2021
Identification 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 structure
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 polymeraseCrystalsStructural and biochemical insights into inhibition of human primase by citrate
Lee JG, Park KR, An JY, Kang JY, Shen H, Wang J, Eom SH. Structural and biochemical insights into inhibition of human primase by citrate. Biochemical And Biophysical Research Communications 2018, 507: 383-388. PMID: 30446220, DOI: 10.1016/j.bbrc.2018.11.047.Peer-Reviewed Original ResearchMeSH KeywordsAnionsCalorimetryCatalytic DomainCitric AcidCrystallography, X-RayDNA PrimaseDNA PrimersEnzyme InhibitorsHumansNucleotidesConceptsDNA replicationSmall catalytic subunitShort RNA segmentReplicative DNA polymerasesPhosphate binding siteMammalian chromosomesReplication forksCatalytic subunitAccessory subunitsBiochemical insightsOkazaki fragmentsRNA primersKey regulatorRNA segmentsBacterial enzymesHuman primasePrimaseDNA templateBase pairsDNA polymeraseInactive formDNA strandsBinding sitesPolymeraseSubunits
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 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 ResearchCrystallography, X-RayDatabases, FactualModels, MolecularPhotosystem II Protein ComplexSignal-To-Noise RatioEffects 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 ResearchSystematic 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
Oxygen 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 ResearchX‐ray radiation‐induced addition of oxygen atoms to protein residues
Wang J. X‐ray radiation‐induced addition of oxygen atoms to protein residues. Protein Science 2016, 25: 1407-1419. PMID: 27074249, PMCID: PMC4989999, DOI: 10.1002/pro.2934.Peer-Reviewed Original ResearchS3 State of the O2‑Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X‑ray Diffraction
Askerka M, Wang J, Vinyard DJ, Brudvig GW, Batista VS. S3 State of the O2‑Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X‑ray Diffraction. Biochemistry 2016, 55: 981-984. PMID: 26849148, DOI: 10.1021/acs.biochem.6b00041.Peer-Reviewed Original ResearchConceptsExtended X-ray absorption fine structureFemtosecond x-ray diffractionX-ray diffractionOxygen-evolving complexS3 stateHybrid quantum mechanics/molecular mechanics (QM/MM) methodX-ray absorption fine structureQuantum mechanics/molecular mechanics methodsAbsorption fine structureQM/MMPhotosystem IIMolecular mechanics methodElectron paramagnetic resonanceWater ligandsS3 transitionAmmonia bindingParamagnetic resonanceFine structureMechanics methodDiffractionComplexesStateResonanceLigandsMn4
2015
Crystallographic study of a MATE transporter presents a difficult case in structure determination with low‐resolution, anisotropic data and crystal twinning
Symersky J, Guo Y, Wang J, Lu M. Crystallographic study of a MATE transporter presents a difficult case in structure determination with low‐resolution, anisotropic data and crystal twinning. Acta Crystallographica Section D, Structural Biology 2015, 71: 2287-2296. PMID: 26527145, PMCID: PMC4631480, DOI: 10.1107/s1399004715016995.Peer-Reviewed Original ResearchStructure and function of the N‐terminal domain of the human mitochondrial calcium uniporter
Lee Y, Min CK, Kim TG, Song HK, Lim Y, Kim D, Shin K, Kang M, Kang JY, Youn HS, Lee JG, An JY, Park KR, Lim JJ, Kim JH, Kim JH, Park ZY, Kim YS, Wang J, Kim DH, Eom SH. Structure and function of the N‐terminal domain of the human mitochondrial calcium uniporter. EMBO Reports 2015, 16: 1318-1333. PMID: 26341627, PMCID: PMC4662854, DOI: 10.15252/embr.201540436.Peer-Reviewed Original ResearchConceptsN-terminal domainMitochondrial calcium uniporterCalcium uniporterHuman mitochondrial calcium uniporterMitochondrial calcium uptake 1CaMKII phosphorylation siteDominant negative effectCell linesMitochondrial calcium uptakePhosphorylation sitesNovel foldDeletion mutantsMCU functionÅ resolutionTumor suppressorHeLa cell lineUniporterMutantsUptake 1Calcium uptakeS92SuppressorOncogeneRegulatorDomainEstimation of the quality of refined protein crystal structures
Wang J. Estimation of the quality of refined protein crystal structures. Protein Science 2015, 24: 661-669. PMID: 25581292, PMCID: PMC4420517, DOI: 10.1002/pro.2639.Peer-Reviewed Original ResearchAnalysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data
Askerka M, Vinyard DJ, Wang J, Brudvig GW, Batista VS. Analysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data. Biochemistry 2015, 54: 1713-1716. PMID: 25710258, DOI: 10.1021/acs.biochem.5b00089.Peer-Reviewed Original ResearchConceptsPhotosystem II crystalsX-ray absorption fine structureExtended X-ray absorption fine structureAbsorption fine structurePhotosystem IIHigh-resolution structural modelS1 stateS0 stateOxygen-evolving complexRadiation damageX-ray diffraction studiesExtensive dark adaptationFine structureDiffraction studiesOxygen atomsManganese centersX-ray structureAtomsMM dataCrystalsStateEXAFSLightStructureResolution
2014
On the validation of crystallographic symmetry and the quality of structures
Wang J. On the validation of crystallographic symmetry and the quality of structures. Protein Science 2014, 24: 621-632. PMID: 25352397, PMCID: PMC4420513, DOI: 10.1002/pro.2595.Peer-Reviewed Original ResearchMeSH KeywordsCrystallography, X-RayDatabases, ProteinModels, MolecularProtein ConformationProteinsSoftwareX-Ray DiffractionStructural Changes in the Oxygen-Evolving Complex of Photosystem II Induced by the S1 to S2 Transition: A Combined XRD and QM/MM Study
Askerka M, Wang J, Brudvig GW, Batista VS. Structural Changes in the Oxygen-Evolving Complex of Photosystem II Induced by the S1 to S2 Transition: A Combined XRD and QM/MM Study. Biochemistry 2014, 53: 6860-6862. PMID: 25347729, PMCID: PMC4230327, DOI: 10.1021/bi5011915.Peer-Reviewed Original ResearchStructural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original ResearchMeSH KeywordsBase PairingBase SequenceCrystallography, X-RayHumansHydrogen BondingMolecular Sequence DataNucleic Acid ConformationRNA StabilityRNA, Long Noncoding