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 thermodynamicsMotifGlycophorinHigh-Yield Synthesis and Purification of an α-Helical Transmembrane Domain
Fisher L, Engelman D. High-Yield Synthesis and Purification of an α-Helical Transmembrane Domain. Analytical Biochemistry 2001, 293: 102-108. PMID: 11373085, DOI: 10.1006/abio.2001.5122.Peer-Reviewed Original Research
2000
Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations11Edited by G. Von Heijne
Petrache H, Grossfield A, MacKenzie K, Engelman D, Woolf T. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations11Edited by G. Von Heijne. Journal Of Molecular Biology 2000, 302: 727-746. PMID: 10986130, DOI: 10.1006/jmbi.2000.4072.Peer-Reviewed Original ResearchMeSH Keywords1,2-DipalmitoylphosphatidylcholineAlgorithmsAmino Acid MotifsAmino Acid SequenceBinding SitesComputer SimulationDimerizationDimyristoylphosphatidylcholineGlycophorinsLipid BilayersModels, MolecularMolecular Sequence DataNuclear Magnetic Resonance, BiomolecularPeptide FragmentsPhosphatidylcholinesProtein BindingProtein Structure, SecondaryProtein Structure, TertiaryThermodynamicsConceptsMonomer formLipid bilayersLipid chain lengthUnfavorable electrostatic repulsionLipid typeMolecular dynamics simulationsExplicit lipid bilayerElectrostatic repulsionMonomeric helicesLipid-lipid interactionsInteraction enthalpiesChain lengthDimer structureEnergetic propertiesCHARMM potentialInteraction energyAccessible volumeDynamics simulationsLipid propertiesUnsaturated lipidsEnthalpy calculationsLipid environmentBilayer thicknessAcyl chainsThermodynamic treatmentStatistical 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
Detergents modulate dimerization, but not helicity, of the glycophorin A transmembrane domain 11Edited by G. von Heijne
Fisher L, Engelman D, Sturgis J. Detergents modulate dimerization, but not helicity, of the glycophorin A transmembrane domain 11Edited by G. von Heijne. Journal Of Molecular Biology 1999, 293: 639-651. PMID: 10543956, DOI: 10.1006/jmbi.1999.3126.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceButyratesCircular DichroismDetergentsDimerizationEnergy TransferFluorescent DyesGlycophorinsHumansKineticsMicellesMolecular Sequence DataPeptide FragmentsPhosphorylcholineProtein Structure, SecondaryQuaternary Ammonium CompoundsSodium Dodecyl SulfateSolventsSpectrometry, FluorescenceThermodynamicsConceptsSpecific chemical interactionsFörster resonance energy transferResonance energy transferSodium dodecyl sulfateComplex solventChemical interactionFar-UV circular dichroismCircular dichroismDodecyl sulfateTransmembrane helix associationDetergent micellesHelix associationEnergy transferThermodynamic measurementsHelix formationObserved KdZwitterionic detergentSecondary structureDimerizationG. von HeijneHelix dimerizationOrders of magnitudeDetergentsTransmembrane helicesTransmembrane domainA 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-dodecyl
1998
Structure-based prediction of the stability of transmembrane helix–helix interactions: The sequence dependence of glycophorin A dimerization
MacKenzie K, Engelman D. Structure-based prediction of the stability of transmembrane helix–helix interactions: The sequence dependence of glycophorin A dimerization. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 3583-3590. PMID: 9520409, PMCID: PMC19879, DOI: 10.1073/pnas.95.7.3583.Peer-Reviewed Original ResearchConceptsHelix-helix interactionsTransmembrane helix-helix associationTransmembrane helix-helix interactionsHelix-helix associationSingle-point mutantsStructure-based predictionTransmembrane domainMembrane proteinsDimer interfaceDimerization propensitySide-chain hydrophobicityDimer stabilityPoint mutationsSteric clashesMultiple mutationsMutationsSequence dependenceCompensatory effectFavorable van der Waals interactionsMutantsFoldingProteinInteractionDimerizationGlycophorin
1997
The 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 solutionDissociationHelixA Transmembrane Helix Dimer: Structure and Implications
MacKenzie K, Prestegard J, Engelman D. A Transmembrane Helix Dimer: Structure and Implications. Science 1997, 276: 131-133. PMID: 9082985, DOI: 10.1126/science.276.5309.131.Peer-Reviewed Original ResearchConceptsMembrane-spanning alpha helicesSolution nuclear magnetic resonance spectroscopyDimeric transmembrane domainNuclear magnetic resonance spectroscopyTransmembrane helix dimerVan der Waals interactionsDer Waals interactionsAqueous detergent micellesIntermonomer hydrogen bondsTransmembrane helicesTransmembrane domainMagnetic resonance spectroscopyThree-dimensional structureDetergent micellesHelix dimerHydrogen bondsWaals interactionsAlpha-helixResonance spectroscopyGlycophorin ASpecific associationHelixSequence dependenceMicellesSpectroscopyDimerization of the p185neu transmembrane domain is necessary but not sufficient for transformation
Burke C, Lemmon M, Coren B, Engelman D, Stern D. Dimerization of the p185neu transmembrane domain is necessary but not sufficient for transformation. Oncogene 1997, 14: 687-696. PMID: 9038376, DOI: 10.1038/sj.onc.1200873.Peer-Reviewed Original ResearchConceptsReceptor tyrosine kinasesTransmembrane domainEpidermal growth factor receptorSignal transductionWild-type domainSecond-site mutationsPosition 664Dimerization domainGrowth factor receptorTyrosine kinaseGlycophorin AFactor receptorValine substitutionDimerizationMutationsTransductionGlutamic acidDomainWeak dimerizationMutantsKinaseSignalingProteinEGFChimeras
1996
Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching
Adams P, Engelman D, Brünger A. Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching. Proteins Structure Function And Bioinformatics 1996, 26: 257-261. PMID: 8953647, DOI: 10.1002/(sici)1097-0134(199611)26:3<257::aid-prot2>3.0.co;2-b.Peer-Reviewed Original ResearchLeucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carbon—carbon couplings and 13C chemical shifts
MacKenzie K, Prestegard J, Engelman D. Leucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carbon—carbon couplings and 13C chemical shifts. Journal Of Biomolecular NMR 1996, 7: 256-260. PMID: 8785502, DOI: 10.1007/bf00202043.Peer-Reviewed Original ResearchConceptsChemical shiftsPeptide dimersΑ-carbonSide chainsSide-chain rotamer populationsCarbon-carbon couplingLeucine side chainsThree-bond J couplingsNMR pulse sequencesΔ-methyl groupsRotamer populationsMethyl carbonFast exchangeSide-chain rotamersJ-couplingsTransmembrane peptidesDimer interfaceRotameric statesProtein systemsRotamersShift distributionGlycophorin A.DimersChainMethyl
1994
Glycophorin A helical transmembrane domains dimerize in phospholipid bilayers: a resonance energy transfer study.
Adair B, Engelman D. Glycophorin A helical transmembrane domains dimerize in phospholipid bilayers: a resonance energy transfer study. Biochemistry 1994, 33: 5539-44. PMID: 8180176, DOI: 10.1021/bi00184a024.Peer-Reviewed Original Research