2024
Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels
Flesher D, Liu J, Wang J, Gisriel C, Yang K, Batista V, Debus R, Brudvig G. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Journal Of Biological Chemistry 2024, 300: 107475. PMID: 38879008, PMCID: PMC11294709, DOI: 10.1016/j.jbc.2024.107475.Peer-Reviewed Original ResearchOxygen-evolving complexPhotosystem II active sitePhotosystem IIJahn-Teller distortionPhotosystem II complexD1-Asp170Jahn-TellerResolution cryo-EM structureMutation-induced structural changesCryo-EM structureMagnetic propertiesD1 subunitActive siteOxygenic photosynthesisMutagenesis studiesLight-driven water oxidationSpectroscopic propertiesStructural basisSpectroscopic dataAmino acidsWater oxidation mechanismPhotosystemMutationsMutation-induced shiftWater oxidationOccupancy 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
2023
Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
Ranepura G, Mao J, Vermaas J, Wang J, Gisriel C, Wei R, Ortiz-Soto J, Uddin R, Amin M, Brudvig G, Gunner M. Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II. The Journal Of Physical Chemistry B 2023, 127: 10974-10986. PMID: 38097367, DOI: 10.1021/acs.jpcb.3c06273.Peer-Reviewed Original ResearchBridging 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 efficiencyMetalsSubstrate-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 pathwaysCRISPRA quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center
Gisriel C, Flesher D, Long Z, Liu J, Wang J, Bryant D, Batista V, Brudvig G. A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center. Photosynthesis Research 2023, 1-10. PMID: 37749456, DOI: 10.1007/s11120-023-01047-5.Peer-Reviewed Original ResearchCryo-EM mapsCryogenic electron microscopy structureReaction centersHydrogen bond donorCryo-EM structureElectron microscopy structureReaction center complexBond donorPhotosynthetic organismsMicroscopy structureProtein complexesElectron transferMolecular structureFunctional insightsStructural biologyLight harvestingProtein environmentChemical environmentExperimental cryo-EM mapsDownstream investigationsCenter complexPrimary pigmentEnergy transferStructural dataAcetyl moietyValproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism
Maschietto F, Qiu T, Wang J, Shi Y, Allen B, Lisi G, Lolis E, Batista V. Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism. Computational And Structural Biotechnology Journal 2023, 21: 1066-1076. PMID: 36688026, PMCID: PMC9841741, DOI: 10.1016/j.csbj.2023.01.014.Peer-Reviewed Original ResearchTwisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes
Wang J, Arantes P, Ahsan M, Sinha S, Kyro G, Maschietto F, Allen B, Skeens E, Lisi G, Batista V, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Frontiers In Molecular Biosciences 2023, 9: 1072733. PMID: 36699705, PMCID: PMC9868570, DOI: 10.3389/fmolb.2022.1072733.Peer-Reviewed Original Research
2022
Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations
Fredericks A, East K, Shi Y, Liu J, Maschietto F, Ayala A, Cioffi W, Cohen M, Fairbrother W, Lefort C, Nau G, Levy M, Wang J, Batista V, Lisi G, Monaghan S. Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations. Frontiers In Molecular Biosciences 2022, 9: 1080964. PMID: 36589229, PMCID: PMC9800910, DOI: 10.3389/fmolb.2022.1080964.Peer-Reviewed Original ResearchCOVID-19 patientsSARS-CoV-2Severe acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Spike proteinSevere COVID-19Intensive care unitSyndrome coronavirus 2RNA sequencingCertain immune responsesCOVID-19 infectionSARS-CoV-2 spike proteinEffectiveness of treatmentDeep RNA sequencingICU admissionCare unitSingle centerCoronavirus 2Peripheral bloodMultiple time pointsClinical dataImmune responseEarly infection timesSpecific NAbsTranslocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes
Shi Y, Wang J, Batista V. Translocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes. Frontiers In Molecular Biosciences 2022, 9: 999291. PMID: 36387272, PMCID: PMC9640752, DOI: 10.3389/fmolb.2022.999291.Peer-Reviewed Original ResearchHow to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM
Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. Journal Of Structural Biology 2022, 214: 107902. PMID: 36202310, PMCID: PMC10226527, DOI: 10.1016/j.jsb.2022.107902.Peer-Reviewed Original ResearchConceptsCryo-EM mapsAmino acid residuesAcid residuesCryo-electron microscopy mapIndividual amino acid residuesCyanobacteria Synechocystis spPCC 6803Synechocystis spMicroscopy mapsThermosynechococcus elongatusSARS-CoV-2 spike proteinLocal structural changesResiduesSpike proteinAtomic coordinatesElongatusSubunitsSpeciesProteinSpSimilar structureStructural changesStructural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2
Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2. Biochemistry 2022, 61: 1966-1973. PMID: 36044776, PMCID: PMC9469760, DOI: 10.1021/acs.biochem.2c00341.Peer-Reviewed Original ResearchConceptsReplication-transcription complexStructural basisCryo-EM structureAdenosine monophosphateRemdesivir triphosphateStructural insightsDuplex productsPrimer extensionNucleotide selectivityBase pairsNucleotide incorporationIncoming substrateRibosyl moietyActive complexSARS-CoV-2 inhibitorsNew detailed informationTriphosphateComplexesMolecular dynamics simulationsAdenosine triphosphateInsight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1
Wang J, Sachpatzidis A, Christian TD, Lomakin IB, Garen A, Konigsberg WH. Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1. Biochemistry 2022, 61: 1723-1734. PMID: 35998361, DOI: 10.1021/acs.biochem.2c00192.Peer-Reviewed Original ResearchConceptsRNA recognition motifSplicing factorsRNA bindingÅ resolution crystal structureTranscript 1DNA-binding domainRNA-binding pocketTumor suppression mechanismNew regulatory mechanismTumor suppressor proteinResolution crystal structureMurine virusesAcid proteinSuppressor proteinRecognition motifLung adenocarcinoma transcript 1Gene expressionRegulatory mechanismsApo structureRNA virusesHuman diseasesRNABinding pocketsHuman metastasesPositive cooperativityStructural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme
Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022, 61: 785-794. PMID: 35420793, PMCID: PMC9069930, DOI: 10.1021/acs.biochem.2c00127.Peer-Reviewed Original ResearchConceptsShort palindromic repeatsSubstrate specificityPalindromic repeatsAla mutantWT enzymeRNA-binding domainAssociated 9 (Cas9) systemForeign DNA sequencesDNA strandsWild-type enzymeDouble-strand breaksEnhanced substrate specificityHNH active siteDynamics of proteinsType II immunityCas9 proteinDNA substratesDNA sequencesStructural basisMutantsAla substitutionDistinct conformationsSingle LysCatalytic siteEnzymeGlycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex
Flesher DA, Liu J, Wiwczar JM, Reiss K, Yang KR, Wang J, Askerka M, Gisriel CJ, Batista VS, Brudvig GW. Glycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex. Photosynthesis Research 2022, 152: 167-175. PMID: 35322325, PMCID: PMC9427693, DOI: 10.1007/s11120-022-00911-0.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexHydrogen bond networkS2 stateEPR signalPhotosystem II cyclesX-ray crystal structureRelative stabilityState EPR signalsD1-Asp61Water oxidationCatalytic intermediatesPhotochemical oxidationEPR spectraGlycerol moleculesCrystal structureCyanobacterial PSIIMultiline signalState SiPhotosystem IIOxidationRelative intensitiesComplexesEffect of glycerolExperimental conditionsStabilityTwo-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion
Wang J, Konigsberg WH. Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion. Frontiers In Molecular Biosciences 2022, 9: 824794. PMID: 35300112, PMCID: PMC8921852, DOI: 10.3389/fmolb.2022.824794.Peer-Reviewed Original ResearchInsights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations
Wang J, Shi Y, Reiss K, Allen B, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Insights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV‑2 for the Priming Reaction from Molecular Dynamics Simulations. Biochemistry 2022, 61: 424-432. PMID: 35199520, PMCID: PMC8887646, DOI: 10.1021/acs.biochem.1c00755.Peer-Reviewed Original ResearchConceptsReplication-transcription complexPriming reactionRNA duplexesTemplate strandRNA templateHigher-order oligomerizationRNA-dependent RNA polymeraseCryo-EM structureRNA primaseViral RNA templateRNA polymerasePrimer synthesisViral transcriptionSecondary structureViral genomeSubunitsMolecular dynamics simulations
2021
High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 119: e2116765118. PMID: 34937700, PMCID: PMC8740770, DOI: 10.1073/pnas.2116765118.Peer-Reviewed Original ResearchConceptsCryo-electron microscopy structurePCC 6803Photosystem IIWater oxidationMicroscopy structureMesophilic cyanobacteriumHigh-resolution cryo-electron microscopy structuresOxygen-evolving photosystem IILight-driven water oxidationCyanobacterial photosystem IIHigh-resolution structuresD1 subunitPSII structureSynechocystis spLarge water channelsGenetic manipulationC-terminusBiophysical dataActive siteCyanobacteriumSpStructural pictureSubunitsOxidationWater channelsCorrigendum to Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light BBA Advances 1 (2021) 100019
Gisriel C, Huang H, Reiss K, Flesher D, Batista V, Bryant D, Brudvig G, Wang J. Corrigendum to Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light BBA Advances 1 (2021) 100019. BBA Advances 2021, 1: 100024. PMID: 37206888, PMCID: PMC10189863, DOI: 10.1016/j.bbadva.2021.100024.Peer-Reviewed Original ResearchStructure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f
Gisriel CJ, Shen G, Ho MY, Kurashov V, Flesher DA, Wang J, Armstrong WH, Golbeck JH, Gunner MR, Vinyard DJ, Debus RJ, Brudvig GW, Bryant DA. Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f. Journal Of Biological Chemistry 2021, 298: 101424. PMID: 34801554, PMCID: PMC8689208, DOI: 10.1016/j.jbc.2021.101424.Peer-Reviewed Original ResearchConceptsChl f moleculesWater oxidationF moleculesPhotosystem II core complexII core complexesPhotosystem IIÅ resolution cryo-EM structureFar-red light photoacclimationResolution cryo-EM structurePhotochemical catalysisElectron transfer chainCryo-EM structureGlutamate side chainVisible lightCore complexSide chainsRed limitD moleculesSolar energy utilizationAcceptor sidePSII biogenesisFar-red lightPCC 7335Core subunitsMolecules