Specific Noncovalent Interactions Research Articles

Trikafta rescues F508del-CFTR by tightening specific phosphorylation-dependent interdomain interactions.

Trikafta modulators have been approved by the FDA to treat the most common cystic fibrosis- causing mutation F508del CFTR. However, the molecular action mechanisms of these modulators are still unknown. Following the identification of the gating center in CFTR, this study further revealed that the specific noncovalent interactions of the phosphorylated S813 site with cytoplasmic loops 1 and 4 and N-/C- terminal tails of TMD1 upon Trikafta-triggered tight TMD1- TMD2 interactions at the gating center play a pivotal role in rescuing the primary gating defect and then the thermal defect of F508del CFTR. Trikafta strengthened TMD1-TMD2 interactions at the gating center of ΔF508-CFTR Tight TMD1-TMD2 interactions allowed specific interactions of the R domain with the ICL1- ICL4 interface and the N-/C- terminal tails of TMD1 Subsequently, the C-terminal region was released from NBD1 for tight ATP-dependent NBD1-NBD2 dimerization, stabilizing NBD1 of ΔF508-CFTR.

Non-Covalent Interactions of Lotus Root Polysaccharides and Polyphenols and their Regulatory Mechanism on Macrophage Functions.

Despite the interaction between polyphenols and polysaccharides in food products, their specific non-covalent interactions and effects on macrophage functions are not well understood. Therefore, the interaction and mechanism of purified lotus root polysaccharide (PLRP) with polyphenols, and the regulatory mechanisms of the PLRP-polyphenol complex on the macrophage functionals were studied. By combining ferulic acid (FA) and chlorogenic acid (CHA) with PLRP, the complexes PLRP-FA, PLRP-CHA and the physical mixtures PLRP&FA and PLRP&CHA were prepared, where their mass ratios of polyphenols to PLRP were 143.97 and 601.67 mg g-1. Nuclear magnetic resonance (NMR), Fourier-transform infrared (FTIR), Ultraviolet (UV), and Transmission electron microscopy (TEM) analyses confirmed that PLRP and polyphenols may engage in non-covalent interactions via hydrogen bonds and hydrophobic interactions. We confirmed that non-covalent interactions led to high molecular weight, dense complexes. Both PLRP and its polyphenol complexes stimulated NO production by macrophages to varying degrees without exacerbating lipopolysaccharide-induced inflammatory responses. PLRP and PLRP-polyphenol complexes repaired cells with impaired antioxidant capacity, depending on doses. Those results indicated that after the combination of lotus root polysaccharide and polyphenol, the molecular weight and conformation changed significantly, which influenced the biological activity. RNA-seq analysis suggested that the regulatory mechanism of PLRP-polyphenol complex in macrophages may mainly involve oxidative phosphorylation, FoxO, TNF, IL-17, MAPK, NF-kappa B, and other signaling pathways. This study investigated the effects of polyphenol binding on the physicochemical characteristics and functional activities of polysaccharides, which provided references for the development of polysaccharide functional products and the control of nutritional quality.

Electrostatic Surface Potentials and Chalcogen-Bonding Motifs of Substituted 2,1,3-Benzoselenadiazoles Probed via 77Se Solid-State NMR Spectroscopy.

Chalcogen bonds (ChB) are moderately strong, directional, and specific non-covalent interactions that have garnered substantial interest over the last decades. Specifically, the presence of two σ-holes offers great potential for crystal engineering, catalysis, biochemistry, and molecular sensing. However, ChB applications are currently hampered by a lack of methods to characterize and control chalcogen bonds. Here, we report on the influence of various substituents (halogens, cyano, and methyl groups) on the observed self-complementary ChB networks of 2,1,3-benzoselenadiazoles. From molecular electrostatic potential calculations, we show that the electrostatic surface potentials (ESP) of the σ-holes on selenium are largely influenced by the electron-withdrawing character of these substituents. Structural analyses via X-ray diffraction reveal a variety of ChB geometries and binding modes that are rationalized via the computed ESP maps, although the structure of 5,6-dimethyl-2,1,3-benzoselenadiazole also demonstrates the influence of steric interactions. 77Se solid-state magic-angle spinning NMR spectroscopy, in particular the analysis of the selenium chemical shift tensors, is found to be an effective probe able to characterize both structural and electrostatic features of these self-complementary ChB systems. We find a positive correlation between the value of the ESP maxima at the σ-holes and the experimentally measured 77Se isotropic chemical shift, while the skew of the chemical shift tensor is established as a metric which is reflective of the ChB binding motif.

Redox-Responsive Halogen Bonding as a Highly Selective Interaction for Electrochemical Separations.

Leveraging specific noncovalent interactions can broaden the mechanims for selective electrochemical separations beyond solely electrostatic interactions. Here, we explore redox-responsive halogen bonding (XB) for selective electrosorption in nonaqueous media, by taking advantage of directional interactions of XB alongisde a cooperative and synergistic ferrocene redox-center. We designed and evaluated a new redox-active XB donor polymer, poly(5-iodo-4-ferrocenyl-1-(4-vinylbenzyl)-1H-1,2,3-triazole) (P(FcTS-I)), for the electrochemically switchable binding and release of target organic and inorganic ions at a heterogeneous interface. Under applied potential, the oxidized ferrocene amplifies the halogen binding site, leading to significantly enhanced uptake and selectivity towards key inorganic and organic species, including chloride, bisulfate, and benzenesulfonate, compared to the open-circuit potential or the hydrogen bonding donor analog. Density functional theory calculations, as well as spectroscopic analysis, offer mechanistic insight into the degree of amplification of σ-holes at a molecular level, with selectivity modulated by charge transfer and dispersion interactions. Our work highlights the potential of XB in selective electrosorption by uniquely leveraging noncovalent interactions for redox-mediated electrochemical separations.

Supra-biological performance of immobilized enzymes enabled by chaperone-like specific non-covalent interactions

Designing complex synthetic materials for enzyme immobilization could unlock the utility of biocatalysis in extreme environments. Inspired by biology, we investigate the use of random copolymer brushes as dynamic immobilization supports that enable supra-biological catalytic performance of immobilized enzymes. This is demonstrated by immobilizing Bacillus subtilis Lipase A on brushes doped with aromatic moieties, which can interact with the lipase through multiple non-covalent interactions. Incorporation of aromatic groups leads to a 50 °C increase in the optimal temperature of lipase, as well as a 50-fold enhancement in enzyme activity. Single-molecule FRET studies reveal that these supports act as biomimetic chaperones by promoting enzyme refolding and stabilizing the enzyme’s folded and catalytically active state. This effect is diminished when aromatic residues are mutated out, suggesting the importance of π-stacking and π-cation interactions for stabilization. Our results underscore how unexplored enzyme-support interactions may enable uncharted opportunities for using enzymes in industrial biotransformations.

Catalyst-Controlled Intermolecular Homobenzylic C(sp3)-H Amination for the Synthesis of β-Arylethylamines.

The combination of a tailored sulfamate with a C4-symmetrical rhodium(II) tetracarboxylate allows to uncover a selective intermolecular amination of unactivated homobenzylic C(sp3)-H bonds. The reaction has a broad scope (>30 examples) and proceeds with a high level of regioselectivity with homobenzylic/benzylic ratio of up to 35:1, thereby providing a direct access to β-arylethylamines that are of utmost interest in medicinal chemistry. Computational investigations evidenced a concerted mechanism, involving an asynchronous transition state. Based on a combined activation strain model and energy decomposition analysis, the regioselectivity of the reaction was found to rely mainly on the degree of orbital interaction between the [Rh2]-nitrene and the C-H bond. The latter is facilitated at the homobenzylic position due to the establishment of specific noncovalent interactions within the catalytic pocket.

Atomistic-Level Effects of Noncovalent Interactions and Crystalline Packing for Organic Material Structural Integrity upon Exposure to Gamma Radiation.

Developing an atomistic understanding of ionizing radiation induced changes to organic materials is necessary for intentional design of greener and more sustainable materials for radiation shielding and detection. Cocrystals are promising for these purposes, but a detailed understanding of how the specific intermolecular interactions within the lattice upon exposure to radiation affect the structural stability of the organic crystalline material is unknown. This study evaluates atomistic-level effects of γ radiation on both single- and multicomponent organic crystalline materials and how specific noncovalent interactions and packing within the crystalline lattice enhance structural stability. Dose studies were performed on all crystalline systems and evaluated via experimental and computational methods. Changes in crystallinity were evaluated by p-XRD and free radical formation was analyzed via EPR spectroscopy. Type of intermolecular interactions and packing within the crystal lattice was delineated and related to the specific free radical species formed and the structural integrity of each material. Periodic DFT and HOMO-LUMO surface mapping calculations provided atomistic-level identifications of the most probable sites for the radicals formed upon exposure to γ radiation and relate intermolecular interactions and molecular packing within the crystalline lattice to experimental results.

Non-simple flow behavior in a polar van der Waals liquid: Structural relaxation under scrutiny.

The non-exponential character of the structural relaxation is considered one of the hallmarks of the glassy dynamics, and in this context, the relatively narrow shape observed by dielectric techniques for polar glass formers has attracted the attention of the community for long time. This work addresses the phenomenology and role of specific non-covalent interactions in the structural relaxation of glass-forming liquids by the study of polar tributyl phosphate. We show that dipole interactions can couple to shear stress and modify the flow behavior, preventing the occurrence of the simple liquid behavior. We discuss our findings in the general framework of glassy dynamics and the role of intermolecular interactions.

Visualizing Cardiolipin In Situ with HKCL-1M, a Highly Selective and Sensitive Fluorescent Probe.

Reliable probing of cardiolipin (CL) content in dynamic cellular milieux presents significant challenges and great opportunities for understanding mitochondria-related diseases, including cancer, neurodegeneration, and diabetes mellitus. In intact respiring cells, selectivity and sensitivity for CL detection are technically demanding due to structural similarities among phospholipids and compartmental secludedness of the inner mitochondrial membrane. Here, we report a novel "turn-on" fluorescent probe HKCL-1M for detecting CL in situ. HKCL-1M displays outstanding sensitivity and selectivity toward CL through specific noncovalent interactions. In live-cell imaging, its hydrolyzed product HKCL-1 efficiently retained itself in intact cells independent of mitochondrial membrane potential (Δψm). The probe robustly co-localizes with mitochondria and outperforms 10-N-nonyl acridine orange (NAO) and Δψm-dependent dyes with superior photostability and negligible phototoxicity. Our work thus opens up new opportunities for studying mitochondrial biology through efficient and reliable visualization of CL in situ.

Chiral and Morphological Anisotropy of Supramolecular Polymers Shaped by a Singularity in Solvent Composition.

Understanding the role of solvent in translating molecular anisotropy to supramolecular polymers is in the early stages. A solvent's influence on the strength of different noncovalent interactions can explain anisotropic growth in some cases, but its effect on cooperative processes, particularly in mixed solvents, remains obscure. We report the self-assembly of a series of chiral perylene bisimides in water-cosolvent mixtures, and the results highlight the fascinating influence of solvent-solute interactions on supramolecular anisotropy, both chiral and morphological. The initial assembly is agnostic to solvent composition, resulting in weakly chiral, spherical nanostructures. In an extremely narrow solvent composition range, the nanospheres transform into long, prominently chiral supramolecular polymers. Further, chirality can be fully reversed by changing the good (achiral) cosolvent. We elucidate how solvent modulates specific noncovalent interactions and governs the kinetics and thermodynamics of key processes, such as spontaneous phase segregation, secondary nucleation, and cooperative growth. In the context of supramolecular polymerization, our results encourage one to steer the focus away from the physical attributes of a solvent (polarity, phase diagram, etc.) and toward the complexities of solvent-solute interactions.

Hydrophobically modified complex coacervates for designing aqueous pressure-sensitive adhesives.

The rheology of complex coacervates can be elegantly tuned via the design and control of specific non-covalent hydrophobic interactions between the complexed polymer chains. The well-controlled balance between elasticity and energy dissipation makes complex coacervates perfect candidates for pressure-sensitive adhesives (PSAs). In this work, the polyanion poly(3-sulfopropyl methacrylate) (PSPMA) and the polycation quaternized poly(4-vinylpyridine) (QP4VP) were used to prepare complex coacervates in water. Progressive increase of hydrophobicity is introduced to the polyanion via partial deprotection of the protected precursor. Hence, the polymer chains in the complex coacervates can interact via both electrostatic (controlled by the amount of salt) and hydrophobic (controlled by the deprotection degree) interactions. It was observed that: (i) a rheological time-salt-hydrophobicity superposition principle is applicable, and can be used as a predictive tool for rheology, (ii) the slowdown of the stress relaxation dynamics, due to the increase of hydrophobic stickers (lower deprotection degree), can be captured by the sticky-Rouse model, and (iii) the systematic variation of hydrophobic stickers, amount of salt, and molecular weight of the polymers, enables the identification of optimizing parameters to design aqueous PSA systems. The presented results offer new pathways to control the rheology of complex coacervates and their applicability as PSAs.

Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment.

Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.

Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State

Reactions between Zn(II) nitrate, pentaiodobenzoic acid (HPIBA) and different pyridines in dimethylformamide (DMF) result in the formation of the heteroleptic neutral complexes [Zn(3,5-MePy)2PIBA2] (1) and [Zn(DMF)3(NO3)PIBA] (2). Both compounds were isolated in pure form, as shown by the PXRD data. The features of specific non-covalent interactions involving halogen atoms (halogen bonding) were examined by means of DFT calculations (QTAIM analysis and the estimation of corresponding energies).

Implications of Coexistent Halogen and Hydrogen Bonds in Amorphous Solid Dispersions on Drug Solubility, Miscibility, and Mobility.

Specific noncovalent drug-polymer interactions were analytically identified using Raman and Fourier transform infrared spectroscopy for amorphous solid dispersions (ASD) formed between either chlorpropamide or tolbutamide and polyvinylpyrrolidone vinyl acetate random copolymer (PVPVA). Spectral changes in the C-Cl stretching vibrations due to changes in the electronic environment of the Cl atom confirmed halogen bond formation in chlorpropamide-PVPVA ASDs, the extent of which was established to be inversely related to the concentration of the drug using 2D correlation spectroscopy analysis. Hydrogen bonding between the secondary amide of each drug and the pyrrolidone carbonyl of the copolymer was also confirmed in all dispersions. Implications of coexistent interactions were investigated for drug-polymer solubility, mixing free energy, and molecular mobility relative to tolbutamide, which only formed hydrogen bonds with PVPVA. Chlorpropamide had a higher solubility, a larger negative mixing free energy, and lower mobility in PVPVA relative to tolbutamide. These thermodynamic and kinetic differences demonstrate the significance of halogen bond formation even when hydrogen bonding is present.

Selectins and their involvement in the pathogenesis of cardiovascular diseases

The review presents current data on the structure and functional role of cell adhesion molecules belonging to the selectin family (selectins P, L and E), and their involvement in the pathogenesis of cardiovascular diseases. On the one hand, intercellular adhesion molecules of the vascular wall endothelium, platelets and leukocytes are an important link in the processes of vasculogenesis, development and regeneration of the vascular system. On the other hand, these molecules participate in the earliest stages of endothelial dysfunction with the subsequent development of pathology. For this reason, figuring out the mechanisms of activity of this group of molecules is very important for understanding the molecular basis of the cardiovascular diseases pathogenesis. The adhesion of molecules, both between cells and between cells and a component of the extracellular matrix, is the most important stage of physiological and biochemical processes. According to present knowledge, five classes of intercellular adhesion molecules are known: integrins, cadherins, immunoglobulins (including nectins), selectins and addressins. All of them are bonded to a cytoplasmic membrane and provide the interaction of cells with each other. Some of them are transmembrane and associated with the cytoskeleton of the cell. On the cell surface, intercellular adhesion molecules can be located in clusters, forming multipoint binding sites and thereby determining the degree of avidity. One of the most significant functions of selectins is participation in the initial stage of the leukocyte adhesion cascade, which results in their binding to the endothelium, rolling and further extravasation into tissues. The first stage of this process is mediated by specific non-covalent interactions between selectins and their glycan ligands, with the glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains one of the main strategies aimed at developing new methods of treating immune, inflammatory and oncological diseases.

Peptidic Scaffolds Enable Rapid and Multivariate Secondary Sphere Evolution for an Abiotic Metallocatalyst

Metalloenzymes have benefited from the iterative process of evolution to achieve the precise arrangements of secondary sphere non-covalent interactions that enhance metal-centered catalysis. Iterative synthesis of scaffolds that display complex secondary sphere elements in abiotic systems can be highly challenging and time-intensive. To overcome this synthetic bottleneck, we developed a highly modular and rapid synthetic strategy, leveraging the efficiency of solid-phase peptide synthesis and conformational control afforded by non-canonical residues to construct a ligand platform displaying up to four unique residues of varying electronics and sterics in the secondary coordination sphere. As a proof-of-concept that peptidic secondary sphere can cooperate with the metal complex, we applied this scaffold to a well-known, modestly active C-H oxidizing Fe catalyst to evolve specific non-covalent interactions that is more than double its catalytic activity. Solution-state NMR structures of several catalyst variants suggest that higher activity is correlated with a hydrophobic pocket above the Fe center that may enhance the formation of a catalyst-substrate complex. Above all, we show that peptides are a convenient, highly modular, and structurally defined ligand platform for creating secondary coordination spheres that comprise multiple, diverse functional groups.

Metal-Organic Frameworks as Unique Platforms to Gain Insight of σ-Hole Interactions for the Removal of Organic Dyes from Aquatic Ecosystems.

The combination of high crystallinity and rich host‐guest chemistry in metal‐organic frameworks (MOFs), have situated them in an advantageous position, with respect to traditional porous materials, to gain insight on specific weak noncovalent supramolecular interactions. In particular, sulfur σ‐hole interactions are known to play a key role in the biological activity of living beings as well as on relevant molecular recognitions processes. However, so far, they have been barely explored. Here, we describe both how the combination of the intrinsic features of MOFs, especially the possibility of using single‐crystal X‐ray crystallography (SCXRD), can be an extremely valuable tool to gain insight on sulfur σ‐hole interactions, and how their rational exploitation can be enormously useful in the efficient removal of harmful organic molecules from aquatic ecosystems. Thus, we have used a MOF, prepared from the amino acid L‐methionine and possessing channels decorated with −CH2CH2SCH3 thioalkyl chains, to remove a family of organic dyes at very low concentrations (10 ppm) from water. This MOF is able to efficiently capture the four dyes in a very fast manner, reaching within five minutes nearly the maximum removal. Remarkably, the crystal structure of the different organic dyes within MOFs channels could be determined by SCXRD. This has enabled us to directly visualize the important role sulfur σ‐hole interactions play on the removal of organic dyes from aqueous solutions, representing one of the first studies on the rational exploitation of σ‐hole interactions for water remediation.

Binary and Ternary Complexes of Cucurbit[8]uril with Tryptophan, Phenylalanine, and Tyrosine: A Computational Study.

Selective binding of amino acids, peptides, and proteins by synthetic molecules and elucidation of the geometry and dynamics of the resulting complexes and their strengths are active areas of contemporary research. In recent work, we analyzed via molecular dynamics (MD) simulations the complexes formed between cucurbit[7]uril (CB7) and three aromatic amino acids: tryptophan (W), phenylalanine (F), and tyrosine (Y). Herein, we continue this line of research by performing MD simulations lasting 100 ns to investigate the formation, stabilities, binding modes, dynamics, and specific host–guest noncovalent interactions contributing to the formation of the binary (1:1) and ternary (2:1) complexes in aqueous solution between W, F, and Y amino acids and cucurbit[8]uril (CB8). All complexes were found to be stable, with the binding in each complex dominated by one mode (except for the F–CB8 complex, which had two) characterized by encapsulation of the aromatic side chains of the amino acids within the cavity of CB8 and the exclusion of their ammonium and carboxylate groups. Using the molecular mechanics/Poisson–Boltzmann surface area method to estimate the individual contributions to the overall free energies of binding, results revealed that the key role is played by the amino acid side chains in stabilizing the complexes through their favorable van der Waals interactions with the CB8 cavity and the importance of favorable electrostatic interactions between the carbonyl portal of CB8 and the ammonium group of the amino acid. Visual analysis of structures of the ternary complexes indicated the presence of π–π stacking between the aromatic side chains of the included amino acids. The insights provided by this work may be of value for further efforts aiming to employ the recognition properties of CB8 toward amino acids in applications requiring more elaborate recognition of short peptides and proteins.

Multivalent Noncovalent Interfacing and Cross-Linking of Supramolecular Tubes.

Natural supramolecular filaments have the ability to cross-link with each other and to interface with the cellular membrane via biomolecular noncovalent interactions. This behavior allows them to form complex networks within as well as outside the cell, i.e., the cytoskeleton and the extracellular matrix, respectively. The potential of artificial supramolecular polymers to interact through specific noncovalent interactions has so far only seen limited exploration due to the dynamic nature of supramolecular interactions. Here, a system of synthetic supramolecular tubes that cross-link forming supramolecular networks, and at the same time bind to biomimetic surfaces by the aid of noncovalent streptavidin-biotin linkages, is demonstrated. The architecture of the networks can be engineered by controlling the density of the biotin moiety at the exterior of the tubes as well as by the concentration of the streptavidin. The presented strategy provides a pathway for designing adjustable artificial supramolecular superstructures, which can potentially yield more complex biomimetic adaptive materials.

Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands.

Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the arginine-bound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.