Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg2+). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg2+ and ligand also facilitate a more compact structure in the three-way junction region.

Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods

RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.

What is allosteric regulation? Exploring the exceptions that prove the rule!

"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.

Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering

Engineering in vitro selected RNA aptamers into in vivo functional riboswitches represents a long-standing challenge in molecular biology. The highly specific aptamer domain of the riboswitch undergoes a conformational adjustment in response to ligand sensing, which in turn exerts the regulatory function. Besides essential factors like structural complexity and ligand binding kinetics, the active role of magnesium ions in stabilizing RNA tertiary structures and assisting in ligand binding can be a vital criterion. We present spectroscopic studies on the magnesium ion-driven folding of the Tetracycline binding aptamer. Using fluorescent labels, the aptamer pre-folding and subsequent ligand binding is monitored by magnesium titration experiments and time-resolved stopped-flow measurements. A minimum concentration of 0.5 mM magnesium is required to fold into a magnesium ion-stabilized binding-competent state with a preformed binding pocket. Tetracycline binding causes a pronounced conformational change that results in the establishment of the triple helix core motif, and that further propagates towards the closing stem. By a dynamic acquisition of magnesium ions, a kink motif is formed at the intersection of the triple helix and closing stem regions. This ultimately entails a stabilization of the closing stem which is discussed as a key element in the regulatory function of the Tetracycline aptamer.

Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core

Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer surface and complex core both are predominately populated by phosphate groups loosely sequestering bases in the intermediate layers. A number of helical junctions maintain the RNA core and its nano-water-pool. While the folding of RNA is manifested by its counterion environment composed of mixed mono- and divalent salts, the concerted role of ion and water in maintaining an RNA fold is yet to be explored. In this work, detailed atomistic simulations of SAM-I and Add Adenine riboswitch aptamers, and subgenomic flavivirus RNA (sfRNA) have been performed in a physiological mixed mono- and divalent salt environment. All three RNA systems have compact folds with a core diameter of range 1-1.7 nm. The spatiotemporal heterogeneity of RNA hydration was probed in a layer-wise manner by distinguishing the core, the intermediate, and the outer layers. The layer-wise decomposition of hydrogen bonds and collective single-particle reorientational dynamics reveal a nonmonotonic relaxation pattern with the slowest relaxation observed at the intermediate layers that involves functionally important tertiary motifs. The slowness of this intermediate layer is attributed to two types of long-resident water molecules: (i) water from ion-hydration layers and (ii) structurally trapped water (distant from ions). The relaxation kinetics of the core and the surface water essentially exposed to the phosphate groups show well-separated time scales from the intermediate layers. In the slow intermediate layers, site-specific ions and water control the functional dynamics of important RNA motifs like kink-turn, observed in different structure-probing experiments. Most interestingly, we find that as the size of the RNA core increases (SAM1 core < sfRNAcore < Add adenine core), its hydration tends to show faster relaxation. The hierarchical hydration and the layer-wise base-phosphate composition uniquely portray the globular RNA to act like a soft vesicle with a quasi-dynamic nano-water-pool at its core.

Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg2+ thus plays vital roles in SAM/SAH riboswitch function.

Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling

Metal ions, particularly magnesium ions (Mg²⁺), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias toward the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg²⁺-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twister ribozyme. GCMC is used to sample diverse ion distributions around the RNA with deep learning applied to iteratively generate system-specific reaction coordinates to maximize conformational sampling during metadynamics simulations. Results from 6 μs simulations performed on 9 individual systems indicate that Mg²⁺ ions play a crucial role in stabilizing the three-dimensional (3D) structure of the RNA by stabilizing specific interactions of phosphate groups or phosphate groups and bases of neighboring nucleotides. While many phosphates are accessible to interactions with Mg²⁺, it is observed that multiple, specific interactions are required to sample conformations close to the folded state; coordination of Mg²⁺ at individual specific sites facilitates sampling of folded conformations though unfolding ultimately occurs. It is only when multiple specific interactions occur, including the presence of specific inner-shell cation interactions linking two nucleotides, that conformations close to the folded state are stable. While many of the identified Mg²⁺ interactions are observed in the X-ray crystal structure of Twister, the present study suggests two new Mg²⁺ ion sites in the Twister ribozyme that contribute to stabilization. In addition, specific interactions with Mg²⁺ are observed that destabilize the local RNA structure, a process that may facilitate the folding of RNA into its correct structure.

Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg 2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) identified over 10 inner-shell Mg 2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminish the selectivity between SAM and SAH. One Mg 2+ ion unique to the apo form maintains the Shine-Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg 2+ thus plays vital roles in SAM/SAH riboswitch function.

Dynamic effects of the spine of hydrated magnesium on viral RNA pseudoknot structure

In the cellular environment, a viral RNA Pseudoknot (PK) structure is responsive to its prevailing ion atmosphere created by a mixture of monovalent and divalent cations. We investigate the influence of such a mixed-salt environment on RNA-PK structure at an atomic resolution through three sets of 1.5 μs explicit solvent molecular dynamics (MD) simulations and also by building a dynamic counterion-condensation (DCC) model at varying divalent Mg²⁺ concentrations. The DCC model includes explicit interaction of the ligand and adjacent chelated Mg²⁺ by extending the recently developed generalized Manning condensation model. Its implementation within an all-atom structure-based molecular dynamics framework bolsters its opportunity to explore large-length scale and long-timescale phenomena associated with complex RNA systems immersed in its dynamic ion environment. In the present case of RNA-PK, both explicit MD and DCC simulations reveal a spine of hydrated-Mg²⁺ to induce stem-I and stem-II closure where the minor groove between these stems is akin to breathing. Mg²⁺ mediated minor-groove narrowing is coupled with local base-flipping dynamics of a base triple and quadruple, changing the stem structure of such RNA. Contrary to the conversational view of the indispensable need for Mg²⁺ for the tertiary structure of RNA, the study warns about the plausible detrimental effect of specific Mg²⁺-phosphate interactions on the RNA-PK structure beyond a certain concentration of Mg²⁺.

Visualizing RNA Structures by SAXS-Driven MD Simulations

The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg²⁺ cations stabilizes the compact state. The absence of Mg²⁺ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.