2025
Structure and function of the human apoptotic scramblase Xkr4
Chakraborty S, Feng Z, Lee S, Alvarenga O, Panda A, Zhang S, Bruni R, Khelashvili G, Gupta K, Accardi A. Structure and function of the human apoptotic scramblase Xkr4. Nature Communications 2025, 16: 7317. PMID: 40781244, PMCID: PMC12334663, DOI: 10.1038/s41467-025-62739-1.Peer-Reviewed Original ResearchConceptsCombination of biochemical approachesMolecular mechanismsNegative electrostatic surfaceSurface of dying cellsCaspase cleavagePhosphatidylserine externalizationBiochemical approachesAcid residuesNovel conformationActivated scramblasesXKR4Electrostatic surfaceLigand bindingScramblaseMolecular dynamics simulationsCryoEM imagesMembrane thinningMembraneDynamics simulationsCaspaseCryoEMPhosphatidylserineConformationResiduesCleavageMolecular simulations reveal gas transport mechanisms in polyamide membranes
Qian J, Wang R, Wu H, Wang F, Elimelech M. Molecular simulations reveal gas transport mechanisms in polyamide membranes. Journal Of Membrane Science 2025, 731: 124056. DOI: 10.1016/j.memsci.2025.124056.Peer-Reviewed Original ResearchGas separation processesPA membraneGas separationM-phenylenediamineMembrane-based gas separationsTrimesoyl chlorideSingle gas permeationMolecular dynamics simulationsMolecular sieving effectNon-equilibrium molecular dynamics simulationsSeparation processPolymerization of m-phenylenediamineMembrane pore structureAromatic polyamidesNanoporous materialsSmall gasesInterfacial polymerization of m-phenylenediamineMolecular simulationsPolymeric membranesDynamics simulationsInterfacial polymerizationGas permeationPA filmSieving effectPore size distributionDesigning Ultraporous Mesostructured Silica Nanoparticles for the Remediation of Per- and Polyfluoroalkyl Substances
Huang C, Lewis R, Thomas S, Tang Z, Jones J, Nason S, Zuverza-Mena N, Piskulich Z, O’Keefe T, Tuga B, Paredes-Beaulieu A, Vasiliou V, Cui Q, Dalluge J, White J, Haynes C. Designing Ultraporous Mesostructured Silica Nanoparticles for the Remediation of Per- and Polyfluoroalkyl Substances. ACS Nano 2025, 19: 19777-19789. PMID: 40402145, DOI: 10.1021/acsnano.5c02008.Peer-Reviewed Original ResearchConceptsMesostructured silica nanoparticlesPFAS moleculesMolecular dynamics simulationsPolyfluoroalkyl substancesLiquid chromatography-tandem mass spectrometryChromatography-tandem mass spectrometrySilica nanoparticlesNitrogen physisorptionDynamic light scatteringSilica surfaceMass spectrometryDynamics simulationsFunctional groupsUptake of PFASsElectrostatic interactionsChain lengthRemediation of per-PFAS uptakeLC-MS/MSMultiple PFASLight scatteringPromote phytoremediationRemediation strategiesEnvironmental matricesNanoparticlesDrugging Disordered Proteins by Conformational Selection to Inform Therapeutic Intervention
Bogin B, Levine Z. Drugging Disordered Proteins by Conformational Selection to Inform Therapeutic Intervention. Journal Of Chemical Theory And Computation 2025, 21: 3204-3215. PMID: 40029731, DOI: 10.1021/acs.jctc.4c01160.Peer-Reviewed Original ResearchConceptsIslet amyloid polypeptideIntrinsically disordered proteinsConformational selectionDisordered proteinsHuman islet amyloid polypeptideMolecular dynamics simulationsStable binding sitesSelf-assembling sequencesIAPP sequenceFixed conformationAmyloid polypeptideUmbrella samplingBinding preferencesConformational specificityTwo-state modelDynamics simulationsConformational heterogeneityNew conformationsBinding sitesMolecular binding mechanismsConformationBinding mechanismFoldamersStructural conformationProteinGypsum heterogenous nucleation pathways regulated by surface functional groups and hydrophobicity
Guan Y, Hong X, Karanikola V, Wang Z, Pan W, Wu H, Wang F, Yu H, Elimelech M. Gypsum heterogenous nucleation pathways regulated by surface functional groups and hydrophobicity. Nature Communications 2025, 16: 713. PMID: 39820035, PMCID: PMC11739488, DOI: 10.1038/s41467-025-55993-w.Peer-Reviewed Original ResearchSurface functional groupsGypsum formationSurface-induced nucleationSelf-assembled monolayersIon adsorption sitesFormation of gypsum crystalsFunctional groupsIn situ microscopyGypsum nucleationOH functional groupsHydrophilic surfaceGypsum crystalsTemporal-spatial resolutionFormation mechanismGypsumIndustrial processesNucleationMolecular dynamics simulationsHydrophobic surfaceHeterogeneous nucleation pathwayNucleation pathwayLimitations of experimental techniquesSurfaceExperimental techniquesDynamics simulationsA highly selective and energy efficient approach to boron removal overcomes the Achilles heel of seawater desalination
Pan W, Roy D, Uralcan B, Patel S, Iddya A, Ahn E, Haji-Akbari A, Kamcev J, Elimelech M. A highly selective and energy efficient approach to boron removal overcomes the Achilles heel of seawater desalination. Nature Water 2025, 3: 99-109. DOI: 10.1038/s44221-024-00362-y.Peer-Reviewed Original ResearchHydroxyl groupsImproved electrode performanceMolecular dynamics simulationsBoron selectivityPristine electrodeHydrogen bondsElectrode performanceFunctional electrodesElectrosorption processIon-exchange adsorptionMicroporous electrodesDynamics simulationsFunctional groupsOxygen-containingRemoval selectivityTrace contaminantsElectrosorptionBoron removalElectrodeBoron removal performanceBoronHydroxylBoron removal methodsRemoval of trace contaminantsReverse osmosis
2024
Assessment of electron–proton correlation functionals for vibrational spectra of shared-proton systems by constrained nuclear-electronic orbital density functional theory
Yang Y, Zhang Y, Yang Y, Xu X. Assessment of electron–proton correlation functionals for vibrational spectra of shared-proton systems by constrained nuclear-electronic orbital density functional theory. The Journal Of Chemical Physics 2024, 161: 244103. PMID: 39713995, DOI: 10.1063/5.0243086.Peer-Reviewed Original ResearchElectron-proton correlation functionalsCNEO-DFTElectron-proton correlationDensity functional theoryProton transferFunctional theoryNuclear-electronic orbital density functional theoryConventional DFTProton transfer modeQuantum chemistry calculationsNuclear quantum effectsCorrelation functionMolecular dynamics simulationsVibrational spectrum calculationsVibrational spectraChemistry calculationsDelocalization effectVibrational modesDynamics simulationsNuclear-electronicDFTQuantum natureEpc17Quantum effectsProtonDrug Development for Hematological Cancer Targets Using Asclepius
Crucitti D, Pérez Míguez C, Piñeiro Fiel M, Diaz Arias J, Gómez Fernández J, Mosquera Orgueira A, Zeidan A. Drug Development for Hematological Cancer Targets Using Asclepius. Blood 2024, 144: 7464-7464. DOI: 10.1182/blood-2024-198610.Peer-Reviewed Original ResearchStructure-based drug design approachBinding energy evaluationComputational chemistry calculationsBiological targetsDrug design approachMolecular dynamics simulationsFree energy techniquesSynthetic stepsChemistry calculationsSynthetic accessibilityADMET profileSynthetic costArray of moleculesMolecular dockingDynamics simulationsDrug designNovel inhibitorsDrug discoveryADMETMoleculesStructural conformationIdentified inhibitorsProtein targetsHematological cancersIntegration of artificial intelligenceMolecular simulations of organic solvent transport in dense polymer membranes: Solution-diffusion or pore-flow mechanism?
He J, Fan H, Elimelech M, Li Y. Molecular simulations of organic solvent transport in dense polymer membranes: Solution-diffusion or pore-flow mechanism? Journal Of Membrane Science 2024, 708: 123055. DOI: 10.1016/j.memsci.2024.123055.Peer-Reviewed Original ResearchDense polymer membranesPolymer membranesOrganic solventsSolution-diffusion modelHigh-performance polymer membranesSolvent transportFractional free volumeMolecular-level guidanceOrganic solvent nanofiltrationMolecular dynamics simulationsPore flow mechanismNon-equilibrium molecular dynamics simulationsMembrane pore sizeSolvent sizeSolvent permeanceSolvent nanofiltrationSeparation applicationsTransport mechanisms of waterMolecular simulationsFree volumeDynamics simulationsWater transport mechanismSolventReverse osmosisSolution-diffusionMechanism of phosphate release from actin filaments
Wang Y, Wu J, Zsolnay V, Pollard T, Voth G. Mechanism of phosphate release from actin filaments. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2408156121. PMID: 38980907, PMCID: PMC11260136, DOI: 10.1073/pnas.2408156121.Peer-Reviewed Original ResearchConceptsCryo-EM structureAll-atom molecular dynamics simulationsATP-actinRate of phosphate releaseActin filamentsMechanism of phosphate releaseMolecular dynamics simulationsPhosphate releaseDissociation of phosphateR177Salt bridgesHydrogen bondsEnergy barrierDynamics simulationsComputational studyRelease of phosphateFilamentsRelease pathwayInternal cavityResiduesStudy residuesOccluding interactionsGatePrimary eventD179The physical basis for solvent flow in organic solvent nanofiltration
Fan H, He J, Heiranian M, Pan W, Li Y, Elimelech M. The physical basis for solvent flow in organic solvent nanofiltration. Science Advances 2024, 10: eado4332. PMID: 38875330, PMCID: PMC11177934, DOI: 10.1126/sciadv.ado4332.Peer-Reviewed Original ResearchOrganic solvent nanofiltrationOrganic solvent nanofiltration membranesMembrane pore structureSolvent nanofiltrationNonequilibrium molecular dynamics simulationsMolecular dynamics simulationsPore structureSolvent transport mechanismsSolvent moleculesSolvent flowSolvent permeanceSolvent affinityOSN membranesFlory-Rehner theoryDynamics simulationsSolvent transportMembrane technologyChemical separationNanofiltrationPressure gradientPermeanceStructureTransport mechanismMoleculesInhibition of silica scaling with functional polymers: Role of ionic strength, divalent ions, and temperature
Kaneda M, Cao T, Dong D, Zhang X, Chen Y, Zhang J, Bryantsev V, Zhong M, Elimelech M. Inhibition of silica scaling with functional polymers: Role of ionic strength, divalent ions, and temperature. Water Research 2024, 258: 121705. PMID: 38776744, DOI: 10.1016/j.watres.2024.121705.Peer-Reviewed Original ResearchInhibition efficiencySilicic acid solutionAcid solutionPolymerization inhibitorIonic strengthMolecular dynamics simulationsDivalent ionsFunctional polymersAmmonium groupsSodium ionsInorganic cationsDynamics simulationsDivalent inorganic cationsInhibition performanceIonsSolution conditionsCationsPolymerSolution temperatureEffective stabilizationElevated temperaturesSilicaSilica scale formationSilica scaleSaline industrial wastewaterIdentification of the potassium-binding site in serotonin transporter
Hellsberg E, Boytsov D, Chen Q, Niello M, Freissmuth M, Rudnick G, Zhang Y, Sandtner W, Forrest L. Identification of the potassium-binding site in serotonin transporter. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319384121. PMID: 38652746, PMCID: PMC11067047, DOI: 10.1073/pnas.2319384121.Peer-Reviewed Original ResearchConceptsSerotonin transporterSite-directed mutagenesis of residuesMutagenesis of residuesSite-directed mutagenesisHeterologous expression systemStudy of vesiclesNa2 siteClearance of serotoninPatch-clamp recordingsExpression systemBinding residuesSequential bindingMolecular dynamics simulationsBinding sitesPotassium binding siteSubstrate accumulationClamp recordingsVesiclesResiduesTurnover rateBindingStructural studiesChemical gradientsBinding configurationsSynaptic cleftRational Design of TDP-43 Derived α‑Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders
Salaikumaran M, Gopal P. Rational Design of TDP-43 Derived α‑Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders. ACS Chemical Neuroscience 2024, 15: 1096-1109. PMID: 38466778, PMCID: PMC10959110, DOI: 10.1021/acschemneuro.3c00659.Peer-Reviewed Original ResearchConceptsMolecular dynamics simulationsTDP-43 aggregationTDP-43Disordered C-terminal regionDynamics simulationsIntramolecular hydrogen bondsAmyloid-like filamentsPeptide inhibitorRNA/DNA-binding proteinC-terminal regionPathology of neurodegenerative diseasesNeurodegenerative diseasesAggregation of TDP-43Binding affinityStructure-based computational approachDesign of peptide inhibitorsRNA/DNA-bindingLow root-mean-square deviationRNA splicingMRNA transportPeptide-based therapeuticsRoot-mean-square deviationDevelopment of novel therapeuticsFree energy landscapeStructure predictionTherapeutic targeting Tudor domains in leukemia via CRISPR-Scan Assisted Drug Discovery
Chan A, Han L, Delaney C, Wang X, Mukhaleva E, Li M, Yang L, Pokharel S, Mattson N, Garcia M, Wang B, Xu X, Zhang L, Singh P, Elsayed Z, Chen R, Kuang B, Wang J, Yuan Y, Chen B, Chan L, Rosen S, Horne D, Müschen M, Chen J, Vaidehi N, Armstrong S, Su R, Chen C. Therapeutic targeting Tudor domains in leukemia via CRISPR-Scan Assisted Drug Discovery. Science Advances 2024, 10: eadk3127. PMID: 38394203, PMCID: PMC10889360, DOI: 10.1126/sciadv.adk3127.Peer-Reviewed Original ResearchConceptsTudor domainDrug discoveryRibosomal gene expressionMolecular dynamics simulationsDomain-focused CRISPR screeningDe novo drug discoveryCompound dockingAcetyltransferase complexCRISPR screensGenetic approachesLead inhibitorDynamics simulationsStructural genetics approachGene expressionH3K9 acetylationEpigenetic dysregulationSgf29Tile scansLeukemia progressionMultiple cancersDrug developmentDiscoveryH3K9DockingLeukemiaOccupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations
Kaur D, Reiss K, Wang J, Batista V, Brudvig G, Gunner M. Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations. The Journal Of Physical Chemistry B 2024, 128: 2236-2248. PMID: 38377592, DOI: 10.1021/acs.jpcb.3c05367.Peer-Reviewed Original ResearchOxygen-evolving centerWater moleculesPhotosystem IIPositions of water moleculesAnalysis of water moleculesCatalyze water oxidationHydrogen bond networkOccupancy of water moleculesMolecular dynamics simulationsD1-D61Electron density mapsMolecular dynamics analysisProton transferWater oxidationCrystallographic dataIce latticeMD simulationsMolecular dynamicsStructural transitionDynamics simulationsSubstrate waterOxygen-evolvingRoom temperatureProtein residuesMoleculesGlycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SME and molecular dynamics simulations
Rosenfeld M, Kearns F, Chongsaritsinsuk J, Steigmeyer A, Mahoney K, Lucas T, Ince D, Battison A, Hollenhorst M, Shon D, Bertozzi C, Farracane M, Lemmon M, Malaker S, Amaro R. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SME and molecular dynamics simulations. Biophysical Journal 2024, 123: 14a. DOI: 10.1016/j.bpj.2023.11.205.Peer-Reviewed Original Research
2023
Molecular Design of Functional Polymers for Silica Scale Inhibition
Kaneda M, Dong D, Chen Y, Zhang X, Xue Y, Bryantsev V, Elimelech M, Zhong M. Molecular Design of Functional Polymers for Silica Scale Inhibition. Environmental Science And Technology 2023, 58: 871-882. PMID: 38150403, DOI: 10.1021/acs.est.3c06504.Peer-Reviewed Original ResearchConceptsFunctional polymersSilica polymerizationSilicic acidNitrogen-containing polymersMolecular design principlesWater treatment membranesExtended chain conformationMolecular dynamics simulationsSuperior inhibition performanceNeutral pH conditionsSilicic acid precursorsCondensation reactionPolymer chainsHydration shellMolecular designMolecular structureAlkyl segmentsAmine groupsSilica inhibitionMaterial synthesisAmide groupInhibition performancePolymersChain conformationHydrophobic natureGlycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
Chongsaritsinsuk J, Steigmeyer A, Mahoney K, Rosenfeld M, Lucas T, Smith C, Li A, Ince D, Kearns F, Battison A, Hollenhorst M, Judy Shon D, Tiemeyer K, Attah V, Kwon C, Bertozzi C, Ferracane M, Lemmon M, Amaro R, Malaker S. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature Communications 2023, 14: 6169. PMID: 37794035, PMCID: PMC10550946, DOI: 10.1038/s41467-023-41756-y.Peer-Reviewed Original ResearchConceptsFamily of proteinsMucin domainO-glycosylationBiological functionsKey regulatorComplex glycansMass spectrometric analysisFunctional relevanceTIM familyDetailed molecular structureCritical roleGlycosylationProteinSpectrometric analysisStructural featuresUnique abilityStructural dynamicsMolecular dynamics simulationsTim-3 functionFamilyPowerful workflowRegulatorImmune cellsCheckpointGlycansHow ligands achieve biased signaling at opioid receptors
Paggi J, Aydin D, Laloudakis Y, Suomivuori C, Che T, Dror R. How ligands achieve biased signaling at opioid receptors. Journal Of Pharmacology And Experimental Therapeutics 2023, 385: 317. DOI: 10.1124/jpet.122.274970.Peer-Reviewed Original ResearchSide effectsOpioid receptorsK-opioidInduce severe side effectsG-proteinK-opioid receptorsM-opioid receptorSevere side effectsReceptor conformationDecrease side effectsDesign of ligandsProtein-ligand interactionsMolecular dynamics simulationsHazardous side effectsG protein signalingLigand-binding pocketTransmembrane helix 7Increased efficacyConformational ensemblesOpioidReceptorsDynamics simulationsMutagenesis experimentsLigandSignal profiles
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