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Simulations of an RNA Enzyme Molecular Switch

Recent research from the research group of Professor Darrin York.

Recently, graduate student George Giambasu, research associate Dr. Tai-Sung Lee and Prof. Darrin York of the Department of Chemistry, along with collaborators Carlos P. Sosa from IBM and William Scott and Michael Robertson of the Center for Molecular Biology of RNA at UCSC have used large scale molecular dynamics simulations to reveal the dynamical hinge points of the L1 ligase all-RNA synthetic molecular switch. The L1 ligase ribozyme is an in vitro selected ribozyme that uses a non-canonically base-paired ligation site to catalyze regioselectively and regiospecifically the 5' to 3' phosphodiester bond ligation, a reaction relevant to origin of life hypotheses that invoke an RNA World scenario. From these simulations, along with crystallographic data, a set of 4 virtual torsion angles that span two evolutionarily conserved and restricted regions were identified as dynamical hinge points in the conformational switch transition. The ligation site visits three distinct states characterized by hydrogen bond patterns that are correlated with the formation of specific contacts that may promote catalysis. The insights gained from these simulations contribute to a more detailed understanding of the coupled catalytic/conformational switch mechanism of L1 ligase that may facilitate the design and engineering of new catalytic riboswitches.

This work is in press in the RNA Journal.


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