2009
The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules
Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynthesis Research 2009, 102: 455-470. PMID: 19633920, PMCID: PMC2954272, DOI: 10.1007/s11120-009-9467-6.Peer-Reviewed Original ResearchConceptsElectrostatic interactionsMM methodQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsForce fieldQM/MM hybrid methodsQM/MM methodologyQM/MM methodsMolecular mechanics force fieldQuantum chemistry techniquesMM force fieldsStructural refinementPhotosystem IIChemistry techniquesStructure/function relationsCharge transferQM layerMolecular fragmentsChemical modificationBiological macromoleculesSteric hindranceComputational protocolSpectroscopic dataMolecular domainsStructural propertiesHigh-resolution spectroscopic data
2008
A Model of the Oxygen-Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. A Model of the Oxygen-Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations. Journal Of The American Chemical Society 2008, 130: 6728-6730. PMID: 18457397, PMCID: PMC2678715, DOI: 10.1021/ja801979n.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexSpectroscopic dataPhotosystem IIOxygen-Evolving CenterIntermediate oxidation statesHigh-resolution spectroscopic dataOxidation stateCatalytic cycleMetal clustersEXAFS simulationsPolarized EXAFSXRD modelStructural refinementEXAFSComputational structural modelsSingle crystalsStructural modelDanglerAmino acidsIonsComplexesCrystalsMnAcidStructure
2006
Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin
Gascón J, Sproviero E, Batista V. Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin. Accounts Of Chemical Research 2006, 39: 184-193. PMID: 16548507, DOI: 10.1021/ar050027t.Peer-Reviewed Original ResearchConceptsG protein-coupled receptorsRecent computational studiesPrimary photochemical eventQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsComputational studyPhotochemical eventsEnergy storage mechanismPrototypical G protein-coupled receptorX-ray structureVisual rhodopsinHigh-resolution X-ray structuresBovine visual rhodopsinWater moleculesSpectroscopic changesRetinyl chromophoreStorage mechanismActive siteMolecular rearrangementTrans isomerizationPhototransduction eventsMolecular originIndividual residuesStructural refinementPhototransduction mechanismChromophore