3 research outputs found
Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops
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
rRNA C‑Loops: Mechanical Properties of a Recurrent Structural Motif
C-loop is an internal loop motif
found in the ribosome and used
in artificial nanostructures. While its geometry has been partially
characterized, its mechanical properties remain elusive. Here we propose
a method to evaluate global shape and stiffness of an internal loop.
The loop is flanked by short A-RNA helices modeled as rigid bodies.
Their relative rotation and displacement are fully described by six
interhelical coordinates. The deformation energy of the loop is assumed
to be a general quadratic function of the interhelical coordinates.
The model parameters for isolated C-loops are inferred from unrestrained
all-atom molecular dynamics simulations. C-loops exhibit high twist
as reported earlier, but also a bend and a lateral displacement of
the flanking helices. Their bending stiffness and lateral displacement
stiffness are nearly isotropic and similar to the control A-RNA duplexes.
Nevertheless, we found systematic variations with the C-loop position
in the ribosome and the organism of origin. The results characterize
global properties of C-loops in the full six-dimensional interhelical
space and enable one to choose an optimally stiff C-loop for use in
a nanostructure. Our approach can be readily applied to other internal
loops and extended to more complex structural motifs
Role of S‑turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A‑Site. A Bioinformatics and Molecular Dynamics Simulation Study
The mRNA decoding site (A-site) in
the small ribosomal subunit
controls fidelity of the translation process. Here, using molecular
dynamics simulations and bioinformatic analyses, we investigated the
structural dynamics of the human mitochondrial A-site (native and
A1490G mutant) and compared it with the dynamics of the bacterial
A-site. We detected and characterized a specific RNA backbone configuration,
S-turn2, which occurs in the human mitochondrial but not in the bacterial
A-site. Mitochondrial and bacterial A-sites show different propensities
to form S-turn2 that may be caused by different base-pairing patterns
of the flanking nucleotides. Also, the S-turn2 structural stability
observed in the simulations supports higher accuracy and lower speed
of mRNA decoding in mitochondria in comparison with bacteria. In the
mitochondrial A-site, we observed collective movement of stacked nucleotides
A1408·C1409·C1410, which may explain the known differences
in aminoglycoside antibiotic binding affinities toward the studied
A-site variants