Featured Publications
Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing
Unbehaun A, Marintchev A, Lomakin IB, Didenko T, Wagner G, Hellen C, Pestova TV. Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. The EMBO Journal 2007, 26: 3109-3123. PMID: 17568775, PMCID: PMC1914099, DOI: 10.1038/sj.emboj.7601751.Peer-Reviewed Original ResearchPhysical Association of Eukaryotic Initiation Factor 4G (eIF4G) with eIF4A Strongly Enhances Binding of eIF4G to the Internal Ribosomal Entry Site of Encephalomyocarditis Virus and Is Required for Internal Initiation of Translation
Lomakin I, Hellen C, Pestova T. Physical Association of Eukaryotic Initiation Factor 4G (eIF4G) with eIF4A Strongly Enhances Binding of eIF4G to the Internal Ribosomal Entry Site of Encephalomyocarditis Virus and Is Required for Internal Initiation of Translation. Molecular And Cellular Biology 2000, 20: 6019-6029. PMID: 10913184, PMCID: PMC86078, DOI: 10.1128/mcb.20.16.6019-6029.2000.Peer-Reviewed Original ResearchConceptsInternal ribosomal entry siteEMCV internal ribosomal entry siteEIF4GAdditional amino-terminal sequenceEukaryotic initiation factor 4GRNA recognition motifEukaryotic initiation factor 4GIInternal ribosomal entryEntry siteComplex formationBeta-globin mRNAAmino-terminal sequenceEncephalomyocarditis virus internal ribosomal entry siteRibosomal entryRecognition motifLike domainMutational analysisPhysical associationInternal initiationHigh-affinity bindingBinding fragmentSpecific interactionsRNASimilar affinitySpecific high-affinity bindingPosition of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing
Lomakin IB, Kolupaeva VG, Marintchev A, Wagner G, Pestova TV. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes & Development 2003, 17: 2786-2797. PMID: 14600024, PMCID: PMC280627, DOI: 10.1101/gad.1141803.Peer-Reviewed Original ResearchAnimalsBinding SitesCodon, InitiatorEukaryotic Initiation Factor-1Eukaryotic Initiation Factor-3HumansHydroxyl RadicalModels, MolecularNucleic Acid ConformationPeptide Chain Initiation, TranslationalProtein BindingProtein FootprintingProtein Structure, TertiaryProtein SubunitsRecombinant Fusion ProteinsRibosomesRNA, MessengerRNA, RibosomalThe 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
2020
Structural properties of target binding by profilaggrin A and B domains and other S100 fused-type calcium-binding proteins
Hinbest AJ, Kim SR, Eldirany SA, Lomakin IB, Watson J, Ho M, Bunick CG. Structural properties of target binding by profilaggrin A and B domains and other S100 fused-type calcium-binding proteins. Journal Of Dermatological Science 2020, 100: 39-49. PMID: 32893105, PMCID: PMC7752840, DOI: 10.1016/j.jdermsci.2020.08.009.Peer-Reviewed Original ResearchAmino Acid SequenceAnnexin A2Binding SitesCrystallography, X-RayFilaggrin ProteinsHumansHydrophobic and Hydrophilic InteractionsIntermediate Filament ProteinsIntermediate FilamentsKeratinocytesKeratinsMolecular Docking SimulationMutationProtein BindingProtein Conformation, alpha-HelicalProtein DomainsProtein PrecursorsRecombinant ProteinsS100 Proteins
2016
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition
Gagnon MG, Roy RN, Lomakin IB, Florin T, Mankin AS, Steitz TA. Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Nucleic Acids Research 2016, 44: 2439-2450. PMID: 26809677, PMCID: PMC4797290, DOI: 10.1093/nar/gkw018.Peer-Reviewed Original ResearchAmino Acid SequenceAnimalsAnti-Bacterial AgentsAntimicrobial Cationic PeptidesBinding SitesCattleCrystallography, X-RayEscherichia coliInsect ProteinsModels, MolecularMolecular Sequence DataPeptides, CyclicProtein BindingProtein BiosynthesisRibosomesRNA, MessengerRNA, TransferSpecies SpecificityThermus thermophilus
2005
Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association
Kolupaeva VG, Unbehaun A, Lomakin IB, Hellen CU, Pestova TV. Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA 2005, 11: 470-486. PMID: 15703437, PMCID: PMC1370736, DOI: 10.1261/rna.7215305.Peer-Reviewed Original Research
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