Bioinformatics and Molecular Dynamics Simulation Study
of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops
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Abstract
The
L1 stalk is a prominent mobile element of the large ribosomal subunit.
We explore the structure and dynamics of its non-canonical rRNA elements,
which include two kink-turns, an internal loop, and a tetraloop. We
use bioinformatics to identify the L1 stalk RNA conservation patterns
and carry out over 11.5 μs of MD simulations for a set of systems
ranging from isolated RNA building blocks up to complexes of L1 stalk
rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk
tetraloop has an unusual GNNA or UNNG conservation pattern deviating
from major GNRA and YNMG RNA tetraloop families. We suggest that this
deviation is related to a highly conserved tertiary contact within
the L1 stalk. The available X-ray structures contain only UCCG tetraloops
which in addition differ in orientation (<i>anti</i> vs <i>syn</i>) of the guanine. Our analysis suggests that the <i>anti</i> orientation might be a mis-refinement, although even
the <i>anti</i> interaction would be compatible with the
sequence pattern and observed tertiary interaction. Alternatively,
the <i>anti</i> conformation may be a real substate whose
population could be pH-dependent, since the guanine <i>syn</i> orientation requires protonation of cytosine in the tertiary contact.
In absence of structural data, we use molecular modeling to explore
the GCCA tetraloop that is dominant in bacteria and suggest that the
GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn
Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate
that the long bulge is a stalk-specific eight-nucleotide insertion
into consensual kink-turn only subtly modifying its structural dynamics.
We discuss a possible evolutionary role of helix H78 and a mechanism
of L1 stalk interaction with tRNA. We also assess the simulation methodology.
The simulations provide a good description of the studied systems
with the latest bsc0χ<sub>OL3</sub> force field showing improved
performance. Still, even bsc0χ<sub>OL3</sub> is unable to fully
stabilize an essential sugar-edge H-bond between the bulge and non-canonical
stem of the kink-turn. Inclusion of Mg<sup>2+</sup> ions may deteriorate
the simulations. On the other hand, monovalent ions can in simulations
readily occupy experimental Mg<sup>2+</sup> binding sites