Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch

Magnesium Regulates RNA Ring Dynamics and Folding in Subgenomic Flaviviral RNA

Mosquito-borne flaviviruses including dengue, Zika, yellow fever, and regional encephalitis produce a large amount of short subgenomic flaviviral RNAs during infection. A segment of these RNAs named as xrRNA1 features a multi-pseudoknot (PK)-associated structure, which resists the host cell enzyme (XRN1) from degrading the viral RNA. We investigate how this long-range RNA PK folds in the presence of counterions, specifically in a mix of monovalent (K+) and divalent (Mg2+) salts at physiological concentrations. In this study, we use extensive explicit solvent molecular dynamics (MD) simulations to characterize the RNA ion environment of the folded RNA conformation, as determined by the crystal structure. This allowed us to identify the precise locations of various coordinated RNA-Mg2+ interactions, including inner-sphere/chelated and outer-sphere coordinated Mg2+. Given that RNA folding involves large-scale conformational changes, making it challenging to explore through classical MD simulations, we investigate the folding mechanism of xrRNA1 using an all-atom structure-based RNA model with a hybrid implicit-explicit treatment of the ion environment via the dynamic counterion condensation model, both with and without physiological Mg2+ concentration. The study reveals potential folding pathways for this xrRNA1, which is consistent with the results obtained from optical tweezer experiments. The equilibrium and free energy simulations both capture a dynamic equilibrium between the ring-open and ring-close states of the RNA, driven by a long-range PK interaction. Free energy calculations reveal that with the addition of Mg2+ ions, the equilibrium shifts more toward the ring-close state. A detailed analysis of the free energy pathways and ion-mediated contact probability map highlights the critical role of Mg2+ in bridging G50 and A33. This Mg2+-mediated connection helps form the long-range PK which in turn controls the transition between the ring-open and ring-close states. The study underscores the critical role of Mg2+ in the RNA folding transition, highlighting specific locations of Mg2+ contributing to the stabilization of long-range PK connections likely to enhance the robustness of Xrn1 resistance of flaviviral xrRNAs.

RNA's Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events

In the TAR RNA of immunodeficiency viruses, an allosteric communication exists between a distant loop and a bulge. The bulge interacts with the TAT protein vital for transactivating viral RNA, while the loop interacts with cyclin-T1, contingent on TAT binding. Through extensive atomistic and free energy simulations, we investigate TAR-TAT binding in nonpathogenic bovine immunodeficiency virus (BIV) and pathogenic human immunodeficiency virus (HIV). Thermodynamic analysis reveals enthalpically driven binding in BIV and entropically favored binding in HIV. The broader global basin in HIV is attributed to binding-induced loop fluctuation, corroborated by nuclear magnetic resonance (NMR), indicating classical entropic allostery onset. While this loop fluctuation affects the TAT binding affinity, it generates a binding-competent conformation that aids subsequent effector (cyclin-T1) binding. This study underscores how two structurally similar apo-RNA scaffolds adopt distinct conformational selection mechanisms to drive enthalpic and entropic allostery, influencing protein affinity in the signaling cascade.

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.

Dynamic Counterion Condensation Model Decodes Functional Dynamics of RNA Pseudoknot in SARS-CoV-2: Control of Ion-Mediated Pierced Lasso Topology

The programmed frameshifting stimulatory element, a promising drug target for COVID-19 treatment, involves a RNA pseudoknot (PK) structure. This RNA PK facilitates frameshifting, enabling RNA viruses to translate multiple proteins from a single mRNA, which is a key strategy for their rapid evolution. Overcoming the challenges of capturing large-scale structural changes of RNA under the influence of a dynamic counterion environment (K+ and Mg2+), the study extended the applications of a newly developed dynamic counterion condensation (DCC) model. DCC simulations reveal potential folding pathways of this RNA PK, supported by the experimental findings obtained using optical tweezers. The study elucidates the pivotal role of Mg2+ ions in crafting a lasso-like RNA topology, a novel RNA motif that governs dynamic transitions between the ring-opened and ring-closed states of the RNA. The pierced lasso component guided by Mg2+-mediated interactions orchestrates inward and outward motion fine-tuning tension on the slippery segment, a critical factor for optimizing frameshifting efficiency.

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.

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.

Alternative RNA Conformations: Companion or Combatant

RNA molecules, in one form or another, are involved in almost all aspects of cell physiology, as well as in disease development. The diversity of the functional roles of RNA comes from its intrinsic ability to adopt complex secondary and tertiary structures, rivaling the diversity of proteins. The RNA molecules form dynamic ensembles of many interconverting conformations at a timescale of seconds, which is a key for understanding how they execute their cellular functions. Given the crucial role of RNAs in various cellular processes, we need to understand the RNA molecules from a structural perspective. Central to this review are studies aimed at revealing the regulatory role of conformational equilibria in RNA in humans to understand genetic diseases such as cancer and neurodegenerative diseases, as well as in pathogens such as bacteria and viruses so as to understand the progression of infectious diseases. Furthermore, we also summarize the prior studies on the use of RNA structures as platforms for the rational design of small molecules for therapeutic applications.

Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch

Riboswitches normally regulate gene expression through structural changes in response to the specific binding of cellular metabolites or metal ions. Taking add adenine riboswitch as an example, we explore the influences of metal ions (especially for K⁺ and Mg²⁺ ions) on the structure and dynamics of riboswitch aptamer (with and without ligand) by using molecular dynamic (MD) simulations. Our results show that a two-state transition marked by the structural deformation at the connection of J12 and P1 (C_J12-P1) is not only related to the binding of cognate ligands, but also strongly coupled with the change of metal ion environments. Moreover, the deformation of the structure at C_J12-P1 can be transmitted to P1 directly connected to the expression platform in multiple ways, which will affect the structure and stability of P1 to varying degrees, and finally change the regulation state of this riboswitch.

Molecular dynamic simulations are employed to assess the influence of metal ions on riboswitch structure and dynamics, suggesting a conformational control of riboswitch aptamers by metal ions before ligand binding.

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⁺.

Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts

Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure-function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed collective variables and metadynamics efforts, to establish a simple metadynamics protocol, which utilizes only one collective variable, based on multiple tertiary contacts, to characterize the underlying free energy landscape of any RNA molecule. We develop a modified collective variable, the tertiary contacts distance (Q_TC), which can probe the formation and breakage of all or selectively chosen tertiary contacts of the RNA. The SAM-I riboswitch in the presence of three ionic and substrate conditions was investigated and validated against the structure ensemble previously generated using SAXS experiments. This efficient and easy to implement all-atom MD simulation based approach incorporating metadynamics to study RNA conformational dynamics can also be transferred to any other type of biomolecule.

Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments

Computational coarse-grained models play a fundamental role as a research tool in protein folding, and they are important in bridging theory and experiments. Folding mechanisms are generally discussed using the energy landscape framework, which is well mapped within a class of simplified structure-based models. In this chapter, simplified computer models are discussed with special focus on structure-based ones.

Exploring the energy landscape of a SAM-I riboswitch

SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg²⁺ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg²⁺ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription.

Getting to the bottom of lncRNA mechanism: structure-function relationships

While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.

Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation

Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions. A mechanism is proposed for the role of experimentally discovered site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers in bacteria. This mechanism is observed with atomistic simulations performed in a physiological mixed salt environment at a high temperature. The simulations were validated with phosphorothioate interference mapping experiments that help to identify crucial inner-sphere Mg²⁺ sites prescribing an appropriate initial distribution of inner- and outer-sphere magnesium ions to maintain a physiological ion concentration of monovalent and divalent salts. A concerted role of two chelated magnesium ions is newly discovered since the presence of both supports the formation of the pseudoknot. This constitutes a logical AND gate. The absence of any of these magnesium ions instigates the dissociation of long-range pseudoknot interaction exposing the inner core of the RNA. A base triple is the epicenter of the magnesium chelation effect. It allosterically controls RNA pseudoknot by bolstering the direct effect of magnesium chelation in protecting the functional fold of RNA to control ON and OFF transcription switching.

Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection

Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. One switch, called riboswitch N1, is regulated by aminoglycosides such as neomycin. Nucleobase mutations in the apical loop, although distant from the binding pocket, significantly affect neomycin affinity and riboswitch regulatory efficiency. To explain this influence, we conducted molecular dynamics simulations using generalized replica exchange with solute tempering (gREST). Translation assay of a reporter protein in a yeast system shows that mutating A17 to G in the riboswitch apical loop reduces 6-fold the translation regulation efficiency of the mutant. Indeed, simulations of the unbound riboswitch show that G17 frequently stacks with base 7, while base 8 is stabilized towards the binding site in a way that it may interfere with the conformational selection mechanism and decrease riboswitch regulatory activity. In the riboswitch complexes, this single-point A to G mutation disrupts a strong hydrogen bond between nucleotides 5 and 17 and, instead, a new hydrogen bond between residue 17 and neomycin is created. This change forces neomycin to occupy a slightly shifted position in the binding pocket, which increases neomycin flexibility. Our simulations of the U14C mutation suggest that the riboswitch complex with neomycin is more stable if cytosine 14 is protonated. A hydrogen bond between the RNA phosphate and protonated cytosine appears as the stabilizing factor. Also, based on the cell-free translation assay and isothermal titration calorimetry experiments, mutations of nucleotides 14 and 15 affect only slightly the riboswitch ability to bind the ligand and its activity. Indeed, the simulation of the unbound U15A mutant suggests conformations preformed for ligand binding, which may explain slightly higher regulatory activity of this mutant. Overall, our results corroborate the in vivo and in vitro experiments on the N1 riboswitch-neomycin system, detail the relationship between nucleobase mutations and RNA dynamics, and reveal the conformations playing the major role in the conformational selection mechanism.

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.