2021
A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Chen E, Reiss K, Shah D, Manjula R, Allen B, Murphy EL, Murphy JW, Batista VS, Bhandari V, Lolis EJ, Lisi GP. A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase. Journal Of Biological Chemistry 2021, 297: 101061. PMID: 34384784, PMCID: PMC8405996, DOI: 10.1016/j.jbc.2021.101061.Peer-Reviewed Original ResearchMeSH KeywordsAllosteric SiteAmino Acid SequenceAntigens, Differentiation, B-LymphocyteBinding SitesCatalytic DomainCrystallography, X-RayCytokinesHistocompatibility Antigens Class IIHumansIntramolecular OxidoreductasesMacrophage Migration-Inhibitory FactorsProtein BindingStructure-Activity RelationshipConceptsAllosteric siteDopachrome tautomeraseDynamic regulatory networksEnzymatic activityLow sequence identityLigand-binding siteMultiple ligand-binding sitesNonoverlapping functionsRegulatory networksAllosteric couplingMacrophage migration inhibitory factor (MIF) familyFactor familySequence identityHomolog DStructural basisPrimary sequenceCD74 activationFunctional similarityConformational changesSolution NMRMIF-2X-ray crystallographyCatalytic siteStructural consequencesSolvent channels
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
Structural 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 ResearchMeSH KeywordsAnimalsCricetinaeCrystallography, X-RayEvolution, MolecularModels, MolecularQuantum TheoryRetinal PigmentsRod OpsinsSchiff BasesUltraviolet RaysConceptsUV pigmentsCone pigmentsSpectral tuningActivation of rhodopsinAncestral pigmentMolecular evolutionVertebrate visionMutagenesis studiesPhotoreceptor rhodopsinMolecular levelStructural rearrangementsUnprotonated Schiff baseTransmembraneTM6PigmentsRhodopsinMutationsEssential componentRetinyl chromophoreHydrogen bonding networkMutantsTM2Structural modelPhysiologicalRearrangement
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 ResearchMeSH KeywordsBinding SitesChloridesCrystallography, X-RayHydrogen BondingModels, MolecularOxygenPhotosystem II Protein ComplexProtonsStructure-Activity Relationship
2008
Quantum 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
Quantum 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