2013
Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics
Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH. Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Research 2013, 41: 9077-9089. PMID: 23921641, PMCID: PMC3799440, DOI: 10.1093/nar/gkt674.Peer-Reviewed Original ResearchConceptsRB69 DNA polymeraseFörster resonance energy transferDNA polymeraseHigh-resolution X-ray crystallographyResolution X-ray crystallographyHigh mutation rateB-family polConformational dynamicsExonuclease domainState kinetic parametersMutation rateG mutantResonance energy transferX-ray crystallographyM variantPolymerasePrimer terminusHydrophobic cavityActive siteBase selectivitySimilar substitutionSide chainsProfound effectDramatic effectInternal cavity
2004
Equilibrium and Kinetic Analysis of Nucleotide Binding to the DEAD-Box RNA Helicase DbpA †
Talavera MA, De La Cruz EM. Equilibrium and Kinetic Analysis of Nucleotide Binding to the DEAD-Box RNA Helicase DbpA †. Biochemistry 2004, 44: 959-970. PMID: 15654752, DOI: 10.1021/bi048253i.Peer-Reviewed Original ResearchConceptsFluorescence resonance energy transferAbsence of RNARNA helicaseATP bindingNucleotide bindingConformational rearrangementsResonance energy transferConformational flexibilityDbpADependent conformationStructural rearrangementsDbpA.Protein AUnfavorable entropic contributionNucleotidesPhysiological temperatureBindingAssociation rate constantsADP