The VS Ribozyme: Catalytic Mechanism, Transition State Structure, and Evolution

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ABSTRACT Endonucleolytic ribozymes represent a class of noncoding RNAs that influence nearly every aspect of RNA metabolism and shape cellular transcriptomes through catalysis of 2'-O-transphosphorylation reactions. High resolution structures of these self-cleavage motifs reveal distinct architectures and provide physical frameworks to investigate the structural basis of catalysis. Most commonly, nucleobases reside at the active site poised to engage directly in catalysis. For some ribozymes these nucleobases have been implicated in general acid base catalysis and shown to engage in catalytic interactions. Nevertheless, major gaps exist in our mechanistic understanding for every endonucleolytic ribozyme and significant limitations in current approaches stand in the way of developing a quantitative understanding for how structure imparts catalysis. For no single ribozyme have the active site interactions been experimentally identified and dissected in a comprehensive manner nor has the transition state structure, arguably the most critical feature in understanding catalysis, been characterized. Consequently, theoreticians lack appropriate data to benchmark and advance computational approaches. Moreover, similarities and differences within the active sites also raise questions about the sequence-structure and evolutionary relationships of these ribozymes. Did endonucleolytic ribozymes arise independently and converge upon common mechanisms due to chemical constraints or do their mutational pathways intersect, making evolution from a common ancestor possible? Our understanding of and ability to manipulate and apply biology hinges critically upon understanding catalysis and its mechanisms of evolution, as chemical reactions must occur at rates that outpace natural dissipative forces to allow living systems to create order, maintain organization, and evolve. In the long term, we hope to develop a quantitative, predictive understanding of the structural and evolutionary origins of ribozyme catalysis. This application has two overall goals: (1) to generate an atomistic picture of catalysis by the VS ribozyme that incorporates transition state bonding information, locations and extents of proton transfer, and transition state interactions in the context of the overall tertiary structure, and (2) to determine whether the fitness landscapes of a plausible evolutionary precursors of the VS and hairpin ribozymes intersect. Accomplishing the first goal in a comprehensive manner would represent a milestone for any catalyst; accomplishing the latter goal would underscore the fluidity by which RNA self-cleavage motifs can emerge and establish the possibility of common ancestry among endonucleolytic ribozymes. Building upon our recent high-resolution structure of the VS ribozyme, we will initiate new experimental strategies that identify catalytic interactions using double mutant cycles that account for concomitant pKa shifts, measure heavy atom kinetic isotope effects, and move the field beyond inferring proton transfer from structural proximity to obtaining actual biochemical signatures for general acid-base catalysis and associated BrØnsted coefficients.