2024
Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4‐induced brain pathology
Miller B, Kim S, Cao K, Mehta H, Thumaty N, Kumagai H, Iida T, McGill C, Pike C, Nurmakova K, Levine Z, Sullivan P, Yen K, Ertekin‐Taner N, Atzmon G, Barzilai N, Cohen P. Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4‐induced brain pathology. Aging Cell 2024, 23: e14153. PMID: 38520065, PMCID: PMC11258485, DOI: 10.1111/acel.14153.Peer-Reviewed Original ResearchAPOE4 carriersAPOE4 alleleAmyloid beta clearanceMouse model of amyloidosisAlzheimer's diseaseAmyloid-beta pathologyIn silico analysisAmyloid-beta accumulationMitochondrial-derived peptideGenes associated with phagocytosisResistance to ADModel of amyloidosisAmyloid-betaBeta pathologyAssociated with longevitySilico analysisHumaninFactors to Alzheimer's diseaseApoE4Transcriptomic assessmentAmino acidsInfluence longevityAllelesPhagocytosisAshkenazi descentDecoupling sequence and conformational determinants of strong IDP binders to inform therapeutic intervention
Bogin B, Levine Z. Decoupling sequence and conformational determinants of strong IDP binders to inform therapeutic intervention. Biophysical Journal 2024, 123: 74a. DOI: 10.1016/j.bpj.2023.11.520.Peer-Reviewed Original Research
2023
Apolipoprotein E polymorphism‐dependent effects on cellular function
Beyer B, Levine Z. Apolipoprotein E polymorphism‐dependent effects on cellular function. Alzheimer's & Dementia 2023, 19 DOI: 10.1002/alz.077424.Peer-Reviewed Original ResearchApolipoprotein EStructure:function relationshipsCombination of cell-basedIsogenic hiPSC linesTransport of lipidsSubcellular localizationE4 isoformCellular functionsFunction of apolipoprotein EBiophysical approachesLiving cellsTransport of E2Cell typesCo-localizationCentral nervous systemLipoprotein particlesIsoformsHuman astrocytesRelationship of apolipoprotein EHiPSC linesCell-basedInvestigate mechanismsApolipoproteinCellsOrganellesComparing the structure and stability of diverse amyloid beta oligomers using fluorescence correlation spectroscopy
Nurmakova K, Levine Z. Comparing the structure and stability of diverse amyloid beta oligomers using fluorescence correlation spectroscopy. Biophysical Journal 2023, 122: 350a. DOI: 10.1016/j.bpj.2022.11.1944.Peer-Reviewed Original Research
2019
The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes
Levine ZA, Teranishi K, Okada AK, Langen R, Shea JE. The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes. Journal Of The American Chemical Society 2019, 141: 14168-14179. PMID: 31456396, DOI: 10.1021/jacs.9b04995.Peer-Reviewed Original Research
2018
A threonine zipper that mediates protein–protein interactions: Structure and prediction
Oi C, Treado JD, Levine ZA, Lim CS, Knecht KM, Xiong Y, O'Hern CS, Regan L. A threonine zipper that mediates protein–protein interactions: Structure and prediction. Protein Science 2018, 27: 1969-1977. PMID: 30198622, PMCID: PMC6201716, DOI: 10.1002/pro.3505.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein-protein interfacesZipper structureBeta-barrel proteinsIntermonomer hydrogen bondsBarrel proteinsThr residueSide-chain dihedral anglesBiotechnological applicationsProtein interfacesMolecular dynamics simulationsDihedral angleSide-chain conformationsThrH-bondingHydrogen bondsChain conformationMD simulationsSteric constraintsDrug discoveryDynamics simulationsResiduesTargeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands
Wójcik S, Birol M, Rhoades E, Miranker AD, Levine ZA. Targeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands. Methods In Enzymology 2018, 611: 703-734. PMID: 30471705, DOI: 10.1016/bs.mie.2018.09.036.Peer-Reviewed Original ResearchConceptsSmall molecule manipulationSingle-molecule techniquesProtein ensemblesPathological functionsMolecule ligandsTractable targetsConformational flexibilityProteomeAttractive targetProteinDrug developmentExperimental approachIDPsTargetLigandsComplimentary partnersConformationBioengineeringWide range
2017
Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding
Seo S, Lee DW, Ahn JS, Cunha K, Filippidi E, Ju SW, Shin E, Kim B, Levine ZA, Lins RD, Israelachvili JN, Waite JH, Valentine MT, Shea JE, Ahn BK. Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding. Advanced Materials 2017, 29 PMID: 28833661, PMCID: PMC5640498, DOI: 10.1002/adma.201703026.Peer-Reviewed Original ResearchMineral surfacesMussel foot proteinsMolecular dynamics simulationsMetal coordinationPolymer networksPolymeric interfacesPriming layerLoad-bearing materialsCatechol groupsDynamic bondingPolymer resinDynamics simulationsFoot proteinsHydrophobic bondsToughness enhancementAdhesion strengthAdhesive primerBondingSignificant performance enhancementSecondary surfacePerformance enhancementOrders of magnitudeSurfaceResinBondsQuantitative Limits on Small Molecule Transport via the Electropermeome — Measuring and Modeling Single Nanosecond Perturbations
Sözer EB, Levine ZA, Vernier PT. Quantitative Limits on Small Molecule Transport via the Electropermeome — Measuring and Modeling Single Nanosecond Perturbations. Scientific Reports 2017, 7: 57. PMID: 28246401, PMCID: PMC5428338, DOI: 10.1038/s41598-017-00092-0.Peer-Reviewed Original Research
2016
Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces
Levine ZA, Rapp MV, Wei W, Mullen RG, Wu C, Zerze GH, Mittal J, Waite JH, Israelachvili JN, Shea JE. Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 4332-4337. PMID: 27036002, PMCID: PMC4843488, DOI: 10.1073/pnas.1603065113.Peer-Reviewed Original ResearchConceptsSelf-assembled monolayersOrganic surfacesHydrophobic self-assembled monolayersReplica exchange molecular dynamics simulationsSurface force measurementsMolecular interactionsFree energy profilesMussel foot proteinsUmbrella sampling simulationsMolecular dynamics simulationsVan der WaalsPeptide adsorptionPeptide adhesionSFA measurementsUnderwater adhesivesAqueous adhesivesDer WaalsSurface forcesDynamics simulationsElectrostatic forcesFoot proteinsProtein analoguesSpecific interactionsAdsorptionAdhesive properties
2015
Picosecond and Terahertz Perturbation of Interfacial Water and Electropermeabilization of Biological Membranes
Vernier PT, Levine ZA, Ho MC, Xiao S, Semenov I, Pakhomov AG. Picosecond and Terahertz Perturbation of Interfacial Water and Electropermeabilization of Biological Membranes. The Journal Of Membrane Biology 2015, 248: 837-847. PMID: 25796485, PMCID: PMC4565733, DOI: 10.1007/s00232-015-9788-7.Peer-Reviewed Original ResearchConceptsSubnanosecond Electric PulsesTerahertz electromagnetic radiationComplementary molecular dynamics simulationsTerahertz frequenciesElectromagnetic radiationField reversalElectric pulsesElectric fieldInterfacial waterElectropore formationMolecular dynamics simulationsPulsesElectric potentialConductive structuresWater dipolesDynamics simulationsPhospholipid bilayersBilayersPicosecondsRemote monitoringBiological membranesModel membranesFieldPSRadiationRegulation and aggregation of intrinsically disordered peptides
Levine ZA, Larini L, LaPointe NE, Feinstein SC, Shea JE. Regulation and aggregation of intrinsically disordered peptides. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 2758-2763. PMID: 25691742, PMCID: PMC4352815, DOI: 10.1073/pnas.1418155112.Peer-Reviewed Original ResearchConceptsStable native structureRole of osmolytesFragment of tauTrimethylamine N-oxideVital physiological functionsMicrotubule-associated tau proteinOsmolyte ureaAggregation propensityMicrotubule growthTau oligomerizationConformational ensemblesIDP structurePhysiological functionsNative structureCompact oligomersHelical filamentsProteinFibril formationCompact conformationNeurodegenerative diseasesTau proteinMonomer structureUnique classPeptidesN-oxide
2014
Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations
Levine ZA, Venable RM, Watson MC, Lerner MG, Shea JE, Pastor RW, Brown FL. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations. Journal Of The American Chemical Society 2014, 136: 13582-13585. PMID: 25202918, PMCID: PMC4183605, DOI: 10.1021/ja507910r.Peer-Reviewed Original Research
2013
Electric Field-Driven Water Dipoles: Nanoscale Architecture of Electroporation
Tokman M, Lee JH, Levine ZA, Ho MC, Colvin ME, Vernier PT. Electric Field-Driven Water Dipoles: Nanoscale Architecture of Electroporation. PLOS ONE 2013, 8: e61111. PMID: 23593404, PMCID: PMC3623848, DOI: 10.1371/journal.pone.0061111.Peer-Reviewed Original ResearchConceptsInterfacial water moleculesMolecular mechanismsWater moleculesLipid bilayersNovel molecular mechanismWater-vacuum interfaceMolecular dynamics simulationsRole of waterEnergetic analysisCell membranePore formationWater dipolesMolecular dipolesBiological applicationsNanoscale architectureDynamics simulationsElectroporationLipid layerMain playersMembranePassive barrierMoleculesFavorable configurationBilayersReorganization
2009
Electroporating Fields Target Oxidatively Damaged Areas in the Cell Membrane
Vernier PT, Levine ZA, Wu YH, Joubert V, Ziegler MJ, Mir LM, Tieleman DP. Electroporating Fields Target Oxidatively Damaged Areas in the Cell Membrane. PLOS ONE 2009, 4: e7966. PMID: 19956595, PMCID: PMC2779261, DOI: 10.1371/journal.pone.0007966.Peer-Reviewed Original ResearchConceptsLiving cellsComplex biomolecular assembliesPlasma membraneMolecular basisGenetic materialMembrane componentsCell membraneBiomolecular assembliesPermeabilization procedureModel membranesElectroporation protocolReversible electropermeabilizationOxidative stressElectropermeabilizationMembraneCell suspensionsDetailed understandingMolecular dynamics simulationsGene therapyCellsConsiderable knowledgeAssemblyDynamics simulationsPharmaceutical agents