Regensburg 2013 – scientific programme
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BP: Fachverband Biologische Physik
BP 8: Posters: Proteins
BP 8.19: Poster
Monday, March 11, 2013, 17:30–19:30, Poster B2
Computational Analysis of Co-transcriptional Riboswitch Folding — •Benjamin Lutz1,2, Abhinav Verma1, and Alexander Schug1 — 1Steinbuch Centre for Computing (SCC), Karlsruher Institut für Technologie (KIT), 76128 Karlsuhe, Germany — 2Fakultät für Physik, Karlsruher Institut für Technologie (KIT), 76128 Karlsruhe, Germany
Structured RNA in non-coding regions often plays crucial regulatory roles. Riboswitches are an important example that can prevent expression of the downstream gene by terminating transcription or translation. Typically, one out of two distinct conformations is formed depending on ligand binding. The extrusion out of RNA polymerase (RNAP) takes place at time scales comparable to those of folding and binding. We investigate these interdependent processes by simulating the extrusion out of RNAP and concurrent folding for the SAM-I and adenine riboswitches with molecular dynamics. Atomically resolved structure-based models reduce the computational effort sufficiently to simulate different extrusion velocity scenarios. Depending on the scenario, we observe and quantify different pathways in structural formation. Considering the inherent link of folding and binding, this underlines modulation of extrusion velocity as another degree of freedom in genetic evolution. Our simulational findings therefore complement experimental measurements to understand the dynamic behavior of nascent RNA.