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- W3204012741 abstract "Structural knowledge of an enzyme’s architecturecan help elucidate the details of how it performs its biologicalrole at the molecular level. In a case study of the hairpinribozyme, structures were solved to high resolution in complex withreaction-intermediate analogs revealing key chemical groups incatalytically-relevant configurations. Importantly, thenon-bridging oxygens of the scissile phosphate were tightlyrestrained in a conformation apparently promoting an inductiveeffect to elevate the pKa of a crucial active-site nucleobase whilealso ameliorating the unfavorable buildup of negative charge at theleaving group during the phosphoryl-transfer reaction. Active-sitewater molecules were ascribed a new role in both geometric andelectrostatic stabilization of the reaction intermediate. Bycomparison to proteinaceous ribonuclease structures harboring thesame reaction-intermediate analog, the catalytic strategiesemployed by these two evolutionarily-disparate enzyme classesappear to be a case of convergent evolution. In a secondinvestigation, the aptamer domain of a metabolite-sensingnon-coding regulatory RNA sequence was analyzed. Construct design,initial crystallization and attempts to solve the structure aredescribed followed by improved methods to prepare a homogeneousRNA-metabolite complex. The resulting complex was evaluated bydynamic light scattering as well as small angle X-ray scattering.Subsequent optimization of crystallization conditions anddiffraction analyses are also reported. The final area of focusencompasses biochemical and computational efforts to probe themechanism of action of activation induced deaminase (AID). AID is amember of the cytidine deaminase superfamily and functions in theimmunoglobulin maturation processes of somatic hypermutation (SHM),gene conversion (GC) and class switch recombination (CSR). Despiteconsiderable research, questions remain regarding how AID istargeted to its substrate(s), what other cellular cofactors arenecessary for function and how its activity is regulated sincedysfunction or misregulation of AID has the potential to causecancer. Efforts to crystallize AID were complemented bycomputational modeling, which has provided the basis for targetedbiochemical studies aimed at answering outstanding questions.Perspectives on the success and pitfalls of continued modeling arediscussed in light of recent empirical structural informationreported for related family members." @default.
- W3204012741 created "2021-10-11" @default.
- W3204012741 creator A5046436455 @default.
- W3204012741 date "2009-01-01" @default.
- W3204012741 modified "2023-09-27" @default.
- W3204012741 title "Structural Studies of Transition-State Stabilization by aSmall Catalytic RNA, Metabolite-Binding by a Regulatory RNASequence and the Mechanism of Action of Activation InducedDeaminase." @default.
- W3204012741 hasPublicationYear "2009" @default.
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