2022
How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM
Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. Journal Of Structural Biology 2022, 214: 107902. PMID: 36202310, PMCID: PMC10226527, DOI: 10.1016/j.jsb.2022.107902.Peer-Reviewed Original ResearchConceptsCryo-EM mapsAmino acid residuesAcid residuesCryo-electron microscopy mapIndividual amino acid residuesCyanobacteria Synechocystis spPCC 6803Synechocystis spMicroscopy mapsThermosynechococcus elongatusSARS-CoV-2 spike proteinLocal structural changesResiduesSpike proteinAtomic coordinatesElongatusSubunitsSpeciesProteinSpSimilar structureStructural changes
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
2013
Spectral Tuning in Halorhodopsin: The Chloride Pump Photoreceptor
Pal R, Sekharan S, Batista V. Spectral Tuning in Halorhodopsin: The Chloride Pump Photoreceptor. Journal Of The American Chemical Society 2013, 135: 9624-9627. PMID: 23777372, DOI: 10.1021/ja404600z.Peer-Reviewed Original ResearchConceptsKey amino acid residuesIon translocation pathwayAmino acid residuesSpectral tuningInternal water moleculesTranslocation pathwaySpecific hydrogen bondsHalobacterium salinarumAcid residuesMolecular levelStructural rearrangementsAnion transportCl depletionPhotoreceptorsInduces changesHalorhodopsinRetinyl chromophoreSalinarumMutationsResiduesPathwayFirst time
2008
Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes. Coordination Chemistry Reviews 2008, 252: 395-415. PMID: 19190716, PMCID: PMC2350217, DOI: 10.1016/j.ccr.2007.09.006.Peer-Reviewed Original ResearchBiomimetic oxomanganese complexesOxygen-evolving complexOxomanganese complexesWater oxidationPhotosystem IIQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsCatalytic centerQM/MM modelCatalytic metal clustersPhotosynthetic water oxidationX-ray crystallographyX-ray absorption fine structure measurementsAbsorption fine structure measurementsQuantum mechanical studyO2-evolving complexX-ray diffraction dataAmino acid residuesExtended X-ray absorption fine structure (EXAFS) measurementsDetailed molecular levelComputational chemistsWater splittingCatalytic cycleComparative quantum mechanical studyMetal clustersFine structure measurements
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