Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations

Abstract

RNA modulation via small molecules is a novel approach in pharmacotherapies, where the determination of the structural properties of RNA motifs is considered a promising way to develop drugs capable of targeting RNA structures to control diseases. However, due to the complexity and dynamic nature of RNA molecules, the determination of RNA structures using experimental approaches is not always feasible, and computational models employing force fields can provide important insight. The quality of the force field will determine how well the predictions are compared to experimental observables. Stacking in nucleic acids is one such structural property, originating mainly from London dispersion forces, which are quantum mechanical and are included in molecular mechanics force fields through nonbonded interactions. Geometric descriptions are utilized to decide if two residues are stacked and hence to calculate the stacking free energies for RNA dinucleoside monophosphates (DNMPs) through statistical mechanics for comparison with experimental thermodynamics data. Here, we benchmark four different stacking definitions using molecular dynamics (MD) trajectories for 16 RNA DNMPs produced by two different force fields (RNA-IL and ff99OL3) and show that our stacking definition better correlates with the experimental thermodynamics data. While predictions within an accuracy of 0.2 kcal/mol at 300 K were observed in RNA CC, CU, UC, AG, GA, and GG, stacked states of purine−pyrimidine and pyrimidine− purine DNMPs, respectively, were typically underpredicted and overpredicted. Additionally, population distributions of RNA UU DNMPs were poorly predicted by both force fields, implying a requirement for further force field revisions. We further discuss the differences predicted by each RNA force field. Finally, we show that discrete path sampling (DPS) calculations can provide valuable information and complement the MD simulations. We propose the use of experimental thermodynamics data for RNA DNMPs as benchmarks for testing RNA force fields.

High-throughput single-molecule quantification of individual base stacking energies in nucleic acids

“…Force fields for nucleic acids require precise and separate calibration of base-stacking and base-pairing energies for all nucleotide combinations, which is particularly difficult to compare with experimental studies that typically combine these in terms of a "nearest-neighbor" thermodynamic model [48][49][50][51] . Previous attempts 52 roughly recalibrated only purine/purine and pyrimidine/pyrimidine based on limited experimental data from dinucleotide stacking measurements, which also present challenges in geometrically defining stacking in the absence of the double helix 53 . Our base stacking results provide accurate thermodynamic measurements of single-base stacking for all possible nucleobase combinations in the context of a double helix, which uniquely enables direct calibration of MD force fields in a sequence-specific manner.…”

High-throughput single-molecule quantification of individual base stacking energies in nucleic acids

“…(l) Molecular dynamics simulations of base stacking interactions with different force fields, (m) Simulation scheme showing two 3-mer duplexes with A|A in red and T|T in blue, in the initial (stacked) and the final (unstacked) confirmation. The pulling force is applied on the C1’ atoms of the T|T stacked pair, orthogonal to the base-pairs (n) Potential of mean force (PMF) of the A|A-T|T construct as a function of the distance between the pull groups (ξ), for the Amber99-Chen-Garcia [50] and parmbsc1 [52] force-fields. (o) Designs of base stacking interactions tested in MD simulation (p) Free energy of stacking (ΔG stack ) as calculated from the simulations compared to experimentally determined values (values added from Table 1).…”

“…Force fields for nucleic acids require precise and separate calibration of base-stacking and base-pairing energies for all nucleotide combinations, which is particularly difficult to compare with experimental studies that typically combine these in terms of a "nearest-neighbor" thermodynamic model [47][48][49][50]. Previous attempts [51] roughly recalibrated only purine/purine and pyrimidine/pyrimidine based on limited experimental data from dinucleotide stacking measurements, which also present challenges in geometrically defining stacking in the absence of the double helix [52]. Our base stacking results provide accurate thermodynamic measurements of single-base stacking for all possible nucleobase combinations in the context of a double helix, which uniquely enables direct calibration of MD force fields in a sequencespecific manner.…”

Toward Force Fields with Improved Base Stacking Descriptions

“…44 Criterion (3) was evaluated using our previously published rigid-body protocol. 32 Recently, a new criterion for base stacking was introduced by Taghavi et al 45 The proposed definition correlates better with experimental data for RNA DNMPs. However, it is not clear that this also means that the definition per se is better, it might even be worse and may cancel force field errors.…”