2003
Amphipols: polymeric surfactants for membrane biology research
Popot J, Berry E, Charvolin D, Creuzenet C, Ebel C, Engelman D, Flötenmeyer M, Giusti F, Gohon Y, Hervé P, Hong Q, Lakey J, Leonard K, Shuman H, Timmins P, Warschawski D, Zito F, Zoonens M, Pucci B, Tribet C. Amphipols: polymeric surfactants for membrane biology research. Cellular And Molecular Life Sciences 2003, 60: 1559-1574. PMID: 14513831, PMCID: PMC11138540, DOI: 10.1007/s00018-003-3169-6.Peer-Reviewed Original ResearchConceptsMembrane proteinsQuasi-irreversible mannerPolymeric surfactantsAmphiphilic polymersMembrane biologyAqueous solutionTransmembrane surfaceAmphipolsBiology researchDissociating characterPutative usesNative stateSurfactantsNovel familyProteinCurrent knowledgeRapid inactivationNoncovalentDetergentsPolymersBiologyCompoundsComplexesInactivationAbsence
2001
Specificity in transmembrane helix–helix interactions can define a hierarchy of stability for sequence variants
Fleming K, Engelman D. Specificity in transmembrane helix–helix interactions can define a hierarchy of stability for sequence variants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 14340-14344. PMID: 11724930, PMCID: PMC64683, DOI: 10.1073/pnas.251367498.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesDimerizationDrug StabilityElectrophoresis, Polyacrylamide GelGenetic VariationGlycophorinsHumansIn Vitro TechniquesMagnetic Resonance SpectroscopyMembrane ProteinsMutagenesis, Site-DirectedPoint MutationProtein FoldingProtein Structure, SecondaryRecombinant Fusion ProteinsThermodynamicsUltracentrifugationConceptsHelix-helix interactionsMembrane proteinsTransmembrane helix-helix interactionsSequence variantsHelical membrane proteinsTransmembrane helix dimerizationProtein-protein interactionsDifferent hydrophobic environmentsAlanine-scanning mutagenesisSedimentation equilibrium analytical ultracentrifugationEquilibrium analytical ultracentrifugationTransmembrane helicesHelix dimerizationGxxxG motifDimer interfaceNMR structureDimer stabilityAnalytical ultracentrifugationHydrophobic environmentProteinMutationsSequence dependenceEnergetic principlesHierarchy of stabilityMutagenesisComputation and mutagenesis suggest a right‐handed structure for the synaptobrevin transmembrane dimer
Fleming K, Engelman D. Computation and mutagenesis suggest a right‐handed structure for the synaptobrevin transmembrane dimer. Proteins Structure Function And Bioinformatics 2001, 45: 313-317. PMID: 11746678, DOI: 10.1002/prot.1151.Peer-Reviewed Original ResearchConceptsTransmembrane dimerSingle transmembrane segmentBiological membrane fusionProtein-protein interactionsRight-handed structureInterhelical hydrogen bondsSequence-specific mannerTransmembrane segmentsDimerization motifThree-dimensional structureMutagenesis studiesMembrane fusionSuccessful structure predictionSide-chain atomsStructure predictionSpecific mannerKey playersComputational searchDimersSynaptobrevinMutagenesisComputational methodsAssociation thermodynamicsMotifGlycophorinGenetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random Escherichia coli genomic library 1 1 Edited by G. von Heijne
Leeds J, Boyd D, Huber D, Sonoda G, Luu H, Engelman D, Beckwith J. Genetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random Escherichia coli genomic library 1 1 Edited by G. von Heijne. Journal Of Molecular Biology 2001, 313: 181-195. PMID: 11601855, DOI: 10.1006/jmbi.2001.5007.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAmino Acid SubstitutionBacteriophage lambdaBase SequenceBinding SitesCell MembraneCloning, MolecularDimerizationDNA-Binding ProteinsEscherichia coliEscherichia coli ProteinsGenes, BacterialGenetic VectorsGenomic LibraryMembrane ProteinsModels, MolecularMolecular Sequence DataProtein BindingProtein Sorting SignalsProtein Structure, QuaternaryProtein Structure, TertiaryProtein SubunitsProtein TransportRecombinant Fusion ProteinsRepressor ProteinsViral ProteinsViral Regulatory and Accessory ProteinsConceptsTransmembrane domainTransmembrane helix-helix associationE. coli inner membraneMembrane protein structuresGenomic DNA fragmentsHelix-helix associationG. von HeijneHelix-helix interactionsSite-directed mutagenesisSixth transmembrane domainTransmembrane helicesRepressor DNAGenetic toolsInner membraneVon HeijneProtein structureDNA fragmentsGenetic selectionNovel sequencesMultimerization motifMotifSequenceHomomultimerizationDomainMutagenesisThe 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 ResearchMeSH KeywordsAmino Acid SequenceGlycineHydrogen BondingMembrane ProteinsProtein ConformationSerineThreonineConceptsMembrane protein structuresMembrane protein foldingTransmembrane helix associationTransmembrane helix interactionsHelix-helix interactionsTransmembrane helicesProtein foldingPacking interfaceHelix associationHelix interactionsProtein structureDeterminants of stabilityCalphaStructural motifsHelixSerineFoldingMotifHydrogen bondsImportant determinantInteractionGlycophorinSpecificityCαDeterminantsHelical membrane proteins: diversity of functions in the context of simple architecture
Ubarretxena-Belandia I, Engelman D. Helical membrane proteins: diversity of functions in the context of simple architecture. Current Opinion In Structural Biology 2001, 11: 370-376. PMID: 11406389, DOI: 10.1016/s0959-440x(00)00217-7.Peer-Reviewed Original ResearchConceptsHelical membrane proteinsGenome-wide scaleAlpha-helical conformationDiversity of functionsIdentification of motifsMembrane proteinsProtein regionsHelix interactionsPolar sidechainsStructural roleLipid bilayersProteinDiversityMotifUse of deviationsConformationSidechainsFunctionFurther investigationBilayersSequestrationIdentificationPolar residues drive association of polyleucine transmembrane helices
Zhou F, Merianos H, Brunger A, Engelman D. Polar residues drive association of polyleucine transmembrane helices. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 2250-2255. PMID: 11226225, PMCID: PMC30124, DOI: 10.1073/pnas.041593698.Peer-Reviewed Original ResearchConceptsPolar residuesPolyleucine sequenceHelix associationTransmembrane helix associationInterhelical hydrogen bondingTransmembrane protein functionTransmembrane helicesForm homoProtein functionTransmembrane proteinDrive associationMembrane proteinsDetergent micellesAsparagine residuesGeneral structural featuresBiological membranesResiduesOligomerization specificityProteinSequenceHelixStructural flexibilitySuch interactionsStructural featuresHeterooligomers
2000
HELICAL MEMBRANE PROTEIN FOLDING, STABILITY, AND EVOLUTION
Popot J, Engelman D. HELICAL MEMBRANE PROTEIN FOLDING, STABILITY, AND EVOLUTION. Annual Review Of Biochemistry 2000, 69: 881-922. PMID: 10966478, DOI: 10.1146/annurev.biochem.69.1.881.Peer-Reviewed Original ResearchStatistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with β-branched residues at neighboring positions11Edited by G. von Heijne
Senes A, Gerstein M, Engelman D. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with β-branched residues at neighboring positions11Edited by G. von Heijne. Journal Of Molecular Biology 2000, 296: 921-936. PMID: 10677292, DOI: 10.1006/jmbi.1999.3488.Peer-Reviewed Original ResearchAmino Acid MotifsAmino Acid SubstitutionAmino Acids, Branched-ChainBiasBinding SitesCell MembraneDatabases, FactualDimerizationGlycineGlycophorinsIsoleucineMathematicsMembrane ProteinsModels, MolecularMolecular WeightOdds RatioPliabilityProtein FoldingProtein Structure, SecondaryThermodynamicsValineThe GxxxG motif: A framework for transmembrane helix-helix association11Edited by G. von Heijne
Russ W, Engelman D. The GxxxG motif: A framework for transmembrane helix-helix association11Edited by G. von Heijne. Journal Of Molecular Biology 2000, 296: 911-919. PMID: 10677291, DOI: 10.1006/jmbi.1999.3489.Peer-Reviewed Original ResearchAmino Acid MotifsAmino Acid SequenceAmino Acid SubstitutionBacterial ProteinsBinding SitesChloramphenicol ResistanceCloning, MolecularConsensus SequenceDatabases, FactualDimerizationDNA-Binding ProteinsEscherichia coliGlycophorinsIntracellular MembranesMembrane ProteinsModels, MolecularPeptide LibraryProtein Structure, SecondaryProtein Structure, TertiaryThermodynamicsTranscription FactorsInterhelical 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
1999
The Length of the Flexible SNAREpin Juxtamembrane Region Is a Critical Determinant of SNARE-Dependent Fusion
McNew J, Weber T, Engelman D, Söllner T, Rothman J. The Length of the Flexible SNAREpin Juxtamembrane Region Is a Critical Determinant of SNARE-Dependent Fusion. Molecular Cell 1999, 4: 415-421. PMID: 10518222, DOI: 10.1016/s1097-2765(00)80343-3.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAntigens, SurfaceCarrier ProteinsMembrane FusionMembrane ProteinsMolecular Sequence DataMutagenesis, Site-DirectedNerve Tissue ProteinsPliabilityProlineProtein Structure, SecondaryRecombinant ProteinsR-SNARE ProteinsSNARE ProteinsSynaptosomal-Associated Protein 25Syntaxin 1Vesicular Transport ProteinsConceptsJuxtamembrane regionMembrane fusionSNARE-dependent membrane fusionSNARE-dependent fusionHelix-breaking proline residueSNARE proteinsTransmembrane domainSyntaxin 1ACoil domainProline residuesFlexible linkerLipid bilayersCritical determinantFusion efficiencyFusionVAMPDomainProteinRate of fusionSnareVesiclesResiduesLinkerSame changesRegionA Method for Determining Transmembrane Helix Association and Orientation in Detergent Micelles Using Small Angle X-Ray Scattering
Bu Z, Engelman D. A Method for Determining Transmembrane Helix Association and Orientation in Detergent Micelles Using Small Angle X-Ray Scattering. Biophysical Journal 1999, 77: 1064-1073. PMID: 10423450, PMCID: PMC1300396, DOI: 10.1016/s0006-3495(99)76956-0.Peer-Reviewed Original ResearchMeSH KeywordsBiophysical PhenomenaBiophysicsButyratesDetergentsDimerizationElectrochemistryGlycophorinsHumansIn Vitro TechniquesMembrane ProteinsMicellesMolecular WeightMutationProtein ConformationProtein Structure, SecondaryQuaternary Ammonium CompoundsRecombinant Fusion ProteinsScattering, RadiationSolutionsSolventsX-RaysConceptsDetergent micellesTransmembrane domainAlpha-helical transmembrane domainsSolution small-angle X-ray scatteringTransmembrane helix associationSolution small-angle X-rayHuman erythrocyte glycophorin ASmall-angle X-ray scatteringMembrane proteinsTransmembrane proteinErythrocyte glycophorin ACarboxyl terminusHelix associationAngle X-ray scatteringGlycophorin AStaphylococcal nucleaseSmall-angle X-rayProteinModel systemMicelle contributionX-ray scatteringAngle X-rayDimerizationGyration analysisN-dodecylTOXCAT: A measure of transmembrane helix association in a biological membrane
Russ W, Engelman D. TOXCAT: A measure of transmembrane helix association in a biological membrane. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 863-868. PMID: 9927659, PMCID: PMC15316, DOI: 10.1073/pnas.96.3.863.Peer-Reviewed Original ResearchMeSH KeywordsATP-Binding Cassette TransportersBacterial ProteinsBase SequenceCarrier ProteinsCell MembraneChloramphenicol O-AcetyltransferaseDNA PrimersDNA-Binding ProteinsEscherichia coliEscherichia coli ProteinsGene LibraryGenes, ReporterGenetic Complementation TestMacromolecular SubstancesMaltose-Binding ProteinsMembrane ProteinsModels, MolecularMolecular Sequence DataMonosaccharide Transport ProteinsPeriplasmic Binding ProteinsProtein FoldingProtein Structure, SecondaryRecombinant Fusion ProteinsSpheroplastsTranscription FactorsConceptsTOXCAT systemDetergent micellesHelical membrane proteinsN-terminal DNATransmembrane helix associationTransmembrane alpha-helixReporter gene encoding chloramphenicolNatural membrane environmentGene encoding chloramphenicolTransmembrane domainTM associationTM dimerizationMembrane proteinsMembrane environmentOligomerization motifPolar residuesAlpha-helixHelix associationSequence specificityChimeric constructsCAT expressionBiological membranesFundamental eventNoncovalent associationAssay distinguishes
1997
A Biophysical Study of Integral Membrane Protein Folding †
Hunt J, Earnest T, Bousché O, Kalghatgi K, Reilly K, Horváth C, Rothschild K, Engelman D. A Biophysical Study of Integral Membrane Protein Folding †. Biochemistry 1997, 36: 15156-15176. PMID: 9398244, DOI: 10.1021/bi970146j.Peer-Reviewed Original ResearchConceptsAlpha-helical integral membrane proteinsIntegral membrane proteinsMembrane proteinsIntegral membrane protein foldingMembrane protein foldingNon-native conformationsStable secondary structureCellular chaperonesBiophysical dissectionBeta-sheet structureProtein foldingIndividual polypeptidesBiophysical studiesStructure of bacteriorhodopsinTertiary structureSecondary structureReconstitution protocolsG helicesPolypeptideF helixProteinPhospholipid vesiclesHelixFoldingBacteriorhodopsinSpontaneous, 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 associatesBilayersAssessment of the aggregation state of integral membrane proteins in reconstituted phospholipid vesicles using small angle neutron scattering11Edited by M. F. Moody
Hunt J, McCrea P, Zaccaı̈ G, Engelman D. Assessment of the aggregation state of integral membrane proteins in reconstituted phospholipid vesicles using small angle neutron scattering11Edited by M. F. Moody. Journal Of Molecular Biology 1997, 273: 1004-1019. PMID: 9367787, DOI: 10.1006/jmbi.1997.1330.Peer-Reviewed Original ResearchConceptsMembrane protein complexesIntegral membrane proteinsProtein complexesMembrane proteinsIntegral membrane protein complexPhospholipid vesiclesSmall unilamellar phospholipid vesiclesUnilamellar phospholipid vesiclesMolecular massF. MoodySpatial arrangementNon-ionic detergentIndividual complexesVesiclesModel systemMonomeric bacteriorhodopsinProteinUnknown scopeComplexesAggregation stateRadius of gyrationBacteriorhodopsinDetergentsBilayersAre there dominant membrane protein families with a given number of helices?
Arkin I, Brünger A, Engelman D. Are there dominant membrane protein families with a given number of helices? Proteins Structure Function And Bioinformatics 1997, 28: 465-466. PMID: 9261863, DOI: 10.1002/(sici)1097-0134(199708)28:4<465::aid-prot1>3.0.co;2-9.Peer-Reviewed Original ResearchAnimalsMembrane ProteinsSTRUCTURAL PERSPECTIVES OF PHOSPHOLAMBAN, A HELICAL TRANSMEMBRANE PENTAMER
Arkin I, Adams P, Brünger A, Smith S, Engelman D. STRUCTURAL PERSPECTIVES OF PHOSPHOLAMBAN, A HELICAL TRANSMEMBRANE PENTAMER. Annual Review Of Biophysics 1997, 26: 157-179. PMID: 9241417, DOI: 10.1146/annurev.biophys.26.1.157.Peer-Reviewed Original ResearchStructure 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