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 factorSupercomplexesEffects 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 densityBackbone
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 Research
2014
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme
Eiler D, Wang J, Steitz TA. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 13028-13033. PMID: 25157168, PMCID: PMC4246988, DOI: 10.1073/pnas.1414571111.Peer-Reviewed Original Research
2010
Structural insight into the mechanisms of enveloped virus tethering by tetherin
Yang H, Wang J, Jia X, McNatt MW, Zang T, Pan B, Meng W, Wang HW, Bieniasz PD, Xiong Y. Structural insight into the mechanisms of enveloped virus tethering by tetherin. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 18428-18432. PMID: 20940320, PMCID: PMC2972963, DOI: 10.1073/pnas.1011485107.Peer-Reviewed Original ResearchAntigens, CDBase SequenceCell LineCrystallography, X-RayDimerizationDNA PrimersGPI-Linked ProteinsHIV-1HumansImmunity, InnateIn Vitro TechniquesModels, MolecularMolecular Dynamics SimulationMutagenesis, Site-DirectedMutant ProteinsProtein StabilityProtein Structure, QuaternaryProtein Structure, TertiaryRecombinant ProteinsStatic ElectricityVirus Release
2007
Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core
Stahley MR, Adams PL, Wang J, Strobel SA. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core. Journal Of Molecular Biology 2007, 372: 89-102. PMID: 17612557, PMCID: PMC2071931, DOI: 10.1016/j.jmb.2007.06.026.Peer-Reviewed Original Research
2005
Hoogsteen base-pairing in DNA replication?
Wang J. Hoogsteen base-pairing in DNA replication? Nature 2005, 437: e6-e7. PMID: 16163299, DOI: 10.1038/nature04199.Peer-Reviewed Original Research
2004
Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29
Kamtekar S, Berman AJ, Wang J, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell 2004, 16: 609-618. PMID: 15546620, DOI: 10.1016/j.molcel.2004.10.019.Peer-Reviewed Original ResearchConceptsDNA polymerasePhi29 DNA polymeraseT7 RNA polymeraseB-family polymerasesSpecific serinePriming proteinPolymerase active sitePhage phi29RNA polymerasePhage genomeSpecificity loopNontemplate strandStrand displacement activityFirst nucleotideHomology modelingSequence insertionHigh processivityProtein primerB familyPolymeraseDuplex DNATemplate DNAProcessivityProteinDNAThe structure of a ribosomal protein S8/spc operon mRNA complex
Merianos HJ, Wang J, Moore PB. The structure of a ribosomal protein S8/spc operon mRNA complex. RNA 2004, 10: 954-964. PMID: 15146079, PMCID: PMC1370587, DOI: 10.1261/rna.7030704.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesCrystallography, X-RayEscherichia coliEscherichia coli ProteinsGenes, BacterialLigandsMacromolecular SubstancesModels, MolecularNucleic Acid ConformationOperonProtein BiosynthesisRibosomal ProteinsRNA, BacterialRNA, MessengerSpecies SpecificityStatic ElectricityConceptsSpc operon mRNAOperon mRNARibosomal protein cistronsSmall ribosomal subunitRibosomal initiation complexResolution crystal structureProtein synthesis resultsSpc operonAutogenous regulationTranslational repressionInitiation complexOwn mRNARibosomal subunitS8 bindingSequence differencesCistronInternal sequencesMRNAGenesConformational similarityBindingComplexesRetroregulationRRNAsOperon
2003
Crystal structure of a transcription factor IIIB core interface ternary complex
Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler PB. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 2003, 422: 534-539. PMID: 12660736, DOI: 10.1038/nature01534.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBinding SitesCrystallography, X-RayDNA, FungalFungal ProteinsGenes, FungalHydrogen BondingMacromolecular SubstancesModels, MolecularMolecular Sequence DataNucleic Acid ConformationPromoter Regions, GeneticProtein Structure, TertiaryProtein SubunitsRNA, Small NuclearSaccharomyces cerevisiae ProteinsStatic ElectricitySubstrate SpecificityTATA-Box Binding ProteinTranscription Factor TFIIIBConceptsTranscription factor IIIBGeneral transcription factor TFIIBDomain IIÅ resolution crystal structureTranscription factor TFIIBOpen initiation complexRegion of TBPTFIIB-related factorAmino-terminal halfCarboxy-terminal halfTernary complexResolution crystal structureRegulated transcriptionPromoter DNASequence similarityInitiation complexRNA polymeraseBase pairsBdp1Brf1Essential rolePolymerasePrimary interfaceCrystal structureResidue 435