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

Knotting in Subchains of Proteins and Other Entangled Chains Eric Rawdon . University of St. Thomas, Saint Paul, USA.

Researchers have discovered interesting knotting and slipknotting patterns in proteins by analyzing the knotting of all subchains.The subchains typically form simpler knot types (which we call "subknots'") than the full chain. By analyzing the knotting within subchains of some energy-minimizing closed knots, we are able to draw certain conclusions about the geometry of knotted proteins. This is joint work with Kenneth Millett, Andrzej Stasiak, and Joanna Sulkowska.

Mechanical Unfolding of Single RNA Pseudoknots Reveals that Conformational Plasticity, Not Resistance to Unfolding, is a Determinant of Programmed −1 Frameshifting Michael Woodside 1,2 . 1 University of Alberta, Edmonton, Canada, 2 National Institute for Nanotechnology, Edmonton, AB, Canada. Programmed −1 frameshifting, whereby a ribosome shifts reading frame on a messenger RNA in order to generate an alternate gene product, is often stimulated by a pseudoknot structure in the mRNA. Viruses in particular use frameshifting to regulate gene expression, making pseudoknots potential targets for anti-viral drugs. The efficiency of the frameshift varies widely for different sites, but the factors that determine frameshifting efficiency are not yet fully understood. Previous work has suggested that frameshifting efficiency is related to the resistance of the pseudoknot against mechanical unfolding. We tested this hypothesis by studying the mechanical properties of a panel of pseudoknots with frameshifting efficiencies ranging from 2% to 30%. Using optical tweezers to apply tension across the mRNA, mimicking the tension applied by the ribosomal helicase when unfolding structure in the mRNA, we measured the distribution of forces needed to unfold each pseudoknot. We found that neither the unfolding force, the unfolding kinetics, nor the properties of the energy landscape for unfolding could be correlated to frameshifting efficiency. Surprisingly however, increased frameshifting efficiency was correlated with an increased tendency to form alternate structures, suggesting a more complex role for the pseudoknot involving conformational dynamics. These results were corroborated by studying the effects of a ligand that reduces frameshifting associated with the SARS pseudoknot: binding of the ligand to the pseudoknot abolished the formation of alternate conformers. In addition to providing a novel framework for future studies aimed at understanding mechanisms regulating −1 PRF efficiency, our work suggests that targeting the conformational dynamics of pseudoknots may be an effective strategy for anti-viral drug design.

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