2023
Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease
Wang J, Maschietto F, Qiu T, Arantes P, Skeens E, Palermo G, Lisi G, Batista V. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal 2023, 122: 4635-4644. PMID: 37936350, PMCID: PMC10754686, DOI: 10.1016/j.bpj.2023.11.005.Peer-Reviewed Original ResearchConceptsHNH domainHNH nucleaseHigh fidelity enzymesInduced-fit mechanismActivation pathwayActive stateMolecular dynamics trajectoriesCognate substratesConformation 2Conformational selectionObligate stepAla mutantBackbone amidesΑ-helixSide chainsSingle LysEssential roleNucleasePathwayDynamics trajectoriesResiduesConformationMutantsInterconversion pathwaysCRISPR
2021
Cryo-EM structure of an open conformation of a gap junction hemichannel in lipid bilayer nanodiscs
Khan A, Jagielnicki M, Bennett B, Purdy M, Yeager M. Cryo-EM structure of an open conformation of a gap junction hemichannel in lipid bilayer nanodiscs. Structure 2021, 29: 1040-1047.e3. PMID: 34129834, PMCID: PMC9616683, DOI: 10.1016/j.str.2021.05.010.Peer-Reviewed Original ResearchConceptsLipid bilayer nanodiscsGap junction channelsHexameric hemichannelsExtracellular loopBilayer nanodiscsTransmembrane α-helicesCryo-EM structureGap junction hemichannelsAdjacent cell membranesIntercellular conduitsCell communicationCx hemichannelsPlasma membraneOpen conformationSecond extracellular loopJunction channelsΑ-helixConformational flexibilityCell membraneHemichannelsCx isoformsExtracellular spaceNanodiscsStructural foundationMembrane
2018
On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation
Wang J, Liu Z, Crabtree RH, Frank J, Moore PB. On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation. Protein Science 2018, 27: 2051-2061. PMID: 30242932, PMCID: PMC6237698, DOI: 10.1002/pro.3511.Peer-Reviewed Original ResearchConceptsLocal chemical effectsElectron beamElectron radiationChemical mechanismStructure effectsChemical effectsElectron microscopeBackbone atomsChemical damageΑ-helixThermoplasma acidophilumMoleculesDose-dependent degradationQuaternary structureElectronsBeamAtomsEM mapsRadiationStructureMicroscopeResolutionSmall changesAcidophilum
2017
Determination of chemical identity and occupancy from experimental density maps
Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Science 2017, 27: 411-420. PMID: 29027293, PMCID: PMC5775170, DOI: 10.1002/pro.3325.Peer-Reviewed Original ResearchConceptsCharge densityFourier transformElectrostatic potentialExperimental charge densitySolvent moleculesAtomic B-factorsElectron densityBasic electronic propertiesESP mapsProtein α-helixChemical identityActive siteElectronic propertiesLarge macromolecular complexesExperimental density mapsDensity mapsMoleculesVitreous iceMacromolecular complexesΑ-helixSmall protein subunitESP valuesTransformStructure factorSupercomplexesEffects of aligned α‐helix peptide dipoles on experimental electrostatic potentials
Wang J, Videla PE, Batista VS. Effects of aligned α‐helix peptide dipoles on experimental electrostatic potentials. Protein Science 2017, 26: 1692-1697. PMID: 28556371, PMCID: PMC5563131, DOI: 10.1002/pro.3204.Peer-Reviewed Original ResearchConceptsElectrostatic potentialEM mapsProtein αExperimental electrostatic potentialHelix dipoleDetailed molecular levelHigh-resolution electron microscopyDensity functional theory calculationsProtein functionStructural biologyFunctional theory calculationsElectron microscopyProtein α-helixPartial atomic chargesElectric fieldΑ-helixLong-range featuresMolecular levelNonlocal natureAtomic chargesTheory calculationsDipoleBackbone dipolesRecent breakthroughsProper calculation
2016
Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer
Shelar A, Bansal M. Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. Biochimica Et Biophysica Acta 2016, 1858: 2804-2817. PMID: 27521749, DOI: 10.1016/j.bbamem.2016.08.003.Peer-Reviewed Original ResearchConceptsInter-helical interactionsMembrane proteinsTM regionHelix perturbationTM helicesΠ-helixDistinct sequence signaturesIntegral membrane proteinsLow sequence identityHeme-copper oxidasesTransmembrane helicesProtein functionSequence signaturesSequence identityHydrophobic mismatchΑ-helixProtein chainsAmino acidsHelical fragmentsCopper oxidasesProteinHelix terminiHelixTerminusBilayers
2015
Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2* ♦
Zhang YH, Shetty K, Surleac MD, Petrescu AJ, Schatz DG. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2* ♦. Journal Of Biological Chemistry 2015, 290: 11802-11817. PMID: 25745109, PMCID: PMC4424321, DOI: 10.1074/jbc.m115.638627.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCatalytic DomainDNA-Binding ProteinsGene Expression RegulationGenome, HumanHEK293 CellsHomeodomain ProteinsHumansInterferometryMaleMiceMice, Inbred C57BLMolecular Sequence DataMutationNuclear ProteinsProtein BindingProtein Interaction MappingProtein Structure, SecondaryThymus GlandV(D)J RecombinationVDJ RecombinasesConceptsRegion of RAG1Α-helixZinc finger regionResidues N-terminalActive siteAcidic amino acidsPulldown assaysAccessory factorsHermes transposaseProteins RAG1Finger regionRAG activityQuantitative Western blottingC-terminusRAG endonucleaseN-terminalCatalytic functionRAG1Amino acidsDNA cleavageRAG2Nuclear concentrationRecombination activityCatalytic centerBiolayer interferometry
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
2013
Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy
Yu T, Wu G, Yang H, Wang J, Yu S. Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy. International Journal Of Biological Macromolecules 2013, 56: 57-61. PMID: 23403030, DOI: 10.1016/j.ijbiomac.2013.02.004.Peer-Reviewed Original Research
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
2010
Solution Structure and Phospholipid Interactions of the Isolated Voltage-Sensor Domain from KvAP
Butterwick JA, MacKinnon R. Solution Structure and Phospholipid Interactions of the Isolated Voltage-Sensor Domain from KvAP. Journal Of Molecular Biology 2010, 403: 591-606. PMID: 20851706, PMCID: PMC2971526, DOI: 10.1016/j.jmb.2010.09.012.Peer-Reviewed Original ResearchConceptsNuclear Overhauser effect spectroscopyNuclear magnetic resonance spectroscopySolution structureIsolated voltage-sensor domainBilayer-forming lipidsMagnetic resonance spectroscopyMicelle interactionsEffect spectroscopyChemical environmentCrystal structurePhospholipid interfaceChemical propertiesResonance spectroscopyPhospholipid micellesMembrane environmentPhospholipid bilayersNanosecond timescaleMillisecond timescaleMicellesSpectroscopyAmphipathic α-helixΑ-helixVoltage sensor domainRelaxation experimentsPhysical propertiesDynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients
Kenniston JA, Lemmon MA. Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients. The EMBO Journal 2010, 29: 3054-3067. PMID: 20700106, PMCID: PMC2944063, DOI: 10.1038/emboj.2010.187.Peer-Reviewed Original ResearchConceptsDynamin GTPase activityPH domain mutationsGTPase activityCNM mutationsConformational changesLarge GTPase dynaminGTP hydrolysis cycleC-terminal α-helixPleckstrin homology domainLow-resolution structureDomain mutationsReceptor-mediated endocytosisGTPase dynaminGTPase regulationPH domainScission functionCellular processesGTPase activationDynaminDomain rearrangementsVesicle invaginationGTPase rateCentronuclear myopathyHydrolysis cycleΑ-helix
2008
BAX activation is initiated at a novel interaction site
Gavathiotis E, Suzuki M, Davis ML, Pitter K, Bird GH, Katz SG, Tu HC, Kim H, Cheng E, Tjandra N, Walensky LD. BAX activation is initiated at a novel interaction site. Nature 2008, 455: 1076-1081. PMID: 18948948, PMCID: PMC2597110, DOI: 10.1038/nature07396.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsApoptosisApoptosis Regulatory Proteinsbcl-2-Associated X ProteinBcl-2-Like Protein 11BH3 Interacting Domain Death Agonist ProteinCell LineGene Expression RegulationHumansMembrane ProteinsMiceMutagenesis, Site-DirectedMutationNuclear Magnetic Resonance, BiomolecularProtein BindingProto-Oncogene ProteinsSequence AlignmentConceptsAnti-apoptotic proteinsInteraction sitesBax activationBax-mediated cell deathBCL-2 domainsCell deathBcl-2 familyNovel interaction sitePro-apoptotic proteinsPoint mutagenesisMitochondrial apoptosisBax interactionStress stimuliΑ-helixProteinNew targetsBaxTherapeutic modulationDirect activationActivation siteApoptosisActivationFunctional activitySitesMutagenesis
2000
Interhelical hydrogen bonding drives strong interactions in membrane proteins
Xiao Zhou F, Cocco M, Russ W, Brunger A, Engelman D. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nature Structural & Molecular Biology 2000, 7: 154-160. PMID: 10655619, DOI: 10.1038/72430.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAsparagineCell MembraneChloramphenicol O-AcetyltransferaseCircular DichroismDetergentsDimerizationDNA-Binding ProteinsElectrophoresis, Polyacrylamide GelFungal ProteinsGlycophorinsHydrogen BondingLeucine ZippersMagnetic Resonance SpectroscopyMembrane ProteinsMicellesMicrococcal NucleaseMolecular Sequence DataPeptidesProtein ConformationProtein KinasesProtein Structure, SecondaryRecombinant ProteinsSaccharomyces cerevisiae ProteinsConceptsMembrane proteinsHelix associationTransmembrane α-helicesIntegral membrane proteinsInterhelical hydrogen bondingModel transmembrane helixTransmembrane helicesMembrane helicesGCN4 leucine zipperLeucine zipperPolar residuesSoluble proteinHydrophobic leucineΑ-helixBiological membranesProteinHelixNon-specific interactionsValine (HAV) sequenceMembraneZipperFoldingMotifAsparagineResidues
1997
Spontaneous, pH-Dependent Membrane Insertion of a Transbilayer α-Helix †
Hunt J, Rath P, Rothschild K, Engelman D. Spontaneous, pH-Dependent Membrane Insertion of a Transbilayer α-Helix †. Biochemistry 1997, 36: 15177-15192. PMID: 9398245, DOI: 10.1021/bi970147b.Peer-Reviewed Original ResearchConceptsLipid bilayersIntegral membrane protein bacteriorhodopsinMembrane-spanning regionIntegral membrane proteinsPH-dependent membrane insertionAspartic acid residuesMembrane protein bacteriorhodopsinInsertion reactionMembrane insertionMembrane proteinsAqueous solutionHydrophobic sequenceAqueous bufferPoor solubilityAlpha-helixAcid residuesSignificant solubilityC-helixSpectroscopic assaysΑ-helixSecondary structureProtein bacteriorhodopsinNeutral pHPeptide associatesBilayersThe effect of point mutations on the free energy of transmembrane α-helix dimerization11Edited by M. F. Moody
Fleming K, Ackerman A, Engelman D. The effect of point mutations on the free energy of transmembrane α-helix dimerization11Edited by M. F. Moody. Journal Of Molecular Biology 1997, 272: 266-275. PMID: 9299353, DOI: 10.1006/jmbi.1997.1236.Peer-Reviewed Original ResearchConceptsSodium dodecylsulfateVan der Waals interactionsAnalytical ultracentrifugationDer Waals interactionsFree energyMolecular association eventsEnergy of dimerizationOctyl etherWaals interactionsMolecular modelingRelative energy scaleDetergent environmentReversible associationEnergy differenceSedimentation equilibriumMonomersTransmembrane α-helicesNon-denaturing detergent solutionsDimer formationΑ-helixDimer stateAssociation eventsDetergent solutionDissociationHelixStructure of the Transmembrane Cysteine Residues in Phospholamban
Arkin I, Adams P, Brünger A, Aimoto S, Engelman D, Smith S. Structure of the Transmembrane Cysteine Residues in Phospholamban. The Journal Of Membrane Biology 1997, 155: 199-206. PMID: 9050443, DOI: 10.1007/s002329900172.Peer-Reviewed Original ResearchConceptsTransmembrane domainCysteine residuesSide chainsPentameric complexCysteine side chainsTransmembrane cysteine residuesLong α-helixIntrahelical hydrogen bondsBackbone carbonyl oxygenSelective ion channelsPolar side chainsElectrostatic potential fieldCarbonyl oxygenSulfhydryl groupsHydrogen bondsMembrane proteinsWild-type phospholambanVibrational spectraMutagenesis studiesTransmembrane peptidesAlanine substitutionsMolecular dynamicsReticulum membraneElectrostatic calculationsΑ-helix
1995
Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban
Adams P, Arkin I, Engelman D, Brünger A. Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nature Structural & Molecular Biology 1995, 2: 154-162. PMID: 7749920, DOI: 10.1038/nsb0295-154.Peer-Reviewed Original ResearchConceptsPentameric ion channelsTransmembrane domainThree-dimensional structureMembrane proteinsHydrophobic residuesΑ-helixIon channelsComputational searchingEnvironmental constraintsTwo-bodyGlobal searchPhospholambanMutagenesisComputational methodsHomopentamerProteinExperimental dataResiduesData yields
1994
Specificity and promiscuity in membrane helix interactions
Lemmon M, Engelman D. Specificity and promiscuity in membrane helix interactions. Quarterly Reviews Of Biophysics 1994, 27: 157-218. PMID: 7984776, DOI: 10.1017/s0033583500004522.Peer-Reviewed Original ResearchConceptsIntegral membrane proteinsTransmembrane α-helicesMembrane proteinsΑ-helixMembrane protein foldingMembrane-spanning portionTransmembrane helix associationHelix-helix interactionsParticular helicesProtein foldingHelix associationHelix interactionsProsthetic groupLipid bilayersCharge-charge interactionsStereochemical fitFoldingProteinAccessible statesSpecificityOligomerizationInteractionPromiscuityHelixAssemblyA dimerization motif for transmembrane α–helices
Lemmon M, Treutlein H, Adams P, Brünger A, Engelman D. A dimerization motif for transmembrane α–helices. Nature Structural & Molecular Biology 1994, 1: 157-163. PMID: 7656033, DOI: 10.1038/nsb0394-157.Peer-Reviewed Original ResearchConceptsTransmembrane α-helicesHydrophobic transmembrane α-helicesSpecific helix-helix interactionsΑ-helixIntegral membrane proteinsHelix-helix interactionsHelix-helix interfaceDimerization motifSpecific dimerizationMembrane proteinsHelix associationFunctional analysisAmino acidsSuch motifsLipid bilayersMotifParticular motifsFoldingDimerizationSuch interactionsComplex membranesProteinOligomerizationVariety of systemsInteraction
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply