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 ResearchMeSH KeywordsAmidesCRISPR-Associated Protein 9CRISPR-Cas SystemsHydrogenMolecular Dynamics SimulationConceptsHNH domainHNH nucleaseHigh fidelity enzymesInduced-fit mechanismActivation pathwayActive stateMolecular dynamics trajectoriesCognate substratesConformation 2Conformational selectionObligate stepAla mutantBackbone amidesΑ-helixSide chainsSingle LysEssential roleNucleasePathwayDynamics trajectoriesResiduesConformationMutantsInterconversion pathwaysCRISPR
2022
Structural 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 triphosphateGlycerol 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 conditionsStability