Dynamical Transition and Heterogeneous Hydration Dynamics in RNA

TL;DR

This study uses molecular dynamics simulations to reveal that hydration water around RNA exhibits complex, heterogeneous dynamics with slow relaxation times, which are crucial for RNA's functional flexibility and response to cellular signals.

Contribution

It provides detailed insights into the heterogeneous and glass-like hydration dynamics of RNA surfaces and their role in RNA's functional behavior, highlighting a universal transition temperature.

Findings

Hydration water exhibits slow, heterogeneous dynamics with long hydrogen bond lifetimes.

RNA undergoes a dynamic transition at around 200 K linked to hydration changes.

Hydration dynamics are highly temperature-dependent and exhibit glass-like behavior.

Abstract

Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed molecular dynamics simulations at various temperatures of purine (adenine)- and preQ$_1$ sensing riboswitch aptamers, we show that water molecules in the vicinity of RNAs undergo complex dynamics depending on the local structures of the RNAs. The overall lifetimes of hydrogen bonds (HBs) of surface bound waters are more than at least 1-2 orders of magnitude longer than bulk water. Slow hydration dynamics, revealed in non-Arrhenius behavior of the relaxation time, arises from high activation barriers to break water hydrogen bonds with a nucleotide and by reduced diffusion of water. The relaxation kinetics at specific locations in the two RNAs show a broad spectrum of time scales reminiscent of glass-like behavior, suggesting that the hydration dynamics is highly heterogeneous. Both RNAs undergo dynamic transition at $T = T_D \gtrsim 200$ K as assessed by the mean square fluctuation of hydrogen atoms $\langle x^2\rangle$, which undergoes an abrupt harmonic-to-anharmonic transition at $T_D$. The near universal value of $T_D$ found for these RNAs and previously for tRNA is strongly correlated with changes in hydration dynamics as $T$ is altered. Hierarchical dynamics of waters associated with the RNA surface, revealed in the motions of distinct classes of water with well-separated time scales, reflects the heterogeneous local environment on the molecular surface of RNA. At low temperatures slow water dynamics predominates over structural transitions. Our study demonstrates that the complex interplay of dynamics between water and local environment in the RNA structures could be a key determinant of the functional activities of RNA.