Jimin Wang, PhD
Research Scientist in Molecular Biophysics and BiochemistryCards
About
Research
Publications
2024
An analysis of the structural changes of the oxygen evolving complex of Photosystem II in the S1 and S3 states revealed by serial femtosecond crystallography
Yehia S, Wang J, Brudvig G, Gunner M, Brooks B, Amin M. An analysis of the structural changes of the oxygen evolving complex of Photosystem II in the S1 and S3 states revealed by serial femtosecond crystallography. Biochimica Et Biophysica Acta (BBA) - Bioenergetics 2024, 1866: 149531. PMID: 39694218, DOI: 10.1016/j.bbabio.2024.149531.Peer-Reviewed Original ResearchX-ray crystallographyMn coordinationReaction mechanismEfficient solar energy conversionFemtosecond X-ray crystallographyWater splitting reactionX-raySolar energy conversionElectronic structure changesCoordination chemistrySplitting reactionOxygen-evolving complexArtificial catalystsReaction intermediatesPhotosystem IICatalytic intermediatesWater moleculesOxidation stateFemtosecond crystallographyUltra-short laser pulsesOxidation intermediatesCrystallographyS3 stateStructural changesNatural catalystsPhotosystem II: light‐dependent oscillation of ligand composition at its active site
Wang J. Photosystem II: light‐dependent oscillation of ligand composition at its active site. Acta Crystallographica Section D, Structural Biology 2024, 80: 850-861. PMID: 39607822, DOI: 10.1107/s2059798324011392.Peer-Reviewed Original ResearchComposition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells
Wang J. Composition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells. Biochemistry 2024, 63: 1963-1968. PMID: 39037205, DOI: 10.1021/acs.biochem.4c00261.Peer-Reviewed Original ResearchConceptsX-ray free-electron lasersStructure of photosystem IIOxygen-evolving centerPhotosystem IICrystal structure of photosystem IIFree-electron laserPhotosystem II dimersPhotosystem ILight-harvesting complexesCryo-electron tomographyMetal ionsPSII samplesCryo-electron microscopyCryo-ETDimeric core complexesCryo-EMMetal ion cofactorsLiving cellsCrystal structureCryo-electronCryo-EM structureMetal-ion occupancyIon occupancySpectroscopic interpretationAsymmetric environmentMutation-induced shift of the photosystem II active site reveals insight into conserved water channels
Flesher D, Liu J, Wang J, Gisriel C, Yang K, Batista V, Debus R, Brudvig G. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Journal Of Biological Chemistry 2024, 300: 107475. PMID: 38879008, PMCID: PMC11294709, DOI: 10.1016/j.jbc.2024.107475.Peer-Reviewed Original ResearchOxygen-evolving complexPhotosystem II active sitePhotosystem IIJahn-Teller distortionPhotosystem II complexD1-Asp170Jahn-TellerResolution cryo-EM structureMutation-induced structural changesCryo-EM structureMagnetic propertiesD1 subunitActive siteOxygenic photosynthesisMutagenesis studiesLight-driven water oxidationSpectroscopic propertiesStructural basisSpectroscopic dataAmino acidsWater oxidation mechanismPhotosystemMutationsMutation-induced shiftWater oxidationOccupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations
Kaur D, Reiss K, Wang J, Batista V, Brudvig G, Gunner M. Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations. The Journal Of Physical Chemistry B 2024, 128: 2236-2248. PMID: 38377592, DOI: 10.1021/acs.jpcb.3c05367.Peer-Reviewed Original ResearchOxygen-evolving centerWater moleculesPhotosystem IIPositions of water moleculesAnalysis of water moleculesCatalyze water oxidationHydrogen bond networkOccupancy of water moleculesMolecular dynamics simulationsD1-D61Electron density mapsMolecular dynamics analysisProton transferWater oxidationCrystallographic dataIce latticeMD simulationsMolecular dynamicsStructural transitionDynamics simulationsSubstrate waterOxygen-evolvingRoom temperatureProtein residuesMolecules
2023
Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
Ranepura G, Mao J, Vermaas J, Wang J, Gisriel C, Wei R, Ortiz-Soto J, Uddin R, Amin M, Brudvig G, Gunner M. Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II. The Journal Of Physical Chemistry B 2023, 127: 10974-10986. PMID: 38097367, DOI: 10.1021/acs.jpcb.3c06273.Peer-Reviewed Original ResearchBridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig G, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. Journal Of Chemical Information And Modeling 2023, 64: 2586-2593. PMID: 38054243, DOI: 10.1021/acs.jcim.3c01564.Peer-Reviewed Original ResearchOxidation stateMetal ionsActive siteCambridge Crystallographic Data CentreMetal oxidation stateElectron transfer reactionsStandard reduction potentialLower oxidation statesX-ray crystallographyCoordination chemistryCryogenic electron microscopyMetal clustersTransfer reactionsReaction mechanismReduction potentialXFEL crystallographyMetalloproteinsAppropriate experimental conditionsSmall moleculesCrystallographySmall compoundsSpecific reactionElectron microscopyRemarkable efficiencyMetalsSubstrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease
Wang J, Maschietto F, Qiu T, Arantes P, Skeens E, Palermo G, Lisi G, Batista V. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal 2023, 122: 4635-4644. PMID: 37936350, PMCID: PMC10754686, DOI: 10.1016/j.bpj.2023.11.005.Peer-Reviewed Original ResearchConceptsHNH domainHNH nucleaseHigh fidelity enzymesInduced-fit mechanismActivation pathwayActive stateMolecular dynamics trajectoriesCognate substratesConformation 2Conformational selectionObligate stepAla mutantBackbone amidesΑ-helixSide chainsSingle LysEssential roleNucleasePathwayDynamics trajectoriesResiduesConformationMutantsInterconversion pathwaysCRISPRA quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center
Gisriel C, Flesher D, Long Z, Liu J, Wang J, Bryant D, Batista V, Brudvig G. A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center. Photosynthesis Research 2023, 162: 187-196. PMID: 37749456, DOI: 10.1007/s11120-023-01047-5.Peer-Reviewed Original ResearchCryo-EM mapsCryogenic electron microscopy structureReaction centersHydrogen bond donorCryo-EM structureElectron microscopy structureReaction center complexBond donorPhotosynthetic organismsMicroscopy structureProtein complexesElectron transferMolecular structureFunctional insightsStructural biologyLight harvestingProtein environmentChemical environmentExperimental cryo-EM mapsDownstream investigationsCenter complexPrimary pigmentEnergy transferStructural dataAcetyl moietyValproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism
Maschietto F, Qiu T, Wang J, Shi Y, Allen B, Lisi G, Lolis E, Batista V. Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism. Computational And Structural Biotechnology Journal 2023, 21: 1066-1076. PMID: 36688026, PMCID: PMC9841741, DOI: 10.1016/j.csbj.2023.01.014.Peer-Reviewed Original Research