# Destabilization of Structured RNAs by OPC and TIP4PD Water Models

## TL;DR

This study shows that the OPC and TIP4PD water models can destabilize structured RNA simulations, causing large-scale unfolding and loss of RNA-protein interactions.

## Contribution

The paper reveals that four-point water models may destabilize RNA tertiary structures in simulations, a previously unexplored issue.

## Key findings

- OPC simulations caused large-scale RNA unfolding and loss of RNA-protein interface in three structured RNA systems.
- SPC/E and TIP3P models produced stable simulations for the same RNA systems.
- OPC and TIP4PD models showed higher H-bonding affinity to RNA, weakening native solute-solute interactions.

## Abstract

The four-point OPC
water model has recently gained a reputation
as the preferred choice for molecular dynamics (MD) simulations of
nucleic acids and proteins, providing more realistic reproduction
of bulk physical properties of water than the older three-point models.
It has been shown to improve, for example, simulations of unstructured
biomolecules such as RNA tetranucleotides or intrinsically disordered
proteins. However, the performance for folded RNA structures was not
specifically explored. Here we present extensive testing of the OPC
water model on three different RNAs with intricate tertiary structures
– the ribosomal L1 stalk RNA-protein protuberance, the mini
tetraloop-tetraloop receptor (miniTTR-6) folded RNA, and the GAAA
tetraloop-tetraloop receptor homodimer. The OPC performance is directly
compared with SPC/E, TIP3P, and OPC3 water models using the OL3 AMBER
RNA force field (FF). We found substantial effect of the water model
on simulation behavior. For all three systems, we observe large-scale
unfolding of the RNA, and even loss of the L1 stalk protein–RNA
interface, when simulated with the OPC. In contrast, the simulations
are entirely stable with the three-point water models. The underlying
cause seems to be the higher affinity of the OPC waters to H-bond
donor and acceptor groups of the RNA, which weakens the native solute–solute
interactions. An identical issue is observed also for the similar
and widely used TIP4PD water model combined with the DES-Amber RNA
FF. Importantly, the structural consequences of these issues may range
from significant structural perturbations to minimal or undetectable
effects, depending on the RNA system. Accordingly, we do not claim
that the imbalance in water–RNA interactions identified here
is a general feature of all RNA molecules. Indeed, simulations of
three additional, less structurally complex RNA systems revealed more
balanced performance, with no observable differences between water
models for the noncanonical 5S rRNA Loop E double helix. However,
certain caution is warranted when using the four-point OPC and TIP4PD
water models for simulations of structured RNAs, particularly those
rich in 2′-OH hydroxyl-based tertiary interactions. For at
least some structured RNA systems, the three-point water models may
provide more stable behavior in combination with current AMBER RNA
force fields.