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
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 residuesComplexesDeprotonationAnionsCounterionsNaChlorideSitesCl
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 Research
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