Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 7: Poster I

BP 7.56: Poster

Montag, 23. März 2009, 17:45–20:00, P3

A coarse-grained model for RNA tertiary structure formation — •Thomas Schötz and Ulrich Gerland — Arnold Sommerfeld Center for Theoretical Physics and CeNS, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstr. 37, 80333 München

RNA folding is relatively well understood on the secondary structure level, i.e. structure formation in the abstract space of base pairing patterns. However, on the level of the three-dimensional structure in real space, there are hardly any modeling approaches short of full-fletched molecular dynamics simulations, which are challenging even for small RNA molecules. Towards the ultimate goal of filling this gap, we construct a coarse-grained bead-spring type polymer model for RNA, which behaves like a freely jointed rouse chain as long as the bases are unpaired. However, when the short-range sequence-dependent interactions between the bases set in, more complex interactions between adjacent base pairs act to spontaneously create double-helical segments with a non-vanishing bending rigidity and torsion stiffness. We study the rich behavior of this model, including the sequence-dependent folding dynamics as well as static and dynamic properties of the folded tertiary structure, by the use of Brownian dynamics simulation techniques. This approach allows us to examine the dynamic formation and destruction of typical tertiary structure elements, including small pseudo-knotted structures, which play an important role in molecular biology.