Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments

Abstract

Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn: an H-bond, an anion−π interaction, and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulfur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases the dispersion component of the anion−π stacking. The sulfur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to the unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulfur parameters and provide suggestions for improving the force-field performance.

Importance of Anion−π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study

“…This intramolecular contact between the phosphate group and G has been well described and characterized in the field of supramolecular chemistry as an anion−π interaction (an attractive noncovalent force between an electron deficient π-system and an anion) . While anion−π interactions have been contextualized in many chemistry-related fields of research − (e.g., crystal engineering, materials science, catalysis), as well as in biology − (protein–ligand interactions and enzyme chemistry), few studies have analyzed their implications in RNA folding motifs to date. − …”

Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

“…( 87) NBfix is very effective for separate tuning of interactions which cannot be optimally described using a single set of LJ parameters. (30,38,(88)(89)(90)(91)(92) We call the new modification stafix (stacking fix) as it primarily addresses the overstabilization of stacking present in the standard OL3 ff. Simulations with OL3-stafix can be used to observe spontaneous binding as well as to stabilize protein-RNA interfaces (Table 1 and Supplementary Figures S5 and S6).…”

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

“…Similar observations of a systematically too repulsive AFF potential in the short-range region of interatomic contacts have been reported before. 40,[50][51][52]57,126 The awareness about the too steep repulsion of the LJ potential goes all the way back to Buckingham. 54 However, the r −12 form (equation ( 2) in Computational details) has been favored in all major biomolecular FFs over the Buckingham exponential form for computational efficiency reasons.…”