Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 83

important for formation of active in-line attack conformations. In the case of
single Mg 2 þ ion bound in the active site, the Mg 2 þ ion initially stays at the
C-site in the reactant state and migrates to the B-site after the nucleophile
(C17:O2 0 ) is deprotonated. As the reaction proceeds, the Mg 2 þ ion can sta-
bilize the accumulating charge of the leaving group and bind to the general
acid (G8:O2 0 ), significantly increasing its ability to act as a general acid cat-
alyst to transfer a proton to the leaving group (C1.1:O5 0 ). Our QM/MM
studies demonstrate that the Mg 2 þ ion not only facilitates the protonation
of the leaving O5 0 , but it also plays an important role in the final dissociation
step of catalysis.
The mutational simulation results are consistent with observed muta-
tional data and suggest that the active site fold is well tuned for the reaction,
and most disruptions due to mutations have severe impact on HHR catalysis
that can affect different stages of the reaction. Our simulation results propose
mechanisms consistent with available experimental evidence, and have
motivated new experimental work. The insight gained from these studies
provides guiding principles into catalysis of an archetype ribozyme that
may ultimately facilitate the design of new RNA based technologies.

ACKNOWLEDGMENTS
The authors are grateful for financial support provided by the National Institutes of Health
(GM62248 and GM084149 to D. Y.). Computational resources were provided by the
Minnesota Supercomputing Institute (MSI) and by the NSF TeraGrid through the Texas
Advanced Computing Center and National Institute for Computational Sciences under
grant number TG-MCB110101.

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