PhosphohydrolasesGuanosine TriphosphateGuanylyl ImidodiphosphateHumansHydrolysisMolecular Sequence DataPeptide Chain Initiation, TranslationalPeptide Initiation FactorsPuromycinRecombinant ProteinsRibosomesRNA, MessengerConceptsEIF2-bound GTPEukaryotic initiation factor 3RNA ternary complexRibosome-dependent GTPase activityInitiation factor IF2Initiation factor 3Eukaryotic protein synthesisRibosomal subunitInitiation codonGTPase activityProtein synthesisMessenger RNASubunitsTernary complexFactor 3GTPComplexesEukaryotesEIF5EIF5BEIF2EIF4BEIF1ARibosomesIF2
1990
Bovine papillomavirus E2 repressor mutant displays a high-copy-number phenotype and enhanced transforming activity
Riese D, Settleman J, Neary K, DiMaio D. Bovine papillomavirus E2 repressor mutant displays a high-copy-number phenotype and enhanced transforming activity. Journal Of Virology 1990, 64: 944-949. PMID: 2153255, PMCID: PMC249196, DOI: 10.1128/jvi.64.2.944-949.1990.Peer-Reviewed Original ResearchConceptsRepressor proteinWild-type copy numberBovine papillomavirus type 1 genomeCopy numberViral genomeTranscriptional repressor proteinTransient expression experimentsMouse C127 cellsMutant viral DNAViral DNAType 1 genomeNumber phenotypeRepressor activityLow copy numberMethionine codonInitiation codonExpression experimentsC127 cellsGenomeCV1 cellsRepressor mutantsFoci formationColony formationCodonProtein
1987
Genetic and biochemical definition of the bovine papillomavirus E5 transforming protein.
Burkhardt A, DiMaio D, Schlegel R. Genetic and biochemical definition of the bovine papillomavirus E5 transforming protein. The EMBO Journal 1987, 6: 2381-2385. PMID: 2822390, PMCID: PMC553643, DOI: 10.1002/j.1460-2075.1987.tb02515.x.Peer-Reviewed Original ResearchConceptsFirst methionine codonMethionine codonE5 proteinCellular membranesAmino-terminal mutationsFrameshift mutationBovine papillomavirus E5Mutant viral genomesCellular transformationInitiation codonHydrophobic polypeptidesBPV genomeSmall polypeptidesCell transformationCodonViral genomeE5 ORFProteinBovine papillomavirusGenetic alterationsMutationsPolypeptideForm dimersGenomeFrame mutationsCloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae
Weygand-Durasevic I, johnson-Burke D, Söll D. Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae. Nucleic Acids Research 1987, 15: 1887-1904. PMID: 3031581, PMCID: PMC340606, DOI: 10.1093/nar/15.5.1887.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseSingle open reading frameAbundant yeast proteinsGenomic Southern blotsNuclease S1 analysisOpen reading frameTranslation initiation codonAmino acid sequenceKb SalI fragmentNucleotide sequence analysisAT-rich sequencesYeast proteinsStructural geneCodon usageS1 analysisTATA boxInitiation codonReading frameSer geneSalI fragmentAcid sequenceExpression librarySequence analysisRich sequencesSouthern blot
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