2021
Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir
Wang J, Reiss K, Shi Y, Lolis E, Lisi GP, Batista VS. Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir. Biochemistry 2021, 60: 1869-1875. PMID: 34110129, PMCID: PMC8204756, DOI: 10.1021/acs.biochem.1c00292.Peer-Reviewed Original Research
2020
Identification of a Na+‑Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II
Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudvig GW. Identification of a Na+‑Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II. Biochemistry 2020, 59: 2823-2831. PMID: 32650633, DOI: 10.1021/acs.biochem.0c00303.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexSpinach photosystem IIRedox-active Mn ionPhotosystem IIOxygen evolution activityQuantum mechanical calculationsOxomanganese clusterHydroxide anionCommon counterionCryo-electron microscopy mapMechanical calculationsAmino acid residuesMn ionsIonsElectrostatic simulationsMicroscopy mapsAcid residuesComplexesDeprotonationAnionsCounterionsNaChlorideSitesClAllosteric 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
2015
Analysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data
Askerka M, Vinyard DJ, Wang J, Brudvig GW, Batista VS. Analysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data. Biochemistry 2015, 54: 1713-1716. PMID: 25710258, DOI: 10.1021/acs.biochem.5b00089.Peer-Reviewed Original ResearchConceptsPhotosystem II crystalsX-ray absorption fine structureExtended X-ray absorption fine structureAbsorption fine structurePhotosystem IIHigh-resolution structural modelS1 stateS0 stateOxygen-evolving complexRadiation damageX-ray diffraction studiesExtensive dark adaptationFine structureDiffraction studiesOxygen atomsManganese centersX-ray structureAtomsMM dataCrystalsStateEXAFSLightStructureResolutionComputational Insights on Crystal Structures of the Oxygen-Evolving Complex of Photosystem II with Either Ca2+ or Ca2+ Substituted by Sr2+
Vogt L, Ertem MZ, Pal R, Brudvig GW, Batista VS. Computational Insights on Crystal Structures of the Oxygen-Evolving Complex of Photosystem II with Either Ca2+ or Ca2+ Substituted by Sr2+. Biochemistry 2015, 54: 820-825. PMID: 25555204, DOI: 10.1021/bi5011706.Peer-Reviewed Original ResearchMeSH KeywordsCalciumCrystallography, X-RayModels, MolecularOxygenPhotosystem II Protein ComplexQuantum TheoryStrontiumConceptsX-ray crystal structureCrystal structureQuantum mechanics/molecular mechanics calculationsQM/MM modelOxygen-Evolving ComplexMolecular mechanics calculationsPhotosystem IIWater oxidationMechanics calculationsComputational insightsReduced statesHeterocationsMM modelSubstitution resultsComplexesS statesStructureCationsBondsOxidationSr2Experimental dataW5WaterCalculations
2014
Kinetics of Thermal Activation of an Ultraviolet Cone Pigment
Mooney V, Sekharan S, Liu J, Guo Y, Batista V, Yan E. Kinetics of Thermal Activation of an Ultraviolet Cone Pigment. Journal Of The American Chemical Society 2014, 137: 307-313. PMID: 25514632, DOI: 10.1021/ja510553f.Peer-Reviewed Original ResearchConceptsTransmembrane helix 6UV pigmentsUnprotonated Schiff baseVisual pigmentsCone pigmentsDim-light visionExtracellular loop 2Vertebrate visual pigmentsMolecular evolutionUltraviolet pigmentsOpsin proteinHelix 6Retinyl chromophoreLoop 2UV cone pigmentBovine rhodopsinRod pigmentRhodopsinHydrogen bonding networkSalt bridgeIonone ringPigmentsSchiff base chromophoreSteric restraintsActivationStructural Changes in the Oxygen-Evolving Complex of Photosystem II Induced by the S1 to S2 Transition: A Combined XRD and QM/MM Study
Askerka M, Wang J, Brudvig GW, Batista VS. Structural Changes in the Oxygen-Evolving Complex of Photosystem II Induced by the S1 to S2 Transition: A Combined XRD and QM/MM Study. Biochemistry 2014, 53: 6860-6862. PMID: 25347729, PMCID: PMC4230327, DOI: 10.1021/bi5011915.Peer-Reviewed Original Research
2013
Spectral Tuning of Ultraviolet Cone Pigments: An Interhelical Lock Mechanism
Sekharan S, Mooney V, Rivalta I, Kazmi M, Neitz M, Neitz J, Sakmar T, Yan E, Batista V. Spectral Tuning of Ultraviolet Cone Pigments: An Interhelical Lock Mechanism. Journal Of The American Chemical Society 2013, 135: 19064-19067. PMID: 24295328, PMCID: PMC4536979, DOI: 10.1021/ja409896y.Peer-Reviewed Original ResearchConceptsUV pigmentsCone pigmentsSpectral tuningActivation of rhodopsinAncestral pigmentMolecular evolutionVertebrate visionMutagenesis studiesPhotoreceptor rhodopsinMolecular levelStructural rearrangementsUnprotonated Schiff baseTransmembraneTM6PigmentsRhodopsinMutationsEssential componentRetinyl chromophoreHydrogen bonding networkMutantsTM2Structural modelPhysiologicalRearrangementS0‑State Model of the Oxygen-Evolving Complex of Photosystem II
Pal R, Negre CF, Vogt L, Pokhrel R, Ertem MZ, Brudvig GW, Batista VS. S0‑State Model of the Oxygen-Evolving Complex of Photosystem II. Biochemistry 2013, 52: 7703-7706. PMID: 24125018, DOI: 10.1021/bi401214v.Peer-Reviewed Original ResearchMeSH KeywordsManganeseModels, MolecularOxidation-ReductionPhotosystem II Protein ComplexPlant ProteinsConceptsOxygen-evolving complexS1 transitionQuantum mechanics/molecular mechanics modelsX-ray absorption fine structure spectroscopyExtended X-ray absorption fine structure (EXAFS) spectroscopyQM/MM modelAbsorption fine structure spectroscopyElectron transfer processHydrogen bonding networkFine structure spectroscopyPhotosystem IIX-ray diffraction dataMolecular mechanics modelPCET mechanismKok cycleWater moleculesWater splittingBonding networkS1 stateMn centersStructure spectroscopyS0 stateDiffraction dataMM modelSignificant rearrangementElectrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II
Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR. Electrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II. The Journal Of Physical Chemistry B 2013, 117: 6217-6226. PMID: 23570540, PMCID: PMC3753004, DOI: 10.1021/jp403321b.Peer-Reviewed Original ResearchConceptsOxomanganese complexesElectron transferOxygen-evolving complexComplexes 6Electrostatic effectsΜ-oxo bridgeDensity functional theory levelTerminal water ligandsBiomimetic oxomanganese complexesPhotosystem IIOxidation state transitionsContinuum electrostatic modelWater ligandsLigand substituentsOxidation midpoint potentialsOxo bridgeCalculated pKaProton transferElectrostatic interactionsTheory levelElectrostatic contributionMidpoint potentialMn oxidationElectrostatic modelFree energy
2012
Allosteric pathways in imidazole glycerol phosphate synthase
Rivalta I, Sultan MM, Lee NS, Manley GA, Loria JP, Batista VS. Allosteric pathways in imidazole glycerol phosphate synthase. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: e1428-e1436. PMID: 22586084, PMCID: PMC3365145, DOI: 10.1073/pnas.1120536109.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAllosteric RegulationAllosteric SiteAminohydrolasesBacterial ProteinsBinding SitesBiocatalysisCrystallography, X-RayImidazolesKineticsModels, MolecularMolecular Dynamics SimulationProtein BindingProtein ConformationProtein MultimerizationProtein Structure, TertiaryProtein SubunitsRibonucleotidesSignal TransductionThermotoga maritimaConceptsAllosteric pathwayImidazole glycerolNucleotide biosynthetic pathwayGlutaminase active siteProtein-protein interfacesGlutamine-binding siteNew allosteric drugsImportant branch pointSolution NMR techniquesAllosteric drugsBiosynthetic pathwayAllosteric mechanismCommunity analysisCorrelated protein motionsInactive enzymeProtein motionsPRFARAlternative herbicidesPotential therapeutic targetPathwayTherapeutic targetActive siteNMR techniquesBranch pointsFundamental insights
2011
Structural–Functional Role of Chloride in Photosystem II
Rivalta I, Amin M, Luber S, Vassiliev S, Pokhrel R, Umena Y, Kawakami K, Shen JR, Kamiya N, Bruce D, Brudvig GW, Gunner MR, Batista VS. Structural–Functional Role of Chloride in Photosystem II. Biochemistry 2011, 50: 6312-6315. PMID: 21678923, PMCID: PMC3140697, DOI: 10.1021/bi200685w.Peer-Reviewed Original ResearchS1-State Model of the O2-Evolving Complex of Photosystem II
Luber S, Rivalta I, Umena Y, Kawakami K, Shen JR, Kamiya N, Brudvig GW, Batista VS. S1-State Model of the O2-Evolving Complex of Photosystem II. Biochemistry 2011, 50: 6308-6311. PMID: 21678908, PMCID: PMC3139771, DOI: 10.1021/bi200681q.Peer-Reviewed Original ResearchConceptsHigh-resolution spectroscopic dataQuantum mechanics/molecular mechanics modelsExtended X-ray absorption fine structure (EXAFS) dataX-ray absorption fine structure dataFine structure dataPhotosystem IIX-ray diffraction modelOxygen-evolving complexDiffraction modelSingle crystalsMn clusterXRD modelMolecular mechanics modelIntermetallic distanceManganese centersSpectroscopic dataOxidation stateWater splittingCarboxylate moietyCatalytic cycleStructure dataLikely correspondsComplexesSplittingCrystals
2010
Discrimination of Saturated Aldehydes by the Rat I7 Olfactory Receptor
Kurland M, Newcomer M, Peterlin Z, Ryan K, Firestein S, Batista V. Discrimination of Saturated Aldehydes by the Rat I7 Olfactory Receptor. Biochemistry 2010, 49: 6302-6304. PMID: 20608641, PMCID: PMC2912408, DOI: 10.1021/bi100976w.Peer-Reviewed Original ResearchMeSH KeywordsAldehydesAnimalsCattleDiscrimination, PsychologicalModels, MolecularOdorantsRatsReceptors, OdorantRhodopsinSensory Receptor Cells
2008
Acetylacetonate Anchors for Robust Functionalization of TiO2 Nanoparticles with Mn(II)−Terpyridine Complexes
McNamara WR, Snoeberger RC, Li G, Schleicher JM, Cady CW, Poyatos M, Schmuttenmaer CA, Crabtree RH, Brudvig GW, Batista VS. Acetylacetonate Anchors for Robust Functionalization of TiO2 Nanoparticles with Mn(II)−Terpyridine Complexes. Journal Of The American Chemical Society 2008, 130: 14329-14338. PMID: 18831585, DOI: 10.1021/ja805498w.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationElectron Spin Resonance SpectroscopyElectronsHydroxybutyratesLightManganeseMembranes, ArtificialModels, ChemicalModels, MolecularMolecular StructureNanoparticlesOrganometallic CompoundsOxidation-ReductionParticle SizePentanonesPhotochemistryPorosityPyridinesSensitivity and SpecificitySpectrophotometry, UltravioletSurface PropertiesTime FactorsTitaniumWaterConceptsInterfacial electron injectionTiO2 nanoparticlesRobust functionalizationTransition metal ionsVisible light sensitizationElectron injectionInterfacial electron transferColloidal thin filmsTerpy complexesPhotocatalytic complexesOxidation chemistryEffective catalystCoupling reactionElectron transferNanoparticlesVariety of scaffoldsComplex of caPhotovoltaic devicesFunctionalizationSubpicosecond time scaleAqueous suspensionOxidative conditionsThin filmsComplexesTransient measurementsComputational insights into the O2-evolving complex of photosystem II
Sproviero EM, McEvoy JP, Gascón JA, Brudvig GW, Batista VS. Computational insights into the O2-evolving complex of photosystem II. Photosynthesis Research 2008, 97: 91-114. PMID: 18483777, PMCID: PMC2728911, DOI: 10.1007/s11120-008-9307-0.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationModels, MolecularOxygenPhotosystem II Protein ComplexProtein BindingWaterConceptsOxygen-evolving complexX-ray diffractionQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsPhotosystem IIMass spectrometryX-ray absorption fine structure spectroscopyExtended X-ray absorption fine structure (EXAFS) spectroscopyQM/MM modelingElectron paramagnetic resonance spectroscopyAbsorption fine structure spectroscopyCatalytic metal clustersWater splitting reactionIntermediate oxidation statesParamagnetic resonance spectroscopyFine structure spectroscopyO2-evolving complexDensity functional theoryInorganic coreMM modelingOxidation stateMetal clustersStructure spectroscopyOEC structureCrystallographic resultsComputational insightsA Model of the Oxygen-Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. A Model of the Oxygen-Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations. Journal Of The American Chemical Society 2008, 130: 6728-6730. PMID: 18457397, PMCID: PMC2678715, DOI: 10.1021/ja801979n.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexSpectroscopic dataPhotosystem IIOxygen-Evolving CenterIntermediate oxidation statesHigh-resolution spectroscopic dataOxidation stateCatalytic cycleMetal clustersEXAFS simulationsPolarized EXAFSXRD modelStructural refinementEXAFSComputational structural modelsSingle crystalsStructural modelDanglerAmino acidsIonsComplexesCrystalsMnAcidStructureQuantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II. Journal Of The American Chemical Society 2008, 130: 3428-3442. PMID: 18290643, DOI: 10.1021/ja076130q.Peer-Reviewed Original ResearchConceptsSubstrate water moleculesWater moleculesMu-oxo bridgeOxygen-evolving complexWater splittingQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsQuantum Mechanics/Molecular Mechanics StudySolar fuel production systemsPhotosystem IIX-ray diffraction structureMolecular mechanics studySecond coordination shellCyanobacterium Thermosynechococcus elongatusOxomanganese clusterDioxygen evolutionTerminal ligandsXRD structureCatalytic clustersCP43-R357Ligand exchangeCatalytic reactionCatalytic cycleReaction intermediatesS0 stateNucleophilic attack
2007
QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II
Sproviero EM, Shinopoulos K, Gascn J, McEvoy JP, Brudvig GW, Batista VS. QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II. Philosophical Transactions Of The Royal Society B Biological Sciences 2007, 363: 1149-1156. PMID: 17971333, PMCID: PMC2614095, DOI: 10.1098/rstb.2007.2210.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesModels, MolecularOxygenPhotosystem II Protein ComplexQuantum TheorySynechococcusThermodynamicsWaterConceptsOxygen-evolving centerWater moleculesSubstrate waterElectrostatic potential atomic chargesQM/MM computational studiesPhotosystem IIComputational studyX-ray crystal structureCharge transfer interactionFormal oxidation stateCyanobacterium Thermosynechococcus elongatusDioxygen formationMetal centerModel complexesOxidation stateWater exchange rateAtomic chargesMetal clustersSubstrate moleculesMn ionsCrystal structureEnergy barrierThermosynechococcus elongatusManganese ionsWater bindingQuantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. Current Opinion In Structural Biology 2007, 17: 173-180. PMID: 17395452, DOI: 10.1016/j.sbi.2007.03.015.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexPhotosystem IIWater oxidationOEC of PSIIQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsPhotocatalytic water oxidationGreen plant chloroplastsX-ray crystallographyX-ray absorption fine structure measurementsProcess of photosynthesisAmino acid residuesAbsorption fine structure measurementsExtended X-ray absorption fine structure (EXAFS) measurementsIntrinsic electronic propertiesComputational structural modelsFine structure measurementsOEC modelsAvailable mechanistic dataProtein environmentThylakoid membranesCatalytic mechanismX-ray diffraction modelElectronic propertiesInternal membranesCatalytic center