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.
Parallels between Protein Folding and Ribosome Dynamics
Paul Whitford
.
Northeastern University, Boston, USA.
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.
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