2024
Photosystem 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 ResearchMeSH KeywordsCatalytic DomainCrystallography, X-RayLigandsLightModels, MolecularOxygenPhotosystem II Protein ComplexThermosynechococcusComposition 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 ResearchMeSH KeywordsBacterial ProteinsCryoelectron MicroscopyMetalsModels, MolecularOxygenPhotosystem II Protein ComplexThermosynechococcusConceptsX-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 environment
2021
Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir
Wang J, Reiss K, Shi Y, Lolis E, Lisi GP, Batista VS. Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir. Biochemistry 2021, 60: 1869-1875. PMID: 34110129, PMCID: PMC8204756, DOI: 10.1021/acs.biochem.1c00292.Peer-Reviewed Original ResearchIdentification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps
Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps. Acta Crystallographica Section D, Structural Biology 2021, 77: 534-539. PMID: 33825713, PMCID: PMC8025889, DOI: 10.1107/s2059798321001893.Peer-Reviewed Original ResearchMeSH KeywordsCryoelectron MicroscopyCrystallography, X-RayHumansIonsMacromolecular SubstancesModels, MolecularNucleotidesRibosomes
2019
Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds?
Wang J. Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds? Protein Science 2019, 28: 1966-1972. PMID: 31441173, PMCID: PMC6798185, DOI: 10.1002/pro.3716.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCrystallography, X-RayHydrogen BondingModels, MolecularPhotoreceptors, MicrobialProtein ConformationConceptsPhotoactive yellow proteinLow-barrier hydrogen bondH atomsYellow proteinResidual electron density mapsNeutron structureAtomsO bond angleO distancesO atomsHydrogen bondsElectron density mapsBond anglesDensity mapsX-ray structureCrystal structureResolution X-ray structureStructureBondsX-ray crystal structureCrystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups
Wang J. Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups. Protein Science 2019, 28: 472-477. PMID: 30592103, PMCID: PMC6371210, DOI: 10.1002/pro.3568.Peer-Reviewed Original ResearchConceptsLys side chainsSide chainsO bridgesChemical identificationCrystal structureElectron density featuresCross-linking speciesCys side chainDirect chemical identificationProtein crystal structuresMass spectrometric analysisOxidation intermediatesCys-245Primary aminesMethylene groupCrystallographic identificationSpectrometric analysisDehydration mechanismLys-158Protein sulfhydryl groupsSulfhydryl groupsProtein structureChainCHCys residues
2018
Crystallographic evidence for two‐metal‐ion catalysis in human pol η
Wang J, Smithline ZB. Crystallographic evidence for two‐metal‐ion catalysis in human pol η. Protein Science 2018, 28: 439-447. PMID: 30368948, PMCID: PMC6319759, DOI: 10.1002/pro.3541.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCatalysisCrystallography, X-RayDNA-Directed DNA PolymeraseHumansMagnesiumModels, MolecularConceptsMetal ionsProduct pyrophosphateChemical reactionsTwo-metal-ion catalysisTwo-metal-ion catalytic mechanismThird metal ionPhosphoryl transfer reactionsTransfer reactionsCrystallographic dataCatalytic mechanismCrystal structureCrystallographic evidenceHuman Pol ηMeal ionsIonsHuman polymerase ηCatalysisReactionComplexesSubPyrophosphateBindingProductsDNA polymeraseCrystalsOn the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation
Wang J, Liu Z, Crabtree RH, Frank J, Moore PB. On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation. Protein Science 2018, 27: 2051-2061. PMID: 30242932, PMCID: PMC6237698, DOI: 10.1002/pro.3511.Peer-Reviewed Original ResearchMeSH KeywordsElectronsModels, MolecularProteasome Endopeptidase ComplexProtein ConformationThermoplasmaConceptsLocal chemical effectsElectron beamElectron radiationChemical mechanismStructure effectsChemical effectsElectron microscopeBackbone atomsChemical damageΑ-helixThermoplasma acidophilumMoleculesDose-dependent degradationQuaternary structureElectronsBeamAtomsEM mapsRadiationStructureMicroscopeResolutionSmall changesAcidophilumReduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps
Wang J, Reiss K, Brudvig GW, Batista VS. Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps. Biochemistry 2018, 57: 5925-5929. PMID: 30260634, DOI: 10.1021/acs.biochem.8b00609.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexElectrostatic potentialOEC of PSIIPhotosystem IIAtomic scattering factorsElectron scatteringScattering factorsDensity functional theoryESP mapsFunctional theoryAtomic coordinatesAtomistic modelMicroscopy mapsScatteringCryo-electron microscopy mapComputational simulations
2017
Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima
An JY, Sharif H, Kang GB, Park KJ, Lee JG, Lee S, Jin MS, Song JJ, Wang J, Eom SH. Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima. Biochemical And Biophysical Research Communications 2017, 495: 1201-1207. PMID: 29180014, DOI: 10.1016/j.bbrc.2017.11.158.Peer-Reviewed Original ResearchConceptsPeriplasmic domainMisfolded membrane proteinsATP-dependent proteaseMembrane protein complexesResolution crystal structureHydrophobic membrane environmentMembrane homeostasisProtein complexesMembrane proteinsTransmembrane proteinMembrane environmentThermotoga maritimaStructural insightsFtsHProtease domainToxic proteinsProteinOligomerizationHigh energetic barrierDomainTranslocatesEnergetic barrierMaritimaHomeostasisCrystal structureDetermination of chemical identity and occupancy from experimental density maps
Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Science 2017, 27: 411-420. PMID: 29027293, PMCID: PMC5775170, DOI: 10.1002/pro.3325.Peer-Reviewed Original ResearchConceptsCharge densityFourier transformElectrostatic potentialExperimental charge densitySolvent moleculesAtomic B-factorsElectron densityBasic electronic propertiesESP mapsProtein α-helixChemical identityActive siteElectronic propertiesLarge macromolecular complexesExperimental density mapsDensity mapsMoleculesVitreous iceMacromolecular complexesΑ-helixSmall protein subunitESP valuesTransformStructure factorSupercomplexesOn the relationship between cumulative correlation coefficients and the quality of crystallographic data sets
Wang J, Brudvig GW, Batista VS, Moore PB. On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets. Protein Science 2017, 26: 2410-2416. PMID: 28960580, PMCID: PMC5699489, DOI: 10.1002/pro.3314.Peer-Reviewed Original ResearchDynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1
Chase AR, Laudermilch E, Wang J, Shigematsu H, Yokoyama T, Schlieker C. Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1. Molecular Biology Of The Cell 2017, 28: 2765-2772. PMID: 28814508, PMCID: PMC5638581, DOI: 10.1091/mbc.e17-05-0281.Peer-Reviewed Original ResearchEffects of aligned α‐helix peptide dipoles on experimental electrostatic potentials
Wang J, Videla PE, Batista VS. Effects of aligned α‐helix peptide dipoles on experimental electrostatic potentials. Protein Science 2017, 26: 1692-1697. PMID: 28556371, PMCID: PMC5563131, DOI: 10.1002/pro.3204.Peer-Reviewed Original ResearchMeSH KeywordsCrystallography, X-RayMicroscopy, ElectronModels, MolecularPeptidesProtein Conformation, alpha-HelicalStatic ElectricityConceptsElectrostatic potentialEM mapsProtein αExperimental electrostatic potentialHelix dipoleDetailed molecular levelHigh-resolution electron microscopyDensity functional theory calculationsProtein functionStructural biologyFunctional theory calculationsElectron microscopyProtein α-helixPartial atomic chargesElectric fieldΑ-helixLong-range featuresMolecular levelNonlocal natureAtomic chargesTheory calculationsDipoleBackbone dipolesRecent breakthroughsProper calculationExperimental charge density from electron microscopic maps
Wang J. Experimental charge density from electron microscopic maps. Protein Science 2017, 26: 1619-1626. PMID: 28543856, PMCID: PMC5521614, DOI: 10.1002/pro.3198.Peer-Reviewed Original ResearchOn contribution of known atomic partial charges of protein backbone in electrostatic potential density maps
Wang J. On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps. Protein Science 2017, 26: 1098-1104. PMID: 28370507, PMCID: PMC5441424, DOI: 10.1002/pro.3169.Peer-Reviewed Original ResearchConceptsAtomic partial chargesPartial chargesQuantum mechanicsForce field parametersAtomic propertiesPartial atomic chargesDensity mapsAtomic chargesField parametersMolecular dynamicsAtomsElectron microscopyProtein backboneNeutral peptide backboneChargeChain atomsComputer simulationsSide-chain atomsDensityPeptide backboneProtein moleculesModel refinementSimulationsPotential densityBackboneSystematic analysis of residual density suggests that a major limitation in well‐refined X‐ray structures of proteins is the omission of ordered solvent
Wang J. Systematic analysis of residual density suggests that a major limitation in well‐refined X‐ray structures of proteins is the omission of ordered solvent. Protein Science 2017, 26: 1012-1023. PMID: 28244185, PMCID: PMC5405434, DOI: 10.1002/pro.3145.Peer-Reviewed Original ResearchCrystal structure of Pistol, a class of self-cleaving ribozyme
Nguyen LA, Wang J, Steitz TA. Crystal structure of Pistol, a class of self-cleaving ribozyme. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 1021-1026. PMID: 28096403, PMCID: PMC5293083, DOI: 10.1073/pnas.1611191114.Peer-Reviewed Original Research
2016
On the appearance of carboxylates in electrostatic potential maps
Wang J. On the appearance of carboxylates in electrostatic potential maps. Protein Science 2016, 26: 396-402. PMID: 27977901, PMCID: PMC5326552, DOI: 10.1002/pro.3093.Peer-Reviewed Original ResearchOxygen additions in serial femtosecond crystallographic protein structures
Wang J. Oxygen additions in serial femtosecond crystallographic protein structures. Protein Science 2016, 25: 1797-1802. PMID: 27438534, PMCID: PMC5029527, DOI: 10.1002/pro.2987.Peer-Reviewed Original Research