2023
Connected Component Analysis of Dynamical Perturbation Contact Networks
Gheeraert A, Lesieur C, Batista V, Vuillon L, Rivalta I. Connected Component Analysis of Dynamical Perturbation Contact Networks. The Journal Of Physical Chemistry B 2023, 127: 7571-7580. PMID: 37641933, PMCID: PMC10493978, DOI: 10.1021/acs.jpcb.3c04592.Peer-Reviewed Original ResearchTurning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Maschietto F, Morzan U, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro G, Nekrasov P, Brooks B, Loria J, Rivalta I, Batista V. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications 2023, 14: 2239. PMID: 37076500, PMCID: PMC10115891, DOI: 10.1038/s41467-023-37956-1.Peer-Reviewed Original ResearchMeSH KeywordsAllosteric RegulationAllosteric SiteAmino AcidsGlycerolImidazolesMolecular Dynamics SimulationPhosphatesConceptsEffector bindingImidazole Glycerol Phosphate SynthaseLocal amino acidsAmino acid dynamicsImidazole glycerolAllosteric drugsAllosteric activationAllosteric responsePhosphate synthaseAllosteric mechanismMode of activationEnzyme functionAmino acidsAllosteryDrug discoverySynthaseNuclear magnetic resonance spectroscopyBindingMolecular dynamics simulationsActivationAllostericCascadeDynamics simulations
2011
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP. Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid. Biophysical Journal 2011, 101: 411-420. PMID: 21767494, PMCID: PMC3136797, DOI: 10.1016/j.bpj.2011.05.039.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsAmino acidsMeiboom-Gill (CPMG) relaxation dispersion experimentsWild-type ribonuclease AProtein energy landscapesNonnatural amino acidsRelaxation dispersion experimentsSingle residueProtein motionsMillisecond motionsConformational motionsEnzyme motionsHistidine-48Ribonuclease ACatalytic turnoverSimilar pH rangeRate limitingMolecular dynamics simulationsEnergy landscapeCorrelated motionAcidCatalytic cycleDispersion experimentsResiduesDynamics simulations