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

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA Dave Thirumalai . University of Maryland, College Park, USA. Formation of a pseudoknot (PK) in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the PK is in equilibrium with an extended hairpin (HP) structure. We used molecular simulations of a coarse- grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than that of the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in Escherichia coli, the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can partially restore telomerase activity with decreased PK stability. The study of protein folding has provided a rich quantitative and conceptual foundation for describing the physical-chemical properties of biomolecular dynamics. In particular, the folding of complex proteins, such as knotted proteins, has illustrated the strong role that steric interactions have on biological dynamics. By utilizing the foundation provided by theoretical studies of protein folding, we are now able to use molecular simulation to gain deeper insights into the roles that steric factors have during the functional dynamics of large biomolecular assemblies. In our studies of the ribosome, we are finding many common themes between protein folding and conformational dynamics of this assembly. In the case of tRNA accommodation and translocation on the ribosome, we have found that tRNA molecules and elongation factors frequently exploit a delicate balance between entropy enthalpy, similar to the process of protein folding. In addition, through the use of simplified modeling strategies, we are finding that the shape of the ribosome introduces many steric obstacles, which are analogous to the geometric limitations imposed during the folding of knotted proteins. Finally, we are also adopting quantitative tools developed for folding to identify proper coordinates that are capable of precisely capturing the relevant transition states. Together, these studies highlight how an understanding of complex proteins can enable insights into a broad range of biomolecular processes. Parallels between Protein Folding and Ribosome Dynamics Paul Whitford . Northeastern University, Boston, USA.

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