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Long-Residency Hydration, Cation Binding, And Dynamics Of Loop E/Helix Iv Rrna-L25 Protein Complex, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Jaroslav Koča, Jiří Šponer

Chemistry Faculty Publications

Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove geometry whereas in the absence of divalent cations LE extensively interacts with monovalent cations via inner-shell binding. The HeIV region shows bistability of its major groove explaining the observed differences between x-ray and NMR structures. In agreement with the experiments, the simulations suggest that helix-alpha1 of L25 is the least stable part of the protein. …