2014
Conformational Preferences Underlying Reduced Activity of a Thermophilic Ribonuclease H
Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational Preferences Underlying Reduced Activity of a Thermophilic Ribonuclease H. Journal Of Molecular Biology 2014, 427: 853-866. PMID: 25550198, PMCID: PMC4349505, DOI: 10.1016/j.jmb.2014.11.023.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesCrystallography, X-RayEscherichia coliHot TemperatureHydrophobic and Hydrophilic InteractionsModels, MolecularMolecular Dynamics SimulationMutationNuclear Magnetic Resonance, BiomolecularPrincipal Component AnalysisProtein BindingProtein ConformationRibonuclease HThermodynamicsThermus thermophilusConceptsE. coli homologWild-type proteinRibonuclease HE. coli mutantsGlycine-rich regionMesophilic homologsThermophilus enzymeColi mutantsSubstrate bindingThermophilic proteinsImportant residuesThermus thermophilusConformational dynamicsGlycine residueMesophilic enzymesActive conformationLoop regionAtom MD simulationsConformational basisReduced activityEscherichia coliHomologProteinPosition 80MD simulations
2010
Solution Structure and Phospholipid Interactions of the Isolated Voltage-Sensor Domain from KvAP
Butterwick JA, MacKinnon R. Solution Structure and Phospholipid Interactions of the Isolated Voltage-Sensor Domain from KvAP. Journal Of Molecular Biology 2010, 403: 591-606. PMID: 20851706, PMCID: PMC2971526, DOI: 10.1016/j.jmb.2010.09.012.Peer-Reviewed Original ResearchConceptsNuclear Overhauser effect spectroscopyNuclear magnetic resonance spectroscopySolution structureIsolated voltage-sensor domainBilayer-forming lipidsMagnetic resonance spectroscopyMicelle interactionsEffect spectroscopyChemical environmentCrystal structurePhospholipid interfaceChemical propertiesResonance spectroscopyPhospholipid micellesMembrane environmentPhospholipid bilayersNanosecond timescaleMillisecond timescaleMicellesSpectroscopyAmphipathic α-helixΑ-helixVoltage sensor domainRelaxation experimentsPhysical properties
2006
An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H
Butterwick JA, Palmer AG. An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H. Protein Science 2006, 15: 2697-2707. PMID: 17088323, PMCID: PMC2242442, DOI: 10.1110/ps.062398606.Peer-Reviewed Original ResearchConceptsRNase HConformational changesGly residueMesophile Escherichia coliThermophile Thermus thermophilusSolution NMR spectroscopyIntrahelical hydrogen bondsHomologous mesophilicProtein sequencesBiological functionsThermus thermophilusImportant adaptationGly insertionPutative hingeEscherichia coliRibonuclease HMesophilicResiduesDynamic processUnfavorable interactionsThermophilesThermophilicProteinNMR spectroscopyThermophilus
2005
Solution Structure of the Vts1 SAM Domain in the Presence of RNA
Edwards TA, Butterwick JA, Zeng L, Gupta YK, Wang X, Wharton RP, Palmer AG, Aggarwal AK. Solution Structure of the Vts1 SAM Domain in the Presence of RNA. Journal Of Molecular Biology 2005, 356: 1065-1072. PMID: 16405996, DOI: 10.1016/j.jmb.2005.12.004.Peer-Reviewed Original ResearchConceptsSAM domainStructural basisCore helicesMultidimensional heteronuclear NMR spectroscopyRNA-binding surfaceSolution structureChemical shift perturbationsSpecific target RNAHeteronuclear NMR spectroscopyPresence of RNARNA bindingRNA recognitionC-terminusShift perturbationsTarget RNAShort helixMutational dataRNAHelix
2004
Multiple Time Scale Backbone Dynamics of Homologous Thermophilic and Mesophilic Ribonuclease HI Enzymes
Butterwick JA, Loria JP, Astrof NS, Kroenke CD, Cole R, Rance M, Palmer AG. Multiple Time Scale Backbone Dynamics of Homologous Thermophilic and Mesophilic Ribonuclease HI Enzymes. Journal Of Molecular Biology 2004, 339: 855-871. PMID: 15165855, DOI: 10.1016/j.jmb.2004.03.055.Peer-Reviewed Original Research