Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 25

Abstract
Herein we summarize our progress toward the understanding of hammerhead ribozyme
(HHR) catalysis through a multiscale simulation strategy. Simulation results collectively
paint a picture of HHR catalysis: HHR first folds to forman electronegative active site pocket
to recruit a threshold occupation of cationic charges, either a Mg 2þ ion or multiple mono-
valent cations. Catalytically active conformations that have good in-line fitness are
supported by specific metal ion coordination patterns that involve either a bridging
Mg 2þ ion or multiple Na þ ions, one of which is also in a bridging coordination pattern.
In the case of a single Mg 2þ ion bound in the active site, the Mg 2þ ion undergoes a migra-
tion that is coupled with deprotonation of the nucleophile (C17:O 2 ' ). As the reaction pro-
ceeds, the Mg 2þ ion stabilizes the accumulating charge of the leaving group and
significantly increases the general acid ability of G8:O 2 ' . Further computational mutagen-
esis simulations suggest that the disruptions due to mutations may severely impact HHR
catalysis at different stages of the reaction. Catalytic mechanisms supported by the sim-
ulation results are consistent with available structural and biochemical experiments, and
together they advance our understanding of HHR catalysis.
1. INTRODUCTION
In the past two and a half decades, revolutionary changes have been
seen in the original notion that the only function of RNA molecules was
as only messenger intermediates in the pathway from the genetic code to
protein synthesis. Now, the roles of RNA in cellular function are known
to be considerably more diverse, ranging from regulation of gene expression
and signaling pathways to catalyzing important biochemical reactions
including protein synthesis. 1-12 These discoveries have transformed our
view of RNA as a simple messenger to a more profoundly central molecule
in the evolution of life forms, our understanding and appreciation of which
is still in its infancy. 13 Ultimately, the elucidation of the mechanisms of
RNA catalysis 14 will extend our understanding of biological processes
and facilitate the design of new RNA-based technologies. 15-17
Simulations of biological systems at the atomic level could potentially
offer access to the most intimate mechanistic details that may aid in the inter-
pretation of experiments and provide predictive insight into relevant drug
design or therapeutic efforts. 18-22 In particular, a quantum mechanical
description is ultimately required for reliable study of chemical reactions,
including reactions catalyzed by biological macromolecules such as RNA.
At the same time, a high-level fully quantum mechanical treatment of these
systems in molecular simulations is not yet feasible.