2021
High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 119: e2116765118. PMID: 34937700, PMCID: PMC8740770, DOI: 10.1073/pnas.2116765118.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCryoelectron MicroscopyPhotosystem II Protein ComplexProtein ConformationSynechocystisConceptsCryo-electron microscopy structurePCC 6803Photosystem IIWater oxidationMicroscopy structureMesophilic cyanobacteriumHigh-resolution cryo-electron microscopy structuresOxygen-evolving photosystem IILight-driven water oxidationCyanobacterial photosystem IIHigh-resolution structuresD1 subunitPSII structureSynechocystis spLarge water channelsGenetic manipulationC-terminusBiophysical dataActive siteCyanobacteriumSpStructural pictureSubunitsOxidationWater channels
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 ResearchMeSH KeywordsAllosteric RegulationBiocatalysisDual Specificity Phosphatase 3HumansHydrolysisKineticsModels, MolecularMutagenesis, Site-DirectedProtein ConformationConceptsAcid 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 dataCrystalsStateEXAFSLightStructureResolution
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
Amphiphilic Adsorption of Human Islet Amyloid Polypeptide Aggregates to Lipid/Aqueous Interfaces
Xiao D, Fu L, Liu J, Batista V, Yan E. Amphiphilic Adsorption of Human Islet Amyloid Polypeptide Aggregates to Lipid/Aqueous Interfaces. Journal Of Molecular Biology 2011, 421: 537-547. PMID: 22210153, PMCID: PMC3350761, DOI: 10.1016/j.jmb.2011.12.035.Peer-Reviewed Original ResearchConceptsLipid/aqueous interfaceAqueous interfaceΒ-sheet aggregatesAb initio quantum chemistry calculationsChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyQuantum chemistry calculationsFrequency generation spectroscopyHuman islet amyloid polypeptideHuman islet amyloid polypeptide aggregatesChemistry calculationsAmphiphilic propertiesGeneration spectroscopyΒ-sheetPolypeptide aggregatesIslet amyloid polypeptideΒ-strandsAggregatesAmyloid polypeptideAdsorbAdsorptionSpectroscopyAmyloid proteinInterfacePotential disruptive effectsS1-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
2006
Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin
Gascón J, Sproviero E, Batista V. Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin. Accounts Of Chemical Research 2006, 39: 184-193. PMID: 16548507, DOI: 10.1021/ar050027t.Peer-Reviewed Original ResearchMeSH KeywordsIsomerismModels, MolecularNuclear Magnetic Resonance, BiomolecularProtein ConformationRetinal PigmentsRhodopsinSignal TransductionConceptsG protein-coupled receptorsRecent computational studiesPrimary photochemical eventQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsComputational studyPhotochemical eventsEnergy storage mechanismPrototypical G protein-coupled receptorX-ray structureVisual rhodopsinHigh-resolution X-ray structuresBovine visual rhodopsinWater moleculesSpectroscopic changesRetinyl chromophoreStorage mechanismActive siteMolecular rearrangementTrans isomerizationPhototransduction eventsMolecular originIndividual residuesStructural refinementPhototransduction mechanismChromophore
2004
QM/MM Study of Energy Storage and Molecular Rearrangements Due to the Primary Event in Vision
Gascon J, Batista V. QM/MM Study of Energy Storage and Molecular Rearrangements Due to the Primary Event in Vision. Biophysical Journal 2004, 87: 2931-2941. PMID: 15339806, PMCID: PMC1304767, DOI: 10.1529/biophysj.104.048264.Peer-Reviewed Original ResearchConceptsMolecular rearrangementQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsEnergy storageQM/MM studyPolyene chainEnergy storage mechanismElectronic excitation energiesHigh-resolution structural dataBovine visual rhodopsinMolecular structureMM studyNet positive chargePrimary photochemical eventSchiff baseC13 positionSchiff base linkageStorage mechanismSteric interactionsTrans productsSteric constraintsPreferential senseFirst-principles understandingPositive chargePhotochemical eventsStructural data