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Full-Text Articles in Physical Sciences and Mathematics
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
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. …
Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer
Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer
Chemistry Faculty Publications
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of > 80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg2+ rigidifies Loop E and stabilizes its major groove at an intermediate …