BPCPPDYSOE21 – scientific programme

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 16: Charged Soft Matter - organized by Joachim Dzubiella (Albert Ludwigs University Freiburg, Freiburg)

CPP 16.5: Talk

Wednesday, March 24, 2021, 11:40–12:00, CPPa

Identifying Mg²⁺ binding sites on RNA using MD simulations with accelerating force field parameters — •Kara K. Grotz, Sergio Cruz-León, and Nadine Schwierz — Department of Theoretical Biophysics, Max Planck Insitute of Biophysics, Frankfurt am Main, Germany

Mg²⁺ is one of the most abundant cations in living cells. The interaction between Mg²⁺ and RNA is essential for folding and function of the diverse macromolecule. Mg²⁺ binds specifically and often directly (inner-sphere configuration) to individual functional groups on the RNA. Localizing Mg²⁺ binding sites, however, is challenging as Mg²⁺ is silent in most experimental approaches. Computational studies can contribute molecular insight but often struggle with insufficiently accurate atomistic models (force fields) and time scale limitations due to the slow binding kinetics of Mg²⁺ (millisecond time scale). Herein, we use a recently developed Mg²⁺ force field that is based on ion-water and ion-ion properties of Mg²⁺. In addition, the parameters are chosen such that they accelerate the water exchange kinetics (nanosecond time scale). Moreover, by incorporating experimental binding affinities towards specific RNA binding positions, we are able to find Mg²⁺ binding sites on RNA using unbiased simulations and observe outer-to-inner sphere transitions directly.