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
2017
On 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 densityBackbone