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 dimerMutationsResidues
2014
Conformational Preferences Underlying Reduced Activity of a Thermophilic Ribonuclease H
Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational Preferences Underlying Reduced Activity of a Thermophilic Ribonuclease H. Journal Of Molecular Biology 2014, 427: 853-866. PMID: 25550198, PMCID: PMC4349505, DOI: 10.1016/j.jmb.2014.11.023.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesCrystallography, X-RayEscherichia coliHot TemperatureHydrophobic and Hydrophilic InteractionsModels, MolecularMolecular Dynamics SimulationMutationNuclear Magnetic Resonance, BiomolecularPrincipal Component AnalysisProtein BindingProtein ConformationRibonuclease HThermodynamicsThermus thermophilusConceptsE. coli homologWild-type proteinRibonuclease HE. coli mutantsGlycine-rich regionMesophilic homologsThermophilus enzymeColi mutantsSubstrate bindingThermophilic proteinsImportant residuesThermus thermophilusConformational dynamicsGlycine residueMesophilic enzymesActive conformationLoop regionAtom MD simulationsConformational basisReduced activityEscherichia coliHomologProteinPosition 80MD simulations
2013
Receptor tyrosine kinases with intracellular pseudokinase domains
Mendrola JM, Shi F, Park JH, Lemmon MA. Receptor tyrosine kinases with intracellular pseudokinase domains. Biochemical Society Transactions 2013, 41: 1029-1036. PMID: 23863174, PMCID: PMC3777422, DOI: 10.1042/bst20130104.Peer-Reviewed Original ResearchConceptsWeak kinase activityKinase activitySignificant kinase activityReceptor tyrosine kinasesPseudokinase domainHuman proteomeProtein kinaseImportant residuesWnt receptorsTyrosine kinaseEGFR familyKinaseFunctional studiesRTKPseudokinasesPseudokinaseProteomeReceptorsWntNew lightErbB3MutationsResiduesActivityRecent work
2011
Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism
Bhattacharyya M, Vishveshwara S. Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism. Biochemistry 2011, 50: 6225-6236. PMID: 21650159, DOI: 10.1021/bi200306u.Peer-Reviewed Original ResearchConceptsPyrrolysyl-tRNA synthetaseDimeric proteinFunctioning of proteinsSequence/structureAllosteric regulationAllosteric communicationAnticodon recognitionTRNA synthetasesImportant residuesAllosteric mechanismKey residuesSubtle rearrangementsProteinKey playersPyrrolysineFunctional aspectsSynthetaseResiduesAtypical enzymeGlobal perturbationsComprehensive viewComplexesStructure networkMolecular dynamics simulationsPylRSRare mutations in the human Na-K-Cl cotransporter (NKCC2) associated with lower blood pressure exhibit impaired processing and transport function
Monette MY, Rinehart J, Lifton RP, Forbush B. Rare mutations in the human Na-K-Cl cotransporter (NKCC2) associated with lower blood pressure exhibit impaired processing and transport function. American Journal Of Physiology. Renal Physiology 2011, 300: f840-f847. PMID: 21209010, PMCID: PMC3074999, DOI: 10.1152/ajprenal.00552.2010.Peer-Reviewed Original ResearchConceptsHEK-293 cellsNa-K-Cl cotransporterTransport functionMajor salt transport pathwayPlasma membrane localizationHEK cellsLow transport activitySequence conservationMembrane localizationProtein functionHeterologous expressionXenopus laevis oocytesImportant residuesMutantsRenal salt reabsorptionMolecular mechanismsIndependent mutationsConstitutive activityTransport activityBlood pressureFunctional consequencesImpaired transport functionSuch mutationsProcessing defectsLaevis oocytes
2008
25: Functional Analysis of Human Mutations in NAPI-IIC Reveals Important Residues for Surface Expression and Sodium-Phosphate Co-Transport
Bergwitz C, Jaureguiberry G, Carpenter T, Forman S, Jüppner H. 25: Functional Analysis of Human Mutations in NAPI-IIC Reveals Important Residues for Surface Expression and Sodium-Phosphate Co-Transport. American Journal Of Kidney Diseases 2008, 51: b34. DOI: 10.1053/j.ajkd.2008.02.030.Peer-Reviewed Original Research
2005
Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity
Raviscioni M, Gu P, Sattar M, Cooney AJ, Lichtarge O. Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity. Journal Of Molecular Biology 2005, 350: 402-415. PMID: 15946684, DOI: 10.1016/j.jmb.2005.04.054.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionComputational BiologyDNADNA Mutational AnalysisDNA-Binding ProteinsEntropyEvolution, MolecularGenomicsHumansModels, GeneticModels, StatisticalMutationNucleic Acid ConformationPhylogenyProtein BindingProtein EngineeringReceptors, Cytoplasmic and NuclearReceptors, EstrogenResponse ElementsSoftwareThermodynamicsTranscription FactorsConceptsDNA binding specificityTranscription factorsBinding specificityEvolutionary importanceEvolutionary pressureResponse elementInteracting Transcription FactorsRational engineeringRelative evolutionary importanceProtein-DNA interfaceProtein-DNA interactionsTranscription factor proteinsDNA response elementsAmino acid residuesNuclear hormone receptorsTranscriptional regulatorsEvolutionary traceImportant residuesGene expressionRecognition codeMolecular mechanismsAcid residuesFactor proteinProtein residuesLRH-1
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