2024
Occupancy 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
2021
Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f
Gisriel CJ, Shen G, Ho MY, Kurashov V, Flesher DA, Wang J, Armstrong WH, Golbeck JH, Gunner MR, Vinyard DJ, Debus RJ, Brudvig GW, Bryant DA. Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f. Journal Of Biological Chemistry 2021, 298: 101424. PMID: 34801554, PMCID: PMC8689208, DOI: 10.1016/j.jbc.2021.101424.Peer-Reviewed Original ResearchConceptsChl f moleculesWater oxidationF moleculesPhotosystem II core complexII core complexesPhotosystem IIÅ resolution cryo-EM structureFar-red light photoacclimationResolution cryo-EM structurePhotochemical catalysisElectron transfer chainCryo-EM structureGlutamate side chainVisible lightCore complexSide chainsRed limitD moleculesSolar energy utilizationAcceptor sidePSII biogenesisFar-red lightPCC 7335Core subunitsMolecules
2018
On 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 ResearchConceptsLocal chemical effectsElectron beamElectron radiationChemical mechanismStructure effectsChemical effectsElectron microscopeBackbone atomsChemical damageΑ-helixThermoplasma acidophilumMoleculesDose-dependent degradationQuaternary structureElectronsBeamAtomsEM mapsRadiationStructureMicroscopeResolutionSmall changesAcidophilum
2017
Determination 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 factorSupercomplexes
2013
Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy
Yu T, Wu G, Yang H, Wang J, Yu S. Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy. International Journal Of Biological Macromolecules 2013, 56: 57-61. PMID: 23403030, DOI: 10.1016/j.ijbiomac.2013.02.004.Peer-Reviewed Original Research
2000
Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: a scrunching-shuttling model of CCA specificity1 1Edited by T. Richmond
Li F, Wang J, Steitz T. Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: a scrunching-shuttling model of CCA specificity1 1Edited by T. Richmond. Journal Of Molecular Biology 2000, 304: 483-492. PMID: 11090289, DOI: 10.1006/jmbi.2000.4189.Peer-Reviewed Original ResearchConceptsActive siteMulti-angle laser lightSmall-angle X-ray scatteringSize exclusion chromatographyX-ray scatteringFurther dimerizationExclusion chromatographyMoleculesDimeric enzymeC basesOligomerization stateTetramerTransfer RNA moleculesLaser lightTRNA moleculesRNA moleculesMonomersPrimer strandChromatographyEnzymeDimersHigh specificityBindingCCA-adding enzymeDimerization