Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 26

Practical simulation approaches involve the use of so-called multiscale
models 23-25 that integrate a hierarchy of models to work together to provide
a computationally tractable representation of a complex biochemical reac-
tion in a realistic environment. The most simple and widely applied multi-
scale model to study biochemical reactions is the use of a combined quantum
mechanical/molecular mechanical (QM/MM) potential. 25-31 As a specific
example, for enzyme systems, one typically treats the reactive chemical
events in a region localized around the active site with a sufficiently accurate
high-level QM model, the microscopic solvent fluctuations and changes in
molecular conformation using MM force field model, and the macroscopic
dielectric relaxation using a continuum solvation model.
Combined QM/MMmethods have been widely applied to various bio-
logical systems. 25-31 RNA catalysis simulations, however, are particularly
laden with challenges not apparent for most other biological systems such
as protein enzymes. RNA molecules are highly negatively charged and
exhibit strong and often specific interactions with solvent. 20-22,32 This
requires special attention to the microscopic in silico model that requires con-
sideration of a very large number of water molecules, counter-ions, and
co-ions to be included. Electrostatic interactions need to be treated rigor-
ously without cutoff, and long simulation times are typically needed to
insure that the ion environment is properly equilibrated. 33-36 These issues
are further complicated by the fact that RNA molecules bind divalent metal
ions that play an important role in folding, and that may also contribute
actively to the catalytic chemical steps.
The hammerhead ribozyme (HHR) 37-39 is an archetype system to study
the fundamental nature of RNA catalysis 40-45 and is arguably the best char-
acterized ribozyme due to its small size, known crystal structures, and the
wealth of biochemical and biophysical studies. HHR catalyzes the site-
specific attack of an activated 2 0 OH nucleophile to the adjacent 3 0 phos-
phate, resulting in cleavage of the P-O5 0 phosphodiester linkage to form
a2 0 ,3 0 cyclic phosphate and a 5 0 alcohol. A detailed understanding of the
structure-function relationships in the HHR 38,41 will ultimately aid in
the understanding of other cellular RNA catalysts such as the ribosome.
The HHR has gained attention as a potential anti-HIV-1 therapeutic
agent, 46-49 an inhibitor of BCR-ABL1 gene expression, 50 an inhibitor of
hepatitis-B virus gene expressions, 51,52 and as a tool in drug design and target
discovery for other diseases. 50,53,54 The hammerhead-like motif is distrib-
uted throughout various genomes, 55 and recently a discontinuous HHR
motif has been found embedded in the 3 0 untranslated regions of a