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

Thursday Abstracts

Connecting Simplified Models with Explicit-solvent Forcefields: Slipknotting during the Simulations of Folding and Unfolding of Pseudoknots in RNA Janusz M. Bujnicki 1,2 . 1 IIMCB, Warsaw, Poland, 2 Adam Mickiewicz University, Faculty of Biology, Poznan, Poland. RNA pseudoknot is an element of RNA architecture comprising at least two helix-loop structures, in which a region in the loop associated with one helix base-pairs with complementary nucleotides outside that helix, thereby forming a second helix. Pseudoknots can be formed by regions of RNA that are very distant in primary sequence and are difficult to predict computationally from RNA sequence because of their non-linear character. Pseudoknots fold into knot-shaped three-dimensional conformations, but are not true topological knots. The pseudoknot architecture is capable of supporting various stable 3D folds that display a diverse range of functions in a variety of biological processes. First recognized in the genomes of plant viruses in 1982, pseudoknots are now established as evolutionarily conserved elements of functionally important RNAs such as RNase P or telomerase RNA. We used SimRNA, our recently developed method for coarse-grained RNA folding simulations, to model the folding and unfolding of several RNA pseudoknots with experimentally detemrined structures. Our simulations provide insight into the folding trajectories, in particular into the order of helix formation, depending on RNA sequence.

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