Berlin 2018 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 12: Computational Biophysics I

BP 12.6: Vortrag

Dienstag, 13. März 2018, 11:15–11:30, H 1058

Specific RNA-cation interactions: Individual binding site affinities from molecular dynamics simulation — •Sergio Cruz-León and Nadine Schwierz — Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany

Metal cation-RNA interactions are essential for RNA folding and function. In this research, cation-mediated specific interactions between common RNA structural motifs and a set of biologically relevant metal cations including Li⁺, Na⁺, K⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺ and Ba²⁺ are studied with all atom molecular dynamics simulations. Combining advanced sampling techniques and recent force fields for metal cations developed in our group, we investigate ion binding to individual binding sites on RNA by calculating ion binding affinities and kinetic rate coefficients. The calculated binding affinities agree well with available experimental data. Specifically bound cations and ions that diffusively surround the RNA affect the end-to-end distance of double stranded RNA and RNA-RNA interactions consistently with reported experimental findings. This detailed understanding of the metal cation-RNA interactions and its driving forces may provide a starting point to explore the exciting possibility to control structure formation and biological functions which have applications in nanotechnology and RNA based tools medicine.