2025
CryoEM structures of Kv1.2 potassium channels, conducting and non-conducting
Wu Y, Yan Y, Yang Y, Bian S, Rivetta A, Allen K, Sigworth F. CryoEM structures of Kv1.2 potassium channels, conducting and non-conducting. ELife 2025, 12: rp89459. PMID: 39945513, PMCID: PMC11825129, DOI: 10.7554/elife.89459.Peer-Reviewed Original ResearchConceptsIon occupancyIon binding sitesTerminal amineSelectivity filterIon densityLow-resolution structureProtein conformationIonsDetergent micellesPotassium channelsToxin blockVoltage-gated potassium channel Kv1.2Non-conductingStructureVoltage-gated potassium channelsPotassium channel Kv1.2Kv1.2 potassium channelChannel's outer mouthBinding sitesAminesCarbonylCryoEM structures of Kv1.2 potassium channels, conducting and non-conducting
Wu Y, Yan Y, Yang Y, Bian S, Rivetta A, Allen K, Sigworth F. CryoEM structures of Kv1.2 potassium channels, conducting and non-conducting. ELife 2025, 12 DOI: 10.7554/elife.89459.4.Peer-Reviewed Original ResearchIon occupancyIon binding sitesTerminal amineIon densitySelectivity filterLow-resolution structureProtein conformationIonsDetergent micellesPotassium channelsToxin blockVoltage-gated potassium channel Kv1.2Non-conductingStructureVoltage-gated potassium channelsPotassium channel Kv1.2Kv1.2 potassium channelChannel's outer mouthBinding sites
2024
Using in vivo intact structure for system-wide quantitative analysis of changes in proteins
Son A, Kim H, Diedrich J, Bamberger C, McClatchy D, Lipton S, Yates J. Using in vivo intact structure for system-wide quantitative analysis of changes in proteins. Nature Communications 2024, 15: 9310. PMID: 39468068, PMCID: PMC11519357, DOI: 10.1038/s41467-024-53582-x.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseProtein footprinting methodGlobal expression profilingIn vivo conformationStructural alterations of proteinsCo-expressed proteinsMass spectrometry-based methodsAlterations of proteinsProteostasis dysfunctionSpectrometry-based methodsProtein misfoldingConformation of proteinsStructural changesLysine residuesDynamic structural changesBiological functionsProteomics experimentsDimethyl labelingExpression profilesProtein conformationConformational changesProteinIntact proteinDesign of therapeutic interventionsMeasuring dynamic structural changesDNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force
Chung M, Zhou K, Powell J, Lin C, Schwartz M. DNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force. ACS Nano 2024, 18: 27590-27596. PMID: 39344156, PMCID: PMC11518680, DOI: 10.1021/acsnano.4c08663.Peer-Reviewed Original ResearchConceptsTalin rod domainNegative-stain electron microscopyDouble-stranded DNADNA clampProtein functionRod domainCryptic sitesProtein interactionsMolecular clampCellular mechanotransductionStudy proteinsBiochemical studiesCell biologyAdult physiologyProtein conformationTalinProteinBiochemical scaleMultiple diseasesDNAARPC5LVinculinStructural analysisEmbryogenesisDNA-based devicesCellular Prion Protein Conformational Shift after Liquid–Liquid Phase Separation Regulated by a Polymeric Antagonist and Mutations
Liu Y, Tuttle M, Kostylev M, Roseman G, Zilm K, Strittmatter S. Cellular Prion Protein Conformational Shift after Liquid–Liquid Phase Separation Regulated by a Polymeric Antagonist and Mutations. Journal Of The American Chemical Society 2024, 146: 27903-27914. PMID: 39326869, PMCID: PMC11469297, DOI: 10.1021/jacs.4c10590.Peer-Reviewed Original ResearchConceptsLiquid-liquid phase separationCellular prion proteinAssociated with neurodegenerative diseasesAmyloid-bMaturation processDisordered proteinsPrion proteinConformational shiftProtein conformationConformational changesNeurodegenerative diseasesInduction conditionsConformational statesProteinPrPMutationsPhase separationSaturating concentrationsMolecular motionSolid-like stateMaturationDisease-related cognitive deficitsNeurodegenerationInductionAlzheimer
2022
Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers
Wei R, Khaniya U, Mao J, Liu J, Batista V, Gunner M. Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers. Photosynthesis Research 2022, 156: 101-112. PMID: 36307598, DOI: 10.1007/s11120-022-00973-0.Peer-Reviewed Original ResearchConceptsProtonation stateMolecular dynamicsProton affinityReaction centersSide chainsElectron transfer reactionsProton transfer pathwayHydroxy side chainsBacterial reaction centersProton-transfer networkPhotosynthetic reaction centersChains of waterGrotthuss mechanismTransfer reactionsActive siteTransfer pathwayQB siteProton bindingProtein conformationTransmembrane electrochemical gradient
2021
Protein S-Nitrosylation in Neuronal Development
Nakamura T, Zhang X, Oh C, Lipton S. Protein S-Nitrosylation in Neuronal Development. 2021, 91-105. DOI: 10.1201/9781003204091-10.Peer-Reviewed Original ResearchPost-translational modificationsProtein S-nitrosylationS-nitrosylationReactive nitrogen speciesNeuronal developmentNeuronal differentiationTranscription factor MEF2Protein-protein interactionsIon channel activityProtein traffickingEnzymatic functionCysteine thiolsProtein conformationCellular mechanismsChannel activityNormal brain developmentNitrogen speciesSynaptic functionNitric oxide actsPathological processesBiological actionsProteinNeuronal survivalBiological systemsNeurogenesis
2018
Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins
Kisley L, Miller K, Davis CM, Guin D, Murphy EA, Gruebele M, Leckband DE. Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins. Biomacromolecules 2018, 19: 3894-3901. PMID: 30064224, DOI: 10.1021/acs.biomac.8b01120.Peer-Reviewed Original ResearchConceptsProtein melting temperatureBiotechnological applicationsSpecific proteinsProtein conformationTryptophan fluorescenceProteinTryptophan residuesThermal denaturation studiesDenaturation studiesCooperativity increasesProtein bindingPSBLocal polarityInteractsResiduesPEG solutionBindingCooperativityConformationFluorescence
2015
Ion Channels Are Membrane Proteins
Levitan I, Kaczmarek L. Ion Channels Are Membrane Proteins. 2015, 85-102. DOI: 10.1093/med/9780199773893.003.0005.ChaptersMembrane-spanning segmentsHomologous domainsPrimary subunitIon channelsFunctional potassium channelsPotassium channelsVoltage-dependent ion channelsThree-dimensional structureMembrane proteinsSodium channelsMutational analysisProtein regionsVoltage-gated sodiumChannel proteinsChannel gatingProtein conformationStructural modulesChannel poreGlobal changeVoltage-dependent activationVoltage-dependent channelsSubunitsProteinOverall structureIon selectivity
2014
C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation
Qiu B, Zhang K, Wang S, Sun F. C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation. Biochemical And Biophysical Research Communications 2014, 446: 380-386. PMID: 24613384, DOI: 10.1016/j.bbrc.2014.02.125.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBinding SitesConserved SequenceCrystallography, X-RayGuanine Nucleotide Exchange FactorsModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedNuclear Magnetic Resonance, BiomolecularProtein ConformationProtein StabilityProtein Structure, SecondaryRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidStatic ElectricityStructural Homology, ProteinConceptsGuanine exchange factorSec7 domainARF-GEFCatalytic domainActivity regulationGolgi network membranesNucleotide exchange activityC-terminal motifGEF catalytic activityADP-ribosylation factorCatalytic activity regulationExchange activityActivation of ARFARF-GEFsMembrane trafficExchange factorHelix JOrganelle structureMolecular detailsMutagenesis studiesProtein conformationLoop regionMotifRegulationKey role
2011
Chiral Sum Frequency Generation Spectroscopy for Characterizing Protein Secondary Structures at Interfaces
Fu L, Liu J, Yan EC. Chiral Sum Frequency Generation Spectroscopy for Characterizing Protein Secondary Structures at Interfaces. Journal Of The American Chemical Society 2011, 133: 8094-8097. PMID: 21534603, DOI: 10.1021/ja201575e.Peer-Reviewed Original ResearchConceptsChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyFrequency generation spectroscopyProtein secondary structureVibrational signaturesGeneration spectroscopyChiral SFG spectroscopyChiral SFG spectraRandom coilSecondary structureΑ-helixΒ-sheetLipid-water interfaceSFG spectroscopyHuman islet amyloidPeptide backboneSFG spectraH stretchAmide IReal-time characterizationSpectroscopyProtein conformationIslet amyloidStructureSitu
2009
Complex N-Linked Glycans on Asn-89 of Kaposi Sarcoma Herpes Virus-encoded Interleukin-6 Mediate Optimal Function by Affecting Cytokine Protein Conformation*
Dela Cruz CS, Viswanathan SR, El-Guindy AS, Shedd D, Miller G. Complex N-Linked Glycans on Asn-89 of Kaposi Sarcoma Herpes Virus-encoded Interleukin-6 Mediate Optimal Function by Affecting Cytokine Protein Conformation*. Journal Of Biological Chemistry 2009, 284: 29269-29282. PMID: 19690161, PMCID: PMC2785557, DOI: 10.1074/jbc.m109.039115.Peer-Reviewed Original ResearchConceptsVIL-6IL-6RalphaProtein conformationComplex glycansHuman cellular homologueSimilar biological functionsKaposi's sarcoma-associated herpesvirusAsn-89Conformation-specific antibodiesCellular homologueCytokine functionSarcoma-associated herpesvirusProtein functionHigh-mannose glycansBiological functionsViral cytokineDigestion assaysMannose glycansGp130Optimal functionGlycansGlycosylationHuman IL-6HuIL-6Intracellular production
2007
Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions.
Tsutsui Y, Wintrode P. Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Current Medicinal Chemistry 2007, 14: 2344-58. PMID: 17896983, DOI: 10.2174/092986707781745596.Peer-Reviewed Original ResearchConceptsProtein assembliesMolecular basisProtein structureNuclear magnetic resonance spectroscopyHydrogen/deuterium exchangeLarge protein assembliesD exchange processX-ray crystallographyDrugs/inhibitorsDynamics of proteinsBackbone amide hydrogensExchange processMagnetic resonance spectroscopyLocal structural environmentPatho-physiological processesViral capsid structureAmide hydrogensHXMSDeuterium exchangeMass spectrometrySmall sample requirementDrug designHigh-quality crystalsResonance spectroscopyProtein conformation
2006
Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. PLOS ONE 2006, 1: e136. PMID: 17205140, PMCID: PMC1762422, DOI: 10.1371/journal.pone.0000136.Peer-Reviewed Original ResearchConceptsGene regulationNucleoprotein complexesNon-specific DNA-binding proteinE. coli lac repressorWild-type E. coli strainDNA-binding proteinsSmall DNA loopsSame DNA moleculeGene repressionDNA loopingDNA loopsOperator sitesOperator affinityDNA rigidityLac repressorE. coli strainsProtein conformationDNA persistence lengthDNA moleculesRepressor concentrationRepressionColi strainsDNARegulationVivoMechanisms of Mechanotransduction
Orr AW, Helmke BP, Blackman BR, Schwartz MA. Mechanisms of Mechanotransduction. Developmental Cell 2006, 10: 11-20. PMID: 16399074, DOI: 10.1016/j.devcel.2005.12.006.Peer-Reviewed Original Research
2001
Y265H Mutator Mutant of DNA Polymerase β PROPER GEOMETRIC ALIGNMENT IS CRITICAL FOR FIDELITY*
Shah A, Li S, Anderson K, Sweasy J. Y265H Mutator Mutant of DNA Polymerase β PROPER GEOMETRIC ALIGNMENT IS CRITICAL FOR FIDELITY*. Journal Of Biological Chemistry 2001, 276: 10824-10831. PMID: 11154692, DOI: 10.1074/jbc.m008680200.Peer-Reviewed Original ResearchConceptsDNA polymerase betaPolymerase betaVivo genetic screenWild-type proteinWild-type enzymeActive site residuesGenetic screenTyr-265Mutant proteinsMutator mutantsPolymerase structureProper geometric alignmentSite residuesProtein conformationNucleotidyl transferForward mutationDNA polymerasePolymerase fidelityDNTP substratesDNA synthesisProteinDeoxynucleoside triphosphatesFirst evidenceTemplate A.Enzyme
1994
Heat shock proteins and molecular chaperones: Mediators of protein conformation and turnover in the cell
Craig E, Weissman J, Horwich A. Heat shock proteins and molecular chaperones: Mediators of protein conformation and turnover in the cell. Cell 1994, 78: 365-372. PMID: 7914834, DOI: 10.1016/0092-8674(94)90416-2.Peer-Reviewed Original Research
1991
Serine modulates substrate channeling in tryptophan synthase. A novel intersubunit triggering mechanism
Anderson K, Miles E, Johnson K. Serine modulates substrate channeling in tryptophan synthase. A novel intersubunit triggering mechanism. Journal Of Biological Chemistry 1991, 266: 8020-8033. PMID: 1902468, DOI: 10.1016/s0021-9258(18)92934-0.Peer-Reviewed Original ResearchConceptsIndole-3-glycerol phosphateTryptophan synthaseProtein conformationAlpha 2 beta 2 complexReaction of serineAbsence of serineBeta siteFormation of tryptophanAlpha siteSteady-state turnoverActive siteAccumulation of indoleAlpha reactionSubstitution of cysteineSubstrate channelingBeta reactionBeta subunitMetabolic intermediatesSerineAlpha subunitQuench-flowProtein fluorescenceTurnover experimentsProteinTryptophan release
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply