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Carsten Maus (2006)

Simulation of the kinetically controlled riboswitch folding in 5' untranslated mRNA regions

Poster, Monterey, CA, USA, Winter Simulation Conference.

Ribonucleic acids are involved in a huge amount of biological processes. They can fold into complex 3-dimensional structures which have often a very important function. In lots of cases the biological function is not given by the thermodynamical optimal structure (structure with minimum free energy) but by a kinetically stabilized, suboptimal structure. The aim of simulations of kinetically controlled foldings is to identify such metastable structures. In this work [3] we analyzed the folding and function of purine riboswitches. Riboswitches are untranslated regions of mRNAs which can bind directly small metabolite molecules without a cofactor [2]. They regulate gene expression by a conformational change of the RNA structure as a consequence of metabolite binding. The first natural riboswitch was found in 2002 [6]. Till now lots of additional riboswitch classes where discovered in all three kingdoms of life (bacteria, archaebacteria and eukaryotes) [1, 4, 5]. This is a strong evidence for a very old regulation mechanism from an ancient RNA world. We present a method for directed stabilization of defined secondary structure elements during simulation of the sequential folding [3]. Because of that a prediction of the conformational change of the RNA structure induced by ligand binding is possible and we can get information for the detailed regulation mechanism of such molecular switches.

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