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
2008
Structural and Energetic Analysis of Activation by a Cyclic Nucleotide Binding Domain
Altieri SL, Clayton GM, Silverman WR, Olivares AO, De La Cruz EM, Thomas LR, Morais-Cabral JH. Structural and Energetic Analysis of Activation by a Cyclic Nucleotide Binding Domain. Journal Of Molecular Biology 2008, 381: 655-669. PMID: 18619611, PMCID: PMC2555981, DOI: 10.1016/j.jmb.2008.06.011.Peer-Reviewed Original ResearchConceptsBinding domainsCyclic Nucleotide Binding DomainLigand bindingC-terminal cyclicNucleotide-dependent proteinNucleotide Binding DomainAbsence of ligandFull-length channelLigand-protein interactionsCNB domainsUseful model systemProkaryotic homologResidue side chainsApo stateDependent ion channelsApo configurationsSingle proteinMlotiK1Domain fragmentNucleotide selectivityIon channelsDomain structureX-ray crystallographyX-ray structureModel system