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 ResearchDiabetes Mellitus, Type 2HumansIntracellular Signaling Peptides and ProteinsIslet Amyloid PolypeptideMitochondriaMolecular Dynamics Simulation
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 simulationsResidues
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 ResearchMeSH KeywordsAnimalsCalciumCell MembraneElectromagnetic FieldsElectroporationGliomaLipid BilayersMolecular Dynamics SimulationNeuroblastomaNeuronsPhospholipidsRatsTumor Cells, CulturedWaterConceptsSubnanosecond 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 ResearchMeSH KeywordsHumansMethylaminesMolecular Dynamics SimulationPeptidesProtein Aggregation, PathologicalProtein Structure, SecondaryTau ProteinsUreaConceptsStable 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 ResearchLipid BilayersMolecular Dynamics Simulation
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 ResearchMeSH KeywordsBiophysicsCell Membrane PermeabilityElectroporationLipid BilayersMolecular Dynamics SimulationNanostructuresWaterConceptsInterfacial 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