Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Friday Abstracts
Conformational Dynamics of RNA Functional Motifs: Ribosomal A-site and
Thermosensing Hairpin
Joanna Panecka, Filip Leonarski,
Joanna Trylska
.
University of Warsaw, Warsaw, Poland.
Internal dynamics of RNA is often crucial for its function. For instance, various steps of mRNA
translation are regulated by changes in conformational states of single nucleotides in ribosomal
RNA. Inherent dynamics of regulatory elements of mRNA, such as riboswitches, enables
response to environmental conditions. These regulatory elements include RNA thermosensing
sequences that allow for cell's feedback to heat or cold shock conditions.
I will describe two RNA motifs whose dynamics is important for (i) aminoglycoside antibiotic
binding and (ii) switching on translation upon temperature increase. These RNA fragments have
special sequence properties that make their structures uniquely flexible. The methodology used
were molecular dynamics simulations, fluorescence spectroscopy and thermal melting
experiments.
The first example is the aminoacylated-tRNA binding site (A-site) in the small ribosomal subunit
whose sequence differs between bacterial, human cytoplasmic and mitochondrial ribosomes. In
the crystal structures of the mitochondrial A-site we have identified a specific S-turn
conformation of the RNA backbone. This topology is not present in bacterial A-sites (both in
models and 30S subunits). Simulations show that mitochondrial and bacterial A-sites show
different propensities to form S-turn2. Also, mitochondrial A-site with a single mutation
(A1555G) resembles more the bacterial one explaining the ototoxicity of aminoglycosides in
patients carrying this mutation.
The second example are RNA thermosensors which are temperature sensing short RNA
sequences located in the 5' untranslated region of mRNA. They typically form a hairpin with
noncanonical base pairing to allow for unfolding in response to temperature increase. Local
melting of RNA exposes the Shine-Dalgarno sequence and allows for its binding to the
ribosomal RNA (anti-Shine-Dalgarno region) in the small subunit. We have investigated the
mechanism of thermal unwinding of a fourU thermometer and repression of heat shock gene
expression element (ROSE).
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