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• W2036683766 abstract "The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the theoretical conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity." @default.
• W2036683766 created "2016-06-24" @default.
• W2036683766 creator A5018416560 @default.
• W2036683766 creator A5049661679 @default.
• W2036683766 date "1997-06-01" @default.
• W2036683766 modified "2023-10-18" @default.
• W2036683766 title "RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA Asp anticodon hairpin 1 1Edited by J. Karn" @default.
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• W2036683766 doi "https://doi.org/10.1006/jmbi.1997.1022" @default.
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• W2036683766 hasPublicationYear "1997" @default.
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