2024
Occupancy 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 residuesMolecules
2023
Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Maschietto F, Morzan U, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro G, Nekrasov P, Brooks B, Loria J, Rivalta I, Batista V. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications 2023, 14: 2239. PMID: 37076500, PMCID: PMC10115891, DOI: 10.1038/s41467-023-37956-1.Peer-Reviewed Original ResearchConceptsEffector bindingImidazole Glycerol Phosphate SynthaseLocal amino acidsAmino acid dynamicsImidazole glycerolAllosteric drugsAllosteric activationAllosteric responsePhosphate synthaseAllosteric mechanismMode of activationEnzyme functionAmino acidsAllosteryDrug discoverySynthaseNuclear magnetic resonance spectroscopyBindingMolecular dynamics simulationsActivationAllostericCascadeDynamics simulations
2022
Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2
Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2. Biochemistry 2022, 61: 1966-1973. PMID: 36044776, PMCID: PMC9469760, DOI: 10.1021/acs.biochem.2c00341.Peer-Reviewed Original ResearchConceptsReplication-transcription complexStructural basisCryo-EM structureAdenosine monophosphateRemdesivir triphosphateStructural insightsDuplex productsPrimer extensionNucleotide selectivityBase pairsNucleotide incorporationIncoming substrateRibosyl moietyActive complexSARS-CoV-2 inhibitorsNew detailed informationTriphosphateComplexesMolecular dynamics simulationsAdenosine triphosphateInsights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations
Wang J, Shi Y, Reiss K, Allen B, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Insights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations. Biochemistry 2022, 61: 424-432. PMID: 35199520, PMCID: PMC8887646, DOI: 10.1021/acs.biochem.1c00755.Peer-Reviewed Original ResearchConceptsReplication-transcription complexPriming reactionRNA duplexesTemplate strandRNA templateHigher-order oligomerizationRNA-dependent RNA polymeraseCryo-EM structureRNA primaseViral RNA templateRNA polymerasePrimer synthesisViral transcriptionSecondary structureViral genomeSubunitsMolecular dynamics simulations
2020
Allosteric Impact of the Variable Insert Loop in Vaccinia H1-Related (VHR) Phosphatase
Beaumont VA, Reiss K, Qu Z, Allen B, Batista VS, Loria JP. Allosteric Impact of the Variable Insert Loop in Vaccinia H1-Related (VHR) Phosphatase. Biochemistry 2020, 59: 1896-1908. PMID: 32348128, PMCID: PMC7364816, DOI: 10.1021/acs.biochem.0c00245.Peer-Reviewed Original ResearchConceptsAcid loopVariable insertActive siteActive-site hydrogen bondsInsert regionSolution nuclear magnetic resonanceNuclear magnetic resonanceMillisecond motionsActive site environmentNormal catalytic functionActive site altersMolecular dynamics simulationsActive site loopHydrogen bondsVaccinia H1Asparagine 74Protein tyrosineTyrosine phosphataseRapid kinetic measurementsAllosteric regionActivity of enzymesKinetic measurementsDynamics simulationsConformational motionsInsert loop
2019
Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II
Reiss K, Morzan U, Grigas A, Batista V. Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II. Inorganics 2019, 7: 39. DOI: 10.3390/inorganics7030039.Peer-Reviewed Original ResearchOxygen-evolving complexWater network dynamicsMolecular dynamics simulationsPhotosystem IICatalytic performanceHydrogen bondingProtein environmentLarge ionsS2 stateDynamics simulationsLarge channelsProton translocationWater diffusionComplexesPSII assemblyEigenvector centrality analysisWater networkGreat interestWater channelsDynamical natureBondingIonsWater transportMajor channelChloride
2017
Interfacial Structure and Electric Field Probed by in Situ Electrochemical Vibrational Stark Effect Spectroscopy and Computational Modeling
Ge A, Videla P, Lee G, Rudshteyn B, Song J, Kubiak C, Batista V, Lian T. Interfacial Structure and Electric Field Probed by in Situ Electrochemical Vibrational Stark Effect Spectroscopy and Computational Modeling. The Journal Of Physical Chemistry C 2017, 121: 18674-18682. DOI: 10.1021/acs.jpcc.7b05563.Peer-Reviewed Original ResearchSelf-assembled monolayersElectrolyte interfaceMolecular dynamics simulationsHelmholtz layerElectrochemical double-layer structureVibrational Stark effect spectroscopyElectrode/electrolyte interfaceVibrational sum frequency generation spectroscopySum frequency generation spectroscopyDensity functional theory calculationsDynamics simulationsAqueous electrolyte interfaceDirect spectroscopic methodFrequency generation spectroscopyStark tuning rateInterfacial structureFunctional theory calculationsStark effect spectroscopySolar energy conversionInterfacial electric fieldDetailed molecular levelElectrochemical interfaceModel complexesDouble-layer structureElectrolyte penetration
2016
Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulations Reveal a Rotationally Fluid Adsorption State of α‑Pinene on Silica
Ho J, Psciuk B, Chase H, Rudshteyn B, Upshur M, Fu L, Thomson R, Wang H, Geiger F, Batista V. Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulations Reveal a Rotationally Fluid Adsorption State of α‑Pinene on Silica. The Journal Of Physical Chemistry C 2016, 120: 12578-12589. DOI: 10.1021/acs.jpcc.6b03158.Peer-Reviewed Original ResearchMolecular dynamics simulationsΑ-pineneSum frequency generation spectroscopyDynamics simulationsHeterogeneous catalytic pathwayClassical molecular dynamics simulationsSum Frequency Generation StudyFrequency generation spectroscopyVan der Waals contactsFour-membered ringVibrational sum frequency generation studyAdsorption modePrimary oxidantSilica surfaceStrained hydrocarbonsCatalytic pathwayFine chemicalsAdsorption statesGeneration spectroscopyVibrational spectraMethylene groupWaals contactsVapor interfaceVibrational modesRotational diffusion constants
2013
Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides
Poojari C, Xiao D, Batista V, Strodel B. Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides. Biophysical Journal 2013, 105: 2323-2332. PMID: 24268144, PMCID: PMC3838749, DOI: 10.1016/j.bpj.2013.09.045.Peer-Reviewed Original ResearchConceptsChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyMembrane/water interfaceFrequency generation spectroscopyΒ-sheet secondary structureChannel-forming proteinMolecular dynamics simulationsSimulated SFG spectraAmphiphilic propertiesHuman islet amyloidGeneration spectroscopySFG spectraWater interfaceΒ-sandwichHuman islet amyloid polypeptideIslet β-cellsAmyloid polypeptideWater permeationDynamics simulationsHIAPP aggregatesSecondary structureMembrane permeationIslet amyloid polypeptideΒ-cellsFibrillar structures
2011
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP. Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid. Biophysical Journal 2011, 101: 411-420. PMID: 21767494, PMCID: PMC3136797, DOI: 10.1016/j.bpj.2011.05.039.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsAmino acidsMeiboom-Gill (CPMG) relaxation dispersion experimentsWild-type ribonuclease AProtein energy landscapesNonnatural amino acidsRelaxation dispersion experimentsSingle residueProtein motionsMillisecond motionsConformational motionsEnzyme motionsHistidine-48Ribonuclease ACatalytic turnoverSimilar pH rangeRate limitingMolecular dynamics simulationsEnergy landscapeCorrelated motionAcidCatalytic cycleDispersion experimentsResiduesDynamics simulations
2010
Study of Redox Species and Oxygen Vacancy Defects at TiO2−Electrolyte Interfaces
da Silva R, Rego L, Freire J, Rodriguez J, Laria D, Batista V. Study of Redox Species and Oxygen Vacancy Defects at TiO2−Electrolyte Interfaces. The Journal Of Physical Chemistry C 2010, 114: 19433-19442. DOI: 10.1021/jp107385e.Peer-Reviewed Original ResearchRedox speciesElectronic structure calculationsDye-sensitized solar cellsStructure calculationsDifferent redox speciesFree energy barrierMolecular dynamics simulationsPyridine additivesRecombination of photoelectronsSolvent dynamicsTiO2 surfaceElectronic propertiesDynamics simulationsOxygen vacanciesSolar cellsSurface defectsElectrolyteAdsorptionDeeper insightInterfaceCalculationsMolecular processesAdditivesPhotoelectronVacancies
2009
Visible Light Sensitization of TiO2 Surfaces with Alq3 Complexes
Rego L, da Silva R, Freire J, Snoeberger R, Batista V. Visible Light Sensitization of TiO2 Surfaces with Alq3 Complexes. The Journal Of Physical Chemistry C 2009, 114: 1317-1325. DOI: 10.1021/jp9094479.Peer-Reviewed Original ResearchVisible light sensitizationSurface complexesAb initio DFT molecular dynamics simulationsLight sensitizationDFT molecular dynamics simulationsTransient electronic excitationsInterfacial electron transferInterfacial electron injectionTiO2 anatase (101) surfaceMolecular dynamics simulationsTris complexesMolecular assembliesElectron transferAlq3 complexesElectronic excitationTiO2 surfaceCovalent attachmentDynamics simulationsElectron injectionPair recombinationComplexesHost substrateSignificant interestOligothiophenesDerivatization
2005
Influence of Thermal Fluctuations on Interfacial Electron Transfer in Functionalized TiO2 Semiconductors
Abuabara S, Rego L, Batista V. Influence of Thermal Fluctuations on Interfacial Electron Transfer in Functionalized TiO2 Semiconductors. Journal Of The American Chemical Society 2005, 127: 18234-18242. PMID: 16366577, DOI: 10.1021/ja055185u.Peer-Reviewed Original ResearchInterfacial electron transferRoom-temperature thermal fluctuationsElectron transferAb initio DFT molecular dynamics simulationsDFT molecular dynamics simulationsThermal fluctuationsTransient electronic excitationsInterfacial electron transfer dynamicsSemiconductor materialsElectron transfer dynamicsCharge separation mechanismElectron acceptor statesCarrier diffusionAdditional relaxation pathwayCharge diffusionMolecular dynamics simulationsAnatase crystalsDynamic propagationTiO2 semiconductorElectronic excitationNuclear fluctuationsNonadiabatic transitionsDelocalized statesRelaxation pathwaysSeparation mechanism
2003
Quantum Dynamics Simulations of Interfacial Electron Transfer in Sensitized TiO2 Semiconductors
Rego L, Batista V. Quantum Dynamics Simulations of Interfacial Electron Transfer in Sensitized TiO2 Semiconductors. Journal Of The American Chemical Society 2003, 125: 7989-7997. PMID: 12823021, DOI: 10.1021/ja0346330.Peer-Reviewed Original ResearchInterfacial electron transferElectron transferAb initio DFT molecular dynamics simulationsDFT molecular dynamics simulationsAnatase crystalsElectron injection eventsInterfacial electron transfer dynamicsQuantum dynamics calculationsQuantum dynamics simulationsDynamics simulationsElectron transfer dynamicsSurface charge separationMolecular dynamics simulationsCarrier relaxationCharge delocalizationElectronic relaxationAdsorbate moleculesAnatase nanostructuresElectronic statesCharge separationVacuum conditionsSurface ionsTiO2 semiconductorElectron injectionPhotovoltaic devices
2002
Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †
Wu Y, Batista V. Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †. The Journal Of Physical Chemistry B 2002, 106: 8271-8277. DOI: 10.1021/jp0207735.Peer-Reviewed Original ResearchPhotodissociation dynamicsFull quantum mechanical resultsFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState photodissociation dynamicsQuantum mechanical resultsExcited vibrational statesPhotodissociation cross sectionsTotal photodissociation cross sectionsQuantum mechanical calculationsSemiclassical initial value representation methodSemiclassical resultsSemiclassical approachVibrational statesMechanical calculationsCross sectionsH2O spectroscopyExcellent agreementMolecular dynamics simulationsMechanical resultsDynamics simulationsCalculationsBandDynamicsH2OProton-Transfer Dynamics in the Activation of Cytochrome P450eryF
Guallar V, Harris D, Batista V, Miller W. Proton-Transfer Dynamics in the Activation of Cytochrome P450eryF. Journal Of The American Chemical Society 2002, 124: 1430-1437. PMID: 11841312, DOI: 10.1021/ja016474v.Peer-Reviewed Original ResearchConceptsProton transfer eventsProton transfer dynamicsCytochrome P450eryFQuantum chemistry calculationsHydrogen bond networkMechanism of oxidationUltrafast proton transferMolecular dynamics simulationsProton transfer energy profileChemistry calculationsDistal oxygenOxyferrous stateBond networkProton transferEnergy profilesDynamics simulationsHeme groupEnzymatic efficacyP450eryFEnzymatic activationOxidationOxygen speciesReactionOxygenCytochrome P450
2000
Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole. The Journal Of Chemical Physics 2000, 113: 9510-9522. DOI: 10.1063/1.1321049.Peer-Reviewed Original ResearchPotential energy surfaceExcited state potential energy surfacesFull-dimensional potential energy surfaceEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceProton transferVibrational energy redistributionProton transfer dynamicsQuantum mechanical calculationsSemiclassical initial value representation methodIntramolecular proton transferPlane vibrational modesSemiclassical resultsMolecular dynamics simulationsEnergy redistributionMechanical calculationsQuantum chemistryTransfer dynamicsCIS levelTautomerization reactionVibrational modesIsotopic substitutionDynamics simulations
1999
Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers. The Journal Of Chemical Physics 1999, 110: 9922-9936. DOI: 10.1063/1.478866.Peer-Reviewed Original ResearchExcited-state double proton transferState double proton transferDouble proton transferPotential energy surfaceInitial value representationProton transferExcited state potential energy surfacesEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceQuantum mechanical calculationsSemiclassical initial value representationMolecular dynamics simulationsUltrafast dynamicsSymmetric stretch vibrationSemiclassical resultsQuantum chemistryPopulation decayTautomerization reactionMechanical calculationsCIS levelMolecular systemsReduced dimensionalityIsotopic substitution
1998
Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone
Batista V, Miller W. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone. The Journal Of Chemical Physics 1998, 108: 498-510. DOI: 10.1063/1.475413.Peer-Reviewed Original ResearchElectronic potential energy surfacesSemiclassical molecular dynamics simulationsUltrafast photodissociation dynamicsChappuis bandsSemiclassical initial value representation methodTime-dependent picturePotential energy surfaceUltrafast dynamicsPhotodissociation dynamicsSemiclassical resultsExcited statesNonadiabatic processesMolecular dynamics simulationsEnergy surfaceModel HamiltonianVisible lightGas phaseDynamical featuresDynamics simulationsRealistic reactionsOzoneBandPredissociationPhotodissociationPhotoexcitation
1997
Nonadiabatic molecular dynamics simulation of ultrafast pump-probe experiments on I2 in solid rare gases
Batista V, Coker D. Nonadiabatic molecular dynamics simulation of ultrafast pump-probe experiments on I2 in solid rare gases. The Journal Of Chemical Physics 1997, 106: 6923-6941. DOI: 10.1063/1.473717.Peer-Reviewed Original ResearchPump-probe experimentsUltrafast pump-probe experimentsNonadiabatic molecular dynamics simulationsIon-pair statesNonadiabatic molecular dynamicsSolid rare gasesSemiempirical diatomicsElectronic structure techniquesRare gas matricesAbsorption signalPair statesRare gasesDetailed microscopic analysisGolden rule resultsMatrix elementsRemarkable agreementMolecular dynamics simulationsRecent experimental studiesGas matricesStructure techniqueMolecular dynamicsBody dynamicsCrystal systemDIM methodDynamics simulations