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
Computation 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 motifMotifSequenceHomomultimerizationDomainMutagenesis
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 treatmentA view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering11Edited by P. E. Wright
Bu Z, Neumann D, Lee S, Brown C, Engelman D, Han C. A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering11Edited by P. E. Wright. Journal Of Molecular Biology 2000, 301: 525-536. PMID: 10926525, DOI: 10.1006/jmbi.2000.3978.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalciumCattleLactalbuminModels, MolecularNeutronsProtein FoldingProtein Structure, SecondaryScattering, RadiationConceptsVibrational motionDiffusive motionPicosecond time scaleQuasielastic neutron scatteringSuch collective motionLength scalesPotential barrierQuasielastic scattering intensityCorrelation lengthJump motionShort length scalesBovine alpha-lactalbuminNeutron scatteringMolten globuleScattering intensityLong length scalesCollective motionMean-square amplitudesAtom clustersHigh-frequency motionsMolten globule stateNon-exchangeable protonsCluster sizeFrequency motionsProtein dynamicsHELICAL 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 Factors
1999
TOXCAT: 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
1998
A solution SAXS study of borrelia burgdorferi OspA, a protein containing a single‐layer β‐sheet
Bu Z, Engelman D, Koide S. A solution SAXS study of borrelia burgdorferi OspA, a protein containing a single‐layer β‐sheet. Protein Science 1998, 7: 2681-2683. PMID: 9865964, PMCID: PMC2143892, DOI: 10.1002/pro.5560071223.Peer-Reviewed Original ResearchConceptsCrystal structureSingle-layer β-sheetPredominant solution conformationEarlier NMR studiesAngle X-ray Scattering StudySmall-angle X-ray scattering (SAXS) studiesRadius of gyrationNMR studiesSolution conformationX-ray scattering studyStable structureSAXS experimentΒ-sheetLocal structureGlobal conformationScattering StudyUnusual structureBorrelia burgdorferi outer surface protein ABeta topologyConformationBorrelia burgdorferi OspAC-terminal domainSingle layerStructureNMRModels for the Transmembrane Region of the Phospholamban Pentamer: Which Is Correct?a
ADAMS P, LEE A, BRÜNGER A, ENGELMAN D. Models for the Transmembrane Region of the Phospholamban Pentamer: Which Is Correct?a. Annals Of The New York Academy Of Sciences 1998, 853: 178-185. PMID: 10603945, DOI: 10.1111/j.1749-6632.1998.tb08265.x.Peer-Reviewed Original ResearchStructure-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
STRUCTURAL 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 ResearchA 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 dependenceMicellesSpectroscopyStructure 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
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 ResearchSurface point mutations that significantly alter the structure and stability of a protein's denatured state
Smith C, Bu Z, Engelman D, Regan L, Anderson K, Sturtevant J. Surface point mutations that significantly alter the structure and stability of a protein's denatured state. Protein Science 1996, 5: 2009-2019. PMID: 8897601, PMCID: PMC2143264, DOI: 10.1002/pro.5560051007.Peer-Reviewed Original ResearchConceptsPoint mutationsDenatured stateStopped-flow fluorescenceDenaturant concentrationSolvent-exposed sitesStreptococcal protein GMutantsG mutantTertiary structureGuHCl denaturationEquilibrium intermediatesPosition 53B1 domainProteinCircular dichroismMutationsProtein GGuanidine hydrochlorideSmall-angle X-ray scatteringStructural implicationsX-ray scatteringFluorescenceThrRadius of gyrationDenaturantsA Zinc-binding Domain Involved in the Dimerization of RAG1
Rodgers K, Bu Z, Fleming K, Schatz D, Engelman D, Coleman J. A Zinc-binding Domain Involved in the Dimerization of RAG1. Journal Of Molecular Biology 1996, 260: 70-84. PMID: 8676393, DOI: 10.1006/jmbi.1996.0382.Peer-Reviewed Original ResearchConceptsRecombination-activating gene 1Zinc-binding motifDimerization domainZinc fingerProtein-protein interactionsLymphoid-specific genesN-terminal thirdZinc finger sequencesAmino acid residuesC3HC4 motifRAG1 sequencesRAG1 proteinTerminal domainHomodimer formationAcid residuesBiophysical techniquesGene 1Energetics of associationMonomeric subunitsMotifProteinFinger sequencesSequenceC3HC4Zinc ionsMapping the lipid-exposed surfaces of membrane proteins
Arkin I, MacKenzie K, Fisher L, Aimoto S, Engelman D, Smith S. Mapping the lipid-exposed surfaces of membrane proteins. Nature Structural & Molecular Biology 1996, 3: 240-243. PMID: 8605625, DOI: 10.1038/nsb0396-240.Peer-Reviewed Original ResearchConceptsMembrane proteinsLong transmembrane helixLipid-exposed surfaceThree-dimensional foldHigh-resolution structuresRelative rotational orientationTransmembrane helicesTransmembrane segmentsThird cysteineCysteine residuesLipid environmentHelix interfacePentameric complexProteinLipid interfaceStable complexesHelixResiduesUndergoes exchangeSulphydryl groupsPhospholambanComplexesInternal faceCysteineRotational orientation
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