Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
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DOI：
10.1529/biophysj.104.047126
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发表时间：
2004-11
影响因子：
3.4
通讯作者：
K. Réblová;N. Špačková;J. Koča;N. Leontis;J. Šponer
中科院分区：
文献类型：
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作者：
K. Réblová;N. Špačková;J. Koča;N. Leontis;J. Šponer
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. Inclusion of Mg2+ cations into the simulations causes perturbation of basepairing at the LE/HeIV junction, which does not, however, affect the protein binding. The rRNA-protein complex is mediated by a number of highly specific hydration sites with long-residing water molecules and two of them are bound throughout the entire 24-ns simulation. Long-residing water molecules are seen also outside the RNA-protein contact areas with water-binding times substantially enhanced compared to simulations of free RNA. Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA.
