Effects of Temperature on the Thermodynamic and Dynamical Properties of Glycerol–Water Mixtures: A Computer Simulation Study of Three Different Force Fields

Direct Observation of the Mutual Coupling Effect in the Protein-Water-Glycerol Mixture by Combining Neutron Scattering and Selective Deuteration

Numerous studies have discussed the impact of cosolvents on the structure, dynamics, and stability of proteins in aqueous solutions. However, the dynamics of cosolvents in the protein-water-cosolvent ternary system is largely unexplored in experiments due to technical difficulty. Consequently, a comprehensive understanding of the interplay among proteins, water, and cosolvents is still lacking. Here, we employed selective deuteration and neutron scattering techniques to characterize the individual motions of each component in the protein/water/glycerol (GLY) mixture across various temperatures. The consistent dynamic onset temperatures and the correlation between the MSD of the protein and the viscosity of solvents revealed the mutual coupling effects among the three components. Furthermore, our experimental and simulation results showed that the hydrogen bond relaxation energy barrier in the ternary system is ∼43 kJ/mol, whereas in the protein-water binary system it is merely ∼35 kJ/mol. Therefore, we suggest that GLY can enhance hydrogen bond interactions in the ternary system through the mutual coupling effect, thereby serving as one of the protective mechanisms of protein preservation by GLY.

1H-NMR Karplus Analysis of Molecular Conformations of Glycerol under Different Solvent Conditions: A Consistent Rotational Isomerism in the Backbone Governed by Glycerol/Water Interactions

Glycerol is a symmetrical, small biomolecule with high flexibility in molecular conformations. Using a ¹H-NMR spectroscopic Karplus analysis in our way, we analyzed a rotational isomerism in the glycero backbone which generates three kinds of staggered conformers, namely gt (gauche-trans), gg (gauche-gauche), and tg (trans-gauche), at each of sn-1,2 and sn-2,3 positions. The Karplus analysis has disclosed that the three rotamers are consistently equilibrated in water keeping the relation of 'gt:gg:tg = 50:30:20 (%)' at a wide range of concentrations (5 mM~540 mM). The observed relation means that glycerol in water favors those symmetric conformers placing 1,2,3-triol groups in a gauche/gauche geometry. We have found also that the rotational isomerism is remarkably changed when the solvent is replaced with DMSO-d₆ or dimethylformamide (DMF-d₇). In these solvents, glycerol gives a relation of 'gt:gg:tg = 40:30:30 (%)', which means that a remarkable shift occurs in the equilibrium between gt and tg conformers. By this shift, glycerol turns to also take non-symmetric conformers orienting one of the two vicinal diols in an antiperiplanar geometry.

The Glycerol-Induced Perfusion-Kinetics of the Cat Ovaries in the Follicular and Luteal Phases of the Cycle

The method of immersion optical clearing reduces light scattering in tissues, which improves the use of optical technologies in the practice of clinicians. In this work, we studied the optical and molecular diffusion properties of cat ovarian tissues in the follicular (F-ph) and luteal (L-ph) phases under the influence of glycerol using reflectance spectroscopy in a broad wavelength range from 200 to 800 nm. It was found that the reflectance and transmittance of the ovaries are significantly lower in the range from 200 to 600 nm than for longer wavelengths from 600 to 800 nm, and the efficiency of optical clearing is much lower for the ovaries in the luteal phase compared to the follicular phase. For shorter wavelengths, the following tissue transparency windows were observed: centered at 350 nm and wide (46 ± 5) nm, centered at 500 nm and wide (25 ± 7) nm for the F-ph state and with a center of 500 nm and a width of (21 ± 6) nm for the L-ph state. Using the free diffusion model, Fick's law of molecular diffusion and the Bouguer-Beer-Lambert radiation attenuation law, the glycerol/tissue water diffusion coefficient was estimated as D = (1.9 ± 0.2)10^-6 cm²/s for ovaries at F-ph state and D = (2.4 ± 0.2)10^-6 cm²/s-in L-ph state, and the time of complete dehydration of ovarian samples, 0.8 mm thick, as 22.3 min in F-ph state and 17.7 min in L-ph state. The ability to determine the phase in which the ovaries are stated, follicular or luteal, is also important in cryopreservation, new reproductive technologies and ovarian implantation.

Characterization of optical clearing mechanisms in muscle during treatment with glycerol and gadobutrol solutions

The recent increasing interest in the application of radiology contrasting agents to create transparency in biological tissues implies that the diffusion properties of those agents need evaluation. The comparison of those properties with the ones obtained for other optical clearing agents allows to perform an optimized agent selection to create optimized transparency in clinical applications. In this study, the evaluation and comparison of the diffusion properties of gadobutrol and glycerol in skeletal muscle was made, showing that although gadobutrol has a higher molar mass than glycerol, its low viscosity allows for a faster diffusion in the muscle. The characterization of the tissue dehydration and refractive index matching mechanisms of optical clearing was made in skeletal muscle, namely by the estimation of the diffusion coefficients for water, glycerol and gadobutrol. The estimated tortuosity values of glycerol (2.2) and of gadobutrol (1.7) showed a longer path-length for glycerol in the muscle.

Hydrogen-Bond Configurations of Hydration Water around Glycerol Investigated by HOH Bending and OH Stretching Analysis

Toward a comprehensive understanding of the mechanism of glycerol as a moisturizer, studies on the hydrogen-bond (HB) structure of hydration water, which is known to be disordered by glycerol, are insufficient. To this aim, we evaluated the HB configurations based on the HOH bending and OH stretching spectra of the hydration water from those of glycerol/water mixtures by subtracting the contributions of bulk water and glycerol using dielectric relaxation spectroscopy. Analysis of the HOH bending band showed that hydration water-donating HBs lose the intermolecular bending coupling with increasing glycerol by replacing the water-water HBs with water-glycerol HBs. The OH stretching band provided more detailed insight into the HB configuration, indicating that the double-donor double-acceptor and double-donor single-acceptor configurations in bulk water change to a predominantly double-donor single-acceptor configuration in hydration water around glycerol. The formation of more donor HBs than acceptor HBs may be due to the steric constrains by glycerol and/or differences in the partial charge on the oxygen atom between water and glycerol.

Confocal Raman Micro-Spectroscopy for Discrimination of Glycerol Diffusivity in Ex Vivo Porcine Dura Mater

Dura mater (DM) is a connective tissue with dense collagen, which is a protective membrane surrounding the human brain. The optical clearing (OC) method was used to make DM more transparent, thereby allowing to increase in-depth investigation by confocal Raman micro-spectroscopy and estimate the diffusivity of 50% glycerol and water migration. Glycerol concentration was obtained, and the diffusion coefficient was calculated, which ranged from 9.6 × 10^-6 to 3.0 × 10^-5 cm²/s. Collagen-related Raman band intensities were significantly increased for all depths from 50 to 200 µm after treatment. In addition, the changes in water content during OC showed that 50% glycerol induces tissue dehydration. Weakly and strongly bound water types were found to be most concentrated, playing a major role in the glycerol-induced water flux and OC. Results show that OC is an efficient method for controlling the DM optical properties, thereby enhancing the in-depth probing for laser therapy and diagnostics of the brain. DM is a comparable to various collagen-containing tissues and organs, such as sclera of eyes and skin dermis.

Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions

Many biological and biotechnological processes are controlled by protein–protein and protein–solvent interactions. In order to understand, predict, and optimize such processes, it is important to understand how solvents affect protein structure during protein–solvent interactions. In this study, all-atom molecular dynamics are used to investigate the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations by molecular weight. The Generalized Amber Force Field is modified by including restrained electrostatic potential atomic charges for the glycerol molecules. The peptide is considered in detail by monitoring properties like the root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration, hydrodynamic radius, end-to-end distance, solvent-accessible surface area, intra-potential energy, and solvent–peptide interaction energies for hundreds of nanoseconds. Secondary structure analysis is also performed to examine the extent of conformational drift for the individual helices and sheets. We predict that the peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration. We also find that the solvent-peptide becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated when modeled with the modified atomic charges show a very good agreement with experimental results and other simulations at 298.15K.

Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection

Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy-kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.

Protein Preferential Solvation in Water:Glycerol Mixtures

For proteins in solvent mixtures, the relative abundances of each solvent in their solvation shell have a critical impact on their properties. Preferential solvation of a series of proteins in water-glycerol mixtures is studied here over a broad range of solvent compositions via classical molecular dynamics simulations. Our simulation results reveal that the differences between shell and bulk compositions exhibit dramatic changes with solvent composition, temperature, and protein nature. In contrast with the simple and widely used picture where glycerol is completely excluded from the protein interface, we show that for aqueous solutions with less than 50% glycerol in volume, protein solvation shells have approximately the same composition as the bulk solvent and proteins are in direct contact with glycerol. We further demonstrate that at high glycerol concentration, glycerol depletion from the solvation shell is due to an entropic factor arising from the reduced accessibility of bulky glycerol molecules in protein cavities. The resulting molecular picture is important to understand protein activity and cryopreservation in mixed aqueous solvents.

How does hydrogen bond network analysis reveal the golden ratio of water-glycerol mixtures?

Properties of water-glycerol mixtures depend closely on the water/glycerol ratio. Around the 30 mol% glycerol concentration mark, the so-called golden ratio of water-glycerol mixtures, several of the mixture's properties have observed maxima or minima, without a clear fundamental explanation. In this work, a series of molecular dynamics simulations have been performed over a wide range of water-glycerol concentrations to analyze the intermolecular hydrogen bond (H-bond) network. The collected values from simulations are justified from both a probabilistic model of H-bonding and from observing the dynamic behavior of each type of H-bonds. The populations of H-bonds that exist at a given concentration of glycerol are largely governed by the probability of one oxygen atom randomly associating with another oxygen atom. However, the H-bonds that glycerol oxygen can form are dependent on the H-bonds that are formed by the other intramolecular glycerol oxygen. Based on the dynamic analysis of each type of H-bonds, there are deviations from randomly associating with another oxygen. Water preferentially donates a hydrogen to a glycerol than to another water molecule. Yet, glycerol has a near-equal likelihood for donating a hydrogen to either another glycerol or a water. This has an effect of increasing the number of H-bonds between water and glycerol molecules and decreasing H-bonds between two water molecules. A maximum contribution of H-bonds between water and glycerol occurs around 30 mol% glycerol which is a concentration where several of the mixture's properties have an observed maxima or minima.

Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations

One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.

Origins of complex solvent effects on chemical reactivity and computational tools to investigate them: a review

Origins of solvent-induced enhancement in catalytic reactivity and product selectivity are discussed with computational methods to study them.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

Glass polymorphism in glycerol-water mixtures: I. A computer simulation study

We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA-HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol-water mixtures prepared by isobaric cooling at 1 bar.