2025
A highly selective ESIPT-mechanism-based, ratiometric fluorescent sensor for zinc ions
Jović M, Marković O, Newhouse T, Opsenica I, Selaković Ž. A highly selective ESIPT-mechanism-based, ratiometric fluorescent sensor for zinc ions. Dyes And Pigments 2025, 234: 112547. DOI: 10.1016/j.dyepig.2024.112547.Peer-Reviewed Original ResearchExcited-state intramolecular proton transferRatiometric fluorescent sensorFluorescent sensorRatiometric responses to Zn2Tetramic acidsIntramolecular proton transferPolar aprotic solventsBlue-shifted emission maximumResponse to Zn2Low detection limitEfficient fluorescent probeBind metal ionsAprotic solventsProton transferNMR studiesRatiometric sensingEmission bandsMetal ionsEmission maximumDetection limitStructural motifsUV lampZinc ionsStructural modificationsFluorescent probe
2024
RluA is the major mRNA pseudouridine synthase in Escherichia coli
Schaening-Burgos C, LeBlanc H, Fagre C, Li G, Gilbert W. RluA is the major mRNA pseudouridine synthase in Escherichia coli. PLOS Genetics 2024, 20: e1011100. PMID: 39241085, PMCID: PMC11421799, DOI: 10.1371/journal.pgen.1011100.Peer-Reviewed Original ResearchConceptsPseudouridine synthasesHigh-confidence sitesMRNA-modifying enzymesE. coli mRNAsStructure probing dataIdentified target sitesTarget siteDiverse eukaryotesBacterial mRNAsRNA modificationsRluAEscherichia coliSecondary structureE. coliTRNAPseudouridineRRNAStructural motifsMRNAModification capacityRecognition elementsSynthaseRNASequenceEukaryotesThe Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches
Barth K, Hiller D, Strobel S. The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches. Biochemistry 2024, 63: 487-497. PMID: 38329042, PMCID: PMC11306416, DOI: 10.1021/acs.biochem.3c00586.Peer-Reviewed Original ResearchCyclic di-GMPLigand specificityHigh-throughput mutational analysisLigand contactsRegulate downstream gene expressionDownstream gene expressionDistal nucleotidesTerminal helixSequence differencesChemically similar ligandsRiboswitchNucleotideLigand-binding pocketMutation analysisVariant familiesGene expressionSmall molecule ligandsBinding sitesBinding pocketStructural motifsCrystal structureMolecule ligandsLigandSequenceMotif
2023
SLC6 neurotransmitter transporter family in GtoPdb v.2023.1
Bröer S, Rudnick G. SLC6 neurotransmitter transporter family in GtoPdb v.2023.1. IUPHAR/BPS Guide To Pharmacology CITE 2023, 2023 DOI: 10.2218/gtopdb/f144/2023.1.Peer-Reviewed Original ResearchSolute carrier family 6Transporter familyNeurotransmitter transporter familyDependent neurotransmitter transportersAmino acid transportersDependent amino acid transporterNSS transportersTM segmentsPlasma membraneNeurotransmitter transportersAcid transportersFamily 6Neutral amino acidsAmino acidsTransportersStructural motifsGtoPdb v.LeuTAeolicusSubfamiliesFamilyLeuTAaMembersMotifCrystal structure
2019
SLC6 neurotransmitter transporter family (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database
Bröer S, Rudnick G. SLC6 neurotransmitter transporter family (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database. IUPHAR/BPS Guide To Pharmacology CITE 2019, 2019 DOI: 10.2218/gtopdb/f144/2019.4.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsSolute carrier family 6Transporter familyNeurotransmitter transporter familyDependent neurotransmitter transportersAmino acid transportersDependent amino acid transporterNSS transportersTM segmentsPlasma membraneNeurotransmitter transportersAcid transportersFamily 6Neutral amino acidsIUPHAR/BPS GuideAmino acidsTransportersStructural motifsLeuTAeolicusSubfamiliesFamilyPharmacology DatabaseLeuTAaMembersMotifmRNA structure determines modification by pseudouridine synthase 1
Carlile TM, Martinez NM, Schaening C, Su A, Bell TA, Zinshteyn B, Gilbert WV. mRNA structure determines modification by pseudouridine synthase 1. Nature Chemical Biology 2019, 15: 966-974. PMID: 31477916, PMCID: PMC6764900, DOI: 10.1038/s41589-019-0353-z.Peer-Reviewed Original ResearchConceptsMRNA target recognitionMRNA pseudouridylationMRNA targetsPost-transcriptional RNA modificationsRational mutational analysisRNA-protein interactionsPseudouridine synthase 1High-throughput kinetic analysisRNA structural motifsPseudouridine synthasePseudouridine synthasesRNA pseudouridylationRNA modificationsPseudouridylationMRNA structureRNA-RNAMutational analysisGene expressionRNA structurePredominant mRNAStructural context informationSynthase 1Specific sequencesComputational predictionsStructural motifs
2016
Mechanism of substrate specificity of phosphatidylinositol phosphate kinases
Muftuoglu Y, Xue Y, Gao X, Wu D, Ha Y. Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 8711-8716. PMID: 27439870, PMCID: PMC4978281, DOI: 10.1073/pnas.1522112113.Peer-Reviewed Original ResearchConceptsPhosphatidylinositol phosphate kinaseKinase familySubstrate specificityPhosphate kinasePhosphatidylinositol phosphate kinase (PIPK) familyZebrafish type IMembrane trafficking processesExquisite substrate specificityType III kinaseEukaryotic cellsInositol ringPhosphorylation resultsSubstrate recognitionTrafficking processesSpecificity loopPhosphatidylinositol derivativesBiological functionsPhosphatidylinositol 4PhosphatidylinositolKinaseStructural motifsType IBisphosphateLoop functionsComplex patterns
2015
Coilin: The first 25 years
Machyna M, Neugebauer KM, Staněk D. Coilin: The first 25 years. RNA Biology 2015, 12: 590-596. PMID: 25970135, PMCID: PMC4615369, DOI: 10.1080/15476286.2015.1034923.Peer-Reviewed Original Research
2014
Sequence and conformational preferences at termini of α‐helices in membrane proteins: Role of the helix environment
Shelar A, Bansal M. Sequence and conformational preferences at termini of α‐helices in membrane proteins: Role of the helix environment. Proteins Structure Function And Bioinformatics 2014, 82: 3420-3436. PMID: 25257385, DOI: 10.1002/prot.24696.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsComputational BiologyConserved SequenceDatabases, ProteinHumansHydrogen BondingHydrophobic and Hydrophilic InteractionsLipid BilayersMembrane ProteinsModels, BiologicalProtein ConformationProtein FoldingProtein StabilityProtein Structure, SecondarySoftware ValidationTerminology as TopicConceptsMembrane proteinsSequence preferenceΑ-helixC-terminusHelical membrane proteinsCommon secondary structural elementsHelix terminiStructural motifsSecondary structural elementsSecondary structure predictionRat neurotensin receptorTransmembrane helicesMembrane environmentHelix bundleSequencing studiesHelical positionsAmino acidsProteinStructure predictionTerminusMembrane coreGlobular proteinsMotifHelixConformational preferences
2011
Highly Anisotropic Stability and Folding Kinetics of a Single Coiled Coil Protein under Mechanical Tension
Gao Y, Sirinakis G, Zhang Y. Highly Anisotropic Stability and Folding Kinetics of a Single Coiled Coil Protein under Mechanical Tension. Journal Of The American Chemical Society 2011, 133: 12749-12757. PMID: 21707065, PMCID: PMC3670761, DOI: 10.1021/ja204005r.Peer-Reviewed Original Research
2010
Evolutionary divergence and functions of the human interleukin (IL) gene family
Brocker C, Thompson D, Matsumoto A, Nebert DW, Vasiliou V. Evolutionary divergence and functions of the human interleukin (IL) gene family. Human Genomics 2010, 5: 30. PMID: 21106488, PMCID: PMC3390169, DOI: 10.1186/1479-7364-5-1-30.Peer-Reviewed Original ResearchConceptsHelical cytokinesCell typesAmino acid conservationEvolutionary divergenceOrthologous proteinsEvolutionary relationshipsGene familyImmune cell differentiationCommon structural motifBiological functionsCell differentiationUnique structural featuresExact functionStructural featuresGroup of cytokinesMajor groupsCell proliferationImportant roleImmune systemReceptor-binding propertiesHost immune systemStructural motifsStructural informationContinual competitionNumber of interleukinDiscovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening
Ravindranathan KP, Mandiyan V, Ekkati AR, Bae JH, Schlessinger J, Jorgensen WL. Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening. Journal Of Medicinal Chemistry 2010, 53: 1662-1672. PMID: 20121196, PMCID: PMC2842983, DOI: 10.1021/jm901386e.Peer-Reviewed Original ResearchConceptsFibroblast growth factorCo-crystal structureKinase structureFGFR1 kinaseSearch of inhibitorsEmbryonic developmentProtein structureAlternative conformationsCell proliferationStructural motifsKinase inhibitorsGrowth factorNew structural motifDiverse compoundsVirtual screeningFGFR1InhibitorsDockingWound healingThienopyrimidinone derivativesImportant roleConformationKinaseProteinMotif
2009
Metal binding sheds light on mechanisms of amyloid assembly
Calabrese MF, Miranker AD. Metal binding sheds light on mechanisms of amyloid assembly. Prion 2009, 3: 1-4. PMID: 19377278, PMCID: PMC2676736, DOI: 10.4161/pri.3.1.8601.Peer-Reviewed Original Research
2008
Phylogenetic, Structural and Functional Relationships between WD- and Kelch-Repeat Proteins
Hudson AM, Cooley L. Phylogenetic, Structural and Functional Relationships between WD- and Kelch-Repeat Proteins. Subcellular Biochemistry 2008, 48: 6-19. PMID: 18925367, DOI: 10.1007/978-0-387-09595-0_2.Peer-Reviewed Original ResearchConceptsΒ-propeller proteinsKelch repeat proteinWidespread protein familyWD-repeat proteinΒ-propeller structureΒ-propeller foldΒ-propeller domainWD repeatsMolecular functionsCommon ancestorProtein familyEvolutionary advantageDiverse familySimilar functionsProteinΒ-sheetKelchStructural motifsRepeat unitsExhibit similaritiesMotifFunctional relationshipFamilySuperfamilyAncestor
2007
Electron Tomography of Macromolecular Assemblies
Winkler H, Liu J, Taylor K, Zhu P, Roux K. Electron Tomography of Macromolecular Assemblies. 2007, 240-243. DOI: 10.1109/isbi.2007.356833.Peer-Reviewed Original Research
2004
Mutational Analysis of Terminal Deoxynucleotidyltransferase- Mediated N-Nucleotide Addition in V(D)J Recombination
Repasky JA, Corbett E, Boboila C, Schatz DG. Mutational Analysis of Terminal Deoxynucleotidyltransferase- Mediated N-Nucleotide Addition in V(D)J Recombination. The Journal Of Immunology 2004, 172: 5478-5488. PMID: 15100289, DOI: 10.4049/jimmunol.172.9.5478.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibody DiversityCell LineCHO CellsCricetinaeDNA Mutational AnalysisDNA NucleotidylexotransferaseDNA-Binding ProteinsGene RearrangementHomeodomain ProteinsHumansImmunoglobulin Joining RegionImmunoglobulin Variable RegionIsoenzymesMiceNuclear ProteinsNucleotidesOpen Reading FramesPlasmidsRecombination, GeneticSignal TransductionSubstrate SpecificityTemplates, GeneticConceptsNucleotide additionEntire C-terminal regionAg receptor genesProtein-DNA interactionsC-terminal domainStructure-function analysisC-terminal regionN-terminal portionIndividual structural motifsUnique DNA polymeraseBRCT domainHelix domainTdT proteinCatalytic regionDeletional analysisMutational analysisLong isoformNontemplated (N) nucleotidesNucleotide deletionDNA polymeraseDiverse repertoireReceptor geneStructural motifsNonlymphoid cellsCritical role
2001
The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
Senes A, Ubarretxena-Belandia I, Engelman D. The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 9056-9061. PMID: 11481472, PMCID: PMC55372, DOI: 10.1073/pnas.161280798.Peer-Reviewed Original ResearchConceptsMembrane protein structuresMembrane protein foldingTransmembrane helix associationTransmembrane helix interactionsHelix-helix interactionsTransmembrane helicesProtein foldingPacking interfaceHelix associationHelix interactionsProtein structureDeterminants of stabilityCalphaStructural motifsHelixSerineFoldingMotifHydrogen bondsImportant determinantInteractionGlycophorinSpecificityCαDeterminants
1998
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
Basu S, P. Rambo R, Strauss-Soukup J, H.Cate J, R. Ferré-D´Amaré A, Strobel S, Doudna J. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Structural & Molecular Biology 1998, 5: 986-992. PMID: 9808044, DOI: 10.1038/2960.Peer-Reviewed Original ResearchConceptsP4-P6 domainTetraloop receptorCatalytic RNALarge catalytic RNAsGroup I intronRNA tertiary structure formationTertiary structure formationTertiary structural motifsI intronRNAWide diversityFoldingStructural motifsDivalent metal ionsPotassium ionsReceptorsIntronsAzoarcusDomainDiversityMotifSitesActivityMonovalent ions
1996
Association of RNase mitochondrial RNA processing enzyme with ribonuclease P in higher ordered structures in the nucleolus: a possible coordinate role in ribosome biogenesis.
Lee B, Matera AG, Ward DC, Craft J. Association of RNase mitochondrial RNA processing enzyme with ribonuclease P in higher ordered structures in the nucleolus: a possible coordinate role in ribosome biogenesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 11471-11476. PMID: 8876159, PMCID: PMC38081, DOI: 10.1073/pnas.93.21.11471.Peer-Reviewed Original ResearchConceptsMitochondrial RNA processing enzymeRibosomal RNA maturationRNA processing enzymesRNA maturationRibonuclease PRNase PProcessing enzymesSitu hybridization experimentsRNA structural motifsRibosome biogenesisRibosome assemblySmall subpopulationRibonucleoprotein particleRNA componentMacromolecular complexesRNA transcriptsHybridization experimentsFractionation experimentsCoordinate roleCytoplasmic structuresAffinity selectionEnzymeStructural motifsMethyl oligoribonucleotideNucleoli
1995
A new family of outwardly rectifying potassium channel proteins with two pore domains in tandem
Ketchum K, Joiner W, Sellers A, Kaczmarek L, Goldstein S. A new family of outwardly rectifying potassium channel proteins with two pore domains in tandem. Nature 1995, 376: 690-695. PMID: 7651518, DOI: 10.1038/376690a0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCaenorhabditis elegansCells, CulturedDNA PrimersDrosophilaMolecular Sequence DataOocytesPatch-Clamp TechniquesPotassiumPotassium ChannelsProtein ConformationRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidSodiumXenopus laevisConceptsP domainPotassium channel proteinCaenorhabditis elegansCommon structural motifChannel proteinsPore domainCellular membranesPrimary structureExcised membrane patchesSignature sequencesFlow of ionsAmino acidsXenopus laevisSelective currentMembrane potentialStructural motifsMembrane patchesPotassium channelsExternal divalent cationsDivalent cationsFunctional propertiesElegansVoltage-dependent mannerGenomeDomain
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