2023
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig G, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. Journal Of Chemical Information And Modeling 2023, 64: 2586-2593. PMID: 38054243, DOI: 10.1021/acs.jcim.3c01564.Peer-Reviewed Original ResearchOxidation stateMetal ionsActive siteCambridge Crystallographic Data CentreMetal oxidation stateElectron transfer reactionsStandard reduction potentialLower oxidation statesX-ray crystallographyCoordination chemistryCryogenic electron microscopyMetal clustersTransfer reactionsReaction mechanismReduction potentialXFEL crystallographyMetalloproteinsAppropriate experimental conditionsSmall moleculesCrystallographySmall compoundsSpecific reactionElectron microscopyRemarkable efficiencyMetals
2017
Effects 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 calculationOn 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
1998
Crystal Structure Determination ofEscherichia coliClpP Starting from an EM-Derived Mask
Wang J, Hartling J, Flanagan J. Crystal Structure Determination ofEscherichia coliClpP Starting from an EM-Derived Mask. Journal Of Structural Biology 1998, 124: 151-163. PMID: 10049803, DOI: 10.1006/jsbi.1998.4058.Peer-Reviewed Original ResearchConceptsATP-dependent proteolytic complexEscherichia coli ClpPATP-dependent proteaseProteolytic active sitesEvolutionary convergenceClpP structureHeptameric ringsProteolytic complexIntracellular proteolysisProteolytic componentBiophysical techniquesClpPSmall-angle X-rayX-ray crystallographyX-ray crystal structureStriking exampleMatrix refinementActive siteProteaseStructure determinationHslVOverall architectureProteasomeStructural levelElectron microscopy