Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

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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