The ability of trimethylamine N-oxide to resist pressure induced perturbations to water structure

Gut-brain axis and brain health: modulating neuroinflammation, cognitive decline, and neurodegeneration

The microbiota-gut-brain axis is a pivotal medium of crosstalk between the central nervous system (CNS) and the gastrointestinal tract. It is an intricate network of synergistic molecular pathways that exert their effects far beyond their local vicinity and even affect the systemic functioning of the body. The current review explores the involvement of the gut-brain axis (GBA) in the functioning of the nervous system, with a special emphasis on the neurodegeneration, cognitive decline, and neuroinflammation that occur in Alzheimer's disease (AD) and Parkinson's disease (PD). Gut-derived microbial metabolites play an important role in facilitating this interaction. We also highlighted the complex interaction between gut-derived metabolites and CNS processes, demonstrating how microbial dysbiosis might result in clinical disorders. Short-chain fatty acids have neuroprotective properties, whereas branched-chain amino acids, trimethylamine-N-oxide (TMAO), and tryptophan derivatives such as indole have negative effects at high concentrations. Furthermore, we cover pharmaceutical and nonpharmacological approaches for restoring the gut microbial balance and promoting neurological health. We further expanded on nutritional therapies and lifestyle changes, such as the Mediterranean diet and exercise. Next, we focused on food-controlling habits such as caloric restriction and intermittent fasting. Moreover, interventional techniques such as prebiotics, probiotics, and pharmacological medications have also been utilized to modify the GBA. Historical microbiome research from early discoveries to recent studies linking gut health to cognitive and emotional well-being has increased our understanding of the GBA.

Reaction-Based Fluorescence Assays for the Determination of Food Trimethylamine Oxide

Trimethylamine oxide (TMAO), a microbial metabolite commonly found in foods, has been attracting increasing attention as it is associated with the risk of several diseases. Simple and accurate analytical methods are crucial for TMAO study. In the present study, we proposed a chemical reaction-based fluorescence assay for TMAO detection using synthetic small molecular probes. After systematic screening and optimization, the sensitive and selective quantification of TMAO has been achieved based on a fluorescence probe P6 (3-iodopropanyl group modified resorufin). Excellent linearity (R2 = 0.997) was found between 6.25 and 50 μM, and the limit of detection (LOD) was 0.20 μM. Using this method, TMAO levels in several marine fishes and shellfishes have been successfully analyzed. The probe-based assay offers a simple and useful way for TMAO determination. The design is inspired by the unique oxidation reaction between TMAO and halogen, which opens a new perspective in the development of more advanced analytical assays for TMAO in the future.

Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature

In consideration of life in extreme environments, the effects of hydrostatic pressure on proteins at the atomic level have drawn substantial interest. Large deviations of temperature and pressure from ambient conditions can shift the free energy landscape of proteins to reveal otherwise lowly populated structural states and even promote unfolding. We report the crystal structure of the heme-containing peroxidase, cytochrome c peroxidase (CcP) at 1.5 and 3.0 kbar and make comparisons to structures determined at 1.0 bar and cryo-temperatures (100 K). Pressure produces anisotropic changes in CcP, but compressibility plateaus after 1.5 kbar. CcP responds to pressure with volume declines at the periphery of the protein where B-factors are relatively high but maintains nearly intransient core structure, hydrogen bonding interactions and active site channels. Changes in active-site solvation and heme ligation reveal pressure sensitivity to protein-ligand interactions and a potential docking site for the substrate peroxide. Compression at the surface affects neither alternate side-chain conformers nor B-factors. Thus, packing in the core, which resembles a crystalline solid, limits motion and protects the active site, whereas looser packing at the surface preserves side-chain dynamics. These data demonstrate that conformational dynamics and packing densities are not fully correlated in proteins and that encapsulation of cofactors by the polypeptide can provide a precisely structured environment resistant to change across a wide range of physical conditions.

Origin of Pressure Resistance in Deep-Sea Lactate Dehydrogenase

High hydrostatic pressure has a dramatic effect on biochemical systems, as exposure to high pressure can result in structural perturbations ranging from dissociation of protein complexes to complete denaturation. The deep ocean presents an interesting paradox since it is teeming with life despite the high-pressure environment. This is due to evolutionary adaptations in deep-sea organisms, such as amino acid substitutions in their proteins, which aid in resisting the denaturing effects of pressure. However, the physicochemical mechanism by which these substitutions can induce pressure resistance remains unknown. Here, we use molecular dynamics simulations to study pressure-adapted lactate dehydrogenase from the deep-sea abyssal grenadier (Coryphaenoides armatus), in comparison with that of the shallow-water Atlantic cod (Gadus morhua). We examined structural, thermodynamic and volumetric contributions to pressure resistance, and report that the amino acid substitutions result in a decrease in volume of the deep-sea protein accompanied by a decrease in thermodynamic stability of the native protein. Our simulations at high pressure also suggest that differences in compressibility may be important for understanding pressure resistance in deep-sea proteins.

Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations

The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes

Trimethylamine N-oxide (TMAO) as a representative natural osmolyte has received much attention because of its unique properties, including enhancement of hydrogen bonding networks in liquid water and stabilization of three-dimensional structures of proteins in living organisms. As a hydrogen bond maker and/or a protein stabilizer, its hydrated structures and orientation dynamics in aqueous solutions have been investigated by various spectroscopic methods. Particularly, distinct from other natural osmolytes, it has been found that TMAO molecules form complexes with water molecules even at low concentrations, showing extraordinarily long lifetimes and much larger effective dipole moments. In this study, we demonstrated that collective motions of water molecules are closely correlated to TMAO molecules, as revealed by the changes of the librational modes observed in hyper-Raman (HR) spectra in the low-frequency region (<1000 cm-1) for the first time. Based on HR spectra of the TMAO solutions at submolar concentrations, we observed that the librational bands originating from water apparently upshift (∼15 cm-1) upon the addition of TMAO molecules. Compared to the OH stretching band of water showing a negligible downshift (<5 cm-1), the librational bands of water are more sensitive to reflect changes in the hydrogen bonding networks in the TMAO solutions, suggesting formation of transient TMAO-water complexes plays an essential role toward surrounding water molecules in perturbing their librational motions. We expect to provide a supplementary approach to understand that water molecules in TMAO aqueous solutions are strongly affected by TMAO molecules, different from other osmolytes.

Trimethylamine-N-oxide depletes urea in a peptide solvation shell

Trimethylamine-N-oxide (TMAO) and urea are metabolites that are used by some marine animals to maintain their cell volume in a saline environment. Urea is a well-known denaturant, and TMAO is a protective osmolyte that counteracts urea-induced protein denaturation. TMAO also has a general protein-protective effect, for example, it counters pressure-induced protein denaturation in deep-sea fish. These opposing effects on protein stability have been linked to the spatial relationship of TMAO, urea, and protein molecules. It is generally accepted that urea-induced denaturation proceeds through the accumulation of urea at the protein surface and their subsequent interaction. In contrast, it has been suggested that TMAO's protein-stabilizing effects stem from its exclusion from the protein surface, and its ability to deplete urea from protein surfaces; however, these spatial relationships are uncertain. We used neutron diffraction, coupled with structural refinement modeling, to study the spatial associations of TMAO and urea with the tripeptide derivative glycine-proline-glycinamide in aqueous urea, aqueous TMAO, and aqueous urea-TMAO (in the mole ratio 1:2 TMAO:urea). We found that TMAO depleted urea from the peptide's surface and that while TMAO was not excluded from the tripeptide's surface, strong atomic interactions between the peptide and TMAO were limited to hydrogen bond donating peptide groups. We found that the repartition of urea, by TMAO, was associated with preferential TMAO-urea bonding and enhanced urea-water hydrogen bonding, thereby anchoring urea in the bulk solution and depleting urea from the peptide surface.

A novel and efficient electrochemiluminescence sensing strategy for the determination of trimethylamine oxide in seafood

A novel and efficient electrochemiluminescence (ECL) sensing strategy and a solid-state ECL sensor was proposed to detect trimethylamine oxide (TMAO), which is widely presented in marine species and has important physiological functions. TMAO was reduced by Fe(II)-EDTA complex to trimethylamine, acting as coreactant, to amplify the ECL response of the Ru (bpy)32+ system. To improve the detection sensitivity and efficiency, a robust solid-state ECL probe was prepared and a flow injection ECL detection system was established with a specially designed flow ECL unit, under the excitation of stepping pulse potentials. Under optimized experimental conditions, the developed ECL sensor worked well for TMAO detection in a wide linear range of 10.00 μM to 1.00 mM with a limit of detection of 3.41 μM. It was successfully applied to determine TMAO in various species of seafood samples. This work provides a promising strategy for TMAO detection.

Structurally different chemical chaperones show similar mechanical roles with independent molecular mechanisms

Osmolytes are well known to protect the protein structure against different chemical and physical denaturants. Since their actions with protein surfaces are mechanistically complicated and context dependent, the underlying molecular mechanism is not fully understood. Here, we combined single-molecule magnetic tweezers and molecular dynamics (MD) simulation to explore the mechanical role of osmolytes from two different classes, trimethylamine N-oxide (TMAO) and trehalose, as mechanical stabilizers of protein structure. We observed that these osmolytes increase the protein L mechanical stability by decreasing unfolding kinetics while accelerating the refolding kinetics under force, eventually shifting the energy landscape toward the folded state. These osmolytes mechanically stabilize the protein L and plausibly guide them to more thermodynamically robust states. Finally, we observed that osmolyte-modulated protein folding increases mechanical work output up to twofold, allowing the protein to fold under a higher force regime and providing a significant implication for folding-induced structural stability in proteins.

Identifying the key factors affecting the trimethylamine N-oxide content of teleost fishes collected from the marginal seas of China and the epipelagic zone of the northwest Pacific Ocean

To identify the key factors influencing the trimethylamine N-oxide (TMAO) content of teleost fishes living in shallow seas and the epipelagic zone of the deep ocean, the muscle TMAO content was measured in 152 teleost fishes (21 species) collected from the marginal seas of China and the epipelagic zone of the northwest Pacific Ocean (NWPO) during May-July 2021. The results showed that the TMAO content in all fishes varied from 4.99 to 82.97 mmol kg-1, and it varied notably among different species, e.g., the highest average content (72.71 ± 8.22 mmol kg-1 in Argyrosomus argentatus) was 1 order of magnitude higher than the lowest one (Scomber japonicus), but the ratios of the highest content to the lowest content in each species varied from 1.29 to 3.28, suggesting that the interspecific variations in TMAO content were obviously greater than the intraspecific variations. Moreover, no correlation was observed between the TMAO content of the 152 fishes and the corresponding environmental factors of seawater depth, salinity and temperature, indicating that species played a more important role than environmental factors in driving TMAO accumulation. To exclude the influence of species, intraspecies correlations between TMAO content and environmental factors were analyzed. In the marginal seas of China, only ∼8 % of the TMAO content of teleost fishes (1 species) showed a positive correlation with salinity and depth, but ∼50 % of the TMAO content (5 species) was negatively correlated with temperature. Moreover, the TMAO content of the fish increased by 4.66 ± 1.38 % compared with their corresponding intraspecific average values for every 1 °C of temperature decrease. A similar phenomenon was also found in the TMAO content of pelagic teleost fishes in the NWPO, suggesting that temperature was a key environmental factor affecting the TMAO content of teleost fishes in shallow seas and the epipelagic zone of the deep ocean.

Elucidating the hydrotropism behaviour of aqueous caffeine and sodium benzoate solution through NMR and neutron total scattering analysis

Hydrotropism is a convenient way to increase the solubility of drugs by up to several orders of magnitude, and even though it has been researched for decades with both experimental and simulation methods, its mechanism is still unknown. Here, we use caffeine/sodium benzoate (CAF-SB) as model system to explore the behaviour of caffeine solubility enhancement in water through NMR spectroscopy and neutron total scattering. 1H NMR shows strong interaction between caffeine and sodium benzoate in water. Neutron total scattering combined with empirical potential structure refinement, a systematic method to study the solution structure, reveals π-stacking between caffeine and the benzoate anion as well as Coulombic interactions with the sodium cation. The strongest hydrogen bond interaction in the system is between benzoate and water, which help dissolve CAF-SB complex and increase the solubility of CAF in water. Besides, the stronger interaction between CAF and water and the distortion of water structure are further mechanisms of the CAF solubility enhancement. It is likely that the variety of mechanisms for hydrotropism shown in this system can be found for other hydrotropes, and NMR spectroscopy and neutron total scattering can be used as complementary techniques to generate a holistic picture of hydrotropic solutions.

Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

N-Oxides as Control Element for the Direction of a Sigmatropic Rearrangement: Application as a Switch for Fluorescence

An exceptional level of control over the direction of the (2,3)-sigmatropic rearrangement between N-oxides and alkoxylamine is achieved by simply changing the solvent in which they are dissolved. Protic solvents like water, methanol and hexafluoroisopropanol favour the N-oxide form, while other solvents like acetone, acetonitrile and benzene favour the alkoxylamine. The reaction temperature and nature of the substituents on the alkene affect the rate of rearrangement. A N-oxide fragment was attached to two fluorescent molecules and acted as an on/off switch for their fluorescence. The conversion of alkoxylamines into the corresponding N-oxides has not previously been described and is here termed the 'Reverse Meisenheimer Rearrangement'.

Theoretical Spectroscopy Aided Validation of the Hydration Structure of Trimethylamine N-Oxide (TMAO)

The molecular-level understanding of the hydration structure of external solutes is extremely challenging. In the context of molecular simulation, particularly sampling proper solvation structure by classical force fields remains always a matter of concern. In the present work, we use theoretical vibrational spectroscopy to understand the microscopic solvation structure of TMAO in water in the cases of five different classical force fields of TMAO. We find that the Netz (J. Phys. Chem. B 2013, 117, 8310-8321) force field agrees better with the experimental results. We also observe that the O-H stretching frequency gets red-shifted compared to the bulk water response, suggesting that the TMAO-water forms stronger hydrogen bonds than water-water. We further investigate the O-H stretching frequency in different solvation shells and the hydrophobic and hydrophilic regions of TMAO. We find that, in the hydrophilic region, O-H stretching frequencies show a strong orientational correlation; however, that is absent in the hydrophobic region. These are further supplemented by hydrogen-bond analysis and local structure index data.

Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems

Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.