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Simulations de dynamique moléculaires d'ARN – Structures et environnements

Abstract : RNA's, the only type of biomolecules that are at the same time informative and catalytic, play a role at all levels of cellular life. For some RNA's, the function is inscribed in their sequence. For others like transfer RNA's, the function resides in the formation and maintenance of their compact three-dimensional folds. These last RNA's, called structured RNA's, need Mg2+ cations to maintain their tertiary structure and participate to catalytic functions. In Eric WESTHOF's team, numerous three-dimensional models of structured RNA systems have been build through the use of phylogeny and chemical mapping techniques. These models gather almost all available experimental data for a given system and allowed to propose pertinent catalytic and molecular recognition mechanisms. Yet, these models do not allow to access to atomic resolution. This is why molecular dynamics simulation techniques have been developed in order to refine model structures and better understand structure-function relationships.

Recent progress in MD simulation techniques obtained in our laboratory, allows us now to simulate the dynamics of molecules of the tRNA or small ribozymes size with an unprecedented level of precision. For better understanding RNA functions, that are by nature dynamical processes, we developed MD techniques in order to complement fragmentary structural information available on RNA hydration and on the structural role played by ions such as : mono- and divalent cations as well as anions. This knowledge is essential for the comprehension of the folding and stability of RNA systems and should lead to more elaborate three-dimensional models. Among the systems that we propose to investigate, we can cite transfer RNAs, ribosomal fragments as well as RNA/antibiotic and RNA/protein complexes.
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Pascal Auffinger. Simulations de dynamique moléculaires d'ARN – Structures et environnements. Sciences du Vivant [q-bio]. Université Louis Pasteur - Strasbourg I, 2004. ⟨tel-00265627⟩

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