期刊
BIOPHYSICAL JOURNAL
卷 84, 期 6, 页码 3564-3582出版社
CELL PRESS
DOI: 10.1016/S0006-3495(03)75089-9
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- NIGMS NIH HHS [2R15 GM55898, R15 GM055898] Funding Source: Medline
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 width. In the absence of Mg2+, the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg2+, penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na+ cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.
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