2023
Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease
Wang J, Maschietto F, Qiu T, Arantes P, Skeens E, Palermo G, Lisi G, Batista V. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal 2023, 122: 4635-4644. PMID: 37936350, PMCID: PMC10754686, DOI: 10.1016/j.bpj.2023.11.005.Peer-Reviewed Original ResearchConceptsHNH domainHNH nucleaseHigh fidelity enzymesInduced-fit mechanismActivation pathwayActive stateMolecular dynamics trajectoriesCognate substratesConformation 2Conformational selectionObligate stepAla mutantBackbone amidesΑ-helixSide chainsSingle LysEssential roleNucleasePathwayDynamics trajectoriesResiduesConformationMutantsInterconversion pathwaysCRISPR
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 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 ResearchConceptsElectrostatic 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 calculation
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