Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E

Abstract

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 Mg 21 rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg 21 , the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg 21 , 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 1 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.

Molecular dynamics simulations of RNA: An in silico single molecule approach

“…MD simulations, along with phylogenetic analyses and isostericity considerations, were used to predict the structure of spinach chloroplast loop E, based on the structure of loop E from E. coli. 54 The sequences have only 60% identity, but simulations predicted a nearly identical three-dimensional structure, since changes to the non-Watson-Crick base pairs (including four G-to-A substitutions) preserved the overall shape and unique pockets of negative electrostatic potential. This prediction was confirmed by solution NMR experiments.123 MD simulations of the loop E motif also showed long residency water molecules bound to specific hydration sites in the RNA molecule for up to 5 ns,54 much longer than the 50-500 ps water binding times typically observed in nucleic acid simulations.…”

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

“…[3][4][5][6][7][8][9][10][22][23][24][25][26][27][28][29][30][31][32] The AMBER force fields have also been successful in studies of RNA molecules, including those that exhibit a wide range of non-Watson-Crick base pairings, tertiary interactions, and complex backbone topologies. [33][34][35][36][37][38][39][40][41][42][43] These studies have also emphasized the importance of NAs' sugar-phosphate backbone flexibility, which is delimited by six main-chain torsion angles (designated as R through ), in addition to the five internal sugar torsions (denoted as τ 0 through τ 4 , which can be succinctly described by the puckering and the phase angle 44 ), and the glycosidic angle 45 (see Figure 1). Free duplex B-DNA frequently populates two distinct backbone conformational substates, referred to as B I and B II .…”

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

“…Molecular simulation force fields for nucleic acids continue to improve [26][27][28][29][30][31] and a variety of simulations involving ribozymes have been carried out in recent years. [32][33][34][35][36][37][38][39][40] In order to study the structure and dynamics of different catalytic states along the reaction path of a ribozyme, however, reliable empirical force fields parameters must be developed for the transition states and reactive intermediates of these reactions. Furthermore, in order to use molecular simulation to aid in the interpretation of experimentally measured thio effects, parameters for thiosubstituted phosphate and phosphorane models and their interactions with metal ions are required.…”