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.

Effect of ectoine on hydration spheres of peptides-spectroscopic studies

In this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides-diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte influences the hydration shells of both peptides and does so in a different way for both peptides: (1) the interfacial interaction of the NAGMA peptide and ectoine hydration spheres strengthened the hydration shell of this peptide; (2) the inclusion of water molecules from the ectoine hydration sphere into the diglycine hydration sphere had only a marginally enhancing effect. Since ectoine is being used in more and more biopharmaceutical products and cosmetics, knowledge of the properties of its hydration shell and its effect on the hydration shell of other molecules is extremely relevant to understanding its protective mechanism.

Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions

Osmolytes, small organic compounds, play a key role in modulating the protein stability in aqueous solutions, but the operating mechanism of the osmolyte remains inconclusive. Here, we attempt to clarify the mode of osmolyte action by quantitatively estimating the microheterogeneity of osmolyte-water mixtures with the aid of molecular dynamics simulation, graph theoretical analysis, and spatial distribution measurement in the four osmolyte solutions of trimethylamine-N-oxide (TMAO), tetramethylurea (TMU), dimethyl sulfoxide, and urea. TMAO, acting as a protecting osmolyte, tends to remain isolated with no formation of osmolyte aggregates while preferentially interacting with water, but there is a strong aggregation propensity in the denaturant TMU solution, characterized by favored hydrophobic interactions between TMU molecules. Taken together, the mechanism of osmolyte action on protein stability is proposed as a comprehensive one that encompasses the direct interactions between osmolytes and proteins and indirect interactions through the regulation of water properties in the osmolyte-water mixtures.

Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor

The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.

Phase separation propensity of the intrinsically disordered AB region of human RXRβ

RXRβ is one of three subtypes of human retinoid X receptor (RXR), a transcription factor that belongs to the nuclear receptor superfamily. Its expression can be detected in almost all tissues. In contrast to other subtypes - RXRα and RXRγ - RXRβ has the longest and unique N-terminal sequence called the AB region, which harbors a ligand-independent activation function. In contrast to the functional properties of this sequence, the molecular properties of the AB region of human RXRβ (AB_hRXRB) have not yet been characterized. Here, we present a systematic biochemical and biophysical analysis of recombinant AB_hRXRB, along with in silico examinations, which demonstrate that AB_hRXRB exhibits properties of a coil-like intrinsically disordered region. AB_hRXRB possesses a flexible structure that is able to adopt a more ordered conformation under the influence of different environmental factors. Interestingly, AB_hRXRB promotes the formation of liquid-liquid phase separation (LLPS), a phenomenon previously observed for the AB region of another human subtype of RXR - RXRγ (AB_hRXRG). Although both AB regions seem to be similar in terms of their ability to induce phase separation, they clearly differ in the sensitivity to factors driving and regulating LLPS. This distinct LLPS response to environmental factors driven by the unique amino acid compositions of AB_hRXRB and AB_hRXRG can be significant for the specific modulation of the transcriptional activation of target genes by different subtypes of RXR. Video Abstract.

The Role of Taurine in Skeletal Muscle Functioning and Its Potential as a Supportive Treatment for Duchenne Muscular Dystrophy

Taurine (2-aminoethanesulfonic acid) is required for ensuring proper muscle functioning. Knockout of the taurine transporter in mice results in low taurine concentrations in the muscle and associates with myofiber necrosis and diminished exercise capacity. Interestingly, regulation of taurine and its transporter is altered in the mdx mouse, a model for Duchenne Muscular Dystrophy (DMD). DMD is a genetic disorder characterized by progressive muscle degeneration and weakness due to the absence of dystrophin from the muscle membrane, causing destabilization and contraction-induced muscle cell damage. This review explores the physiological role of taurine in skeletal muscle and the consequences of a disturbed balance in DMD. Its potential as a supportive treatment for DMD is also discussed. In addition to genetic correction, that is currently under development as a curative treatment, taurine supplementation has the potential to reduce muscle inflammation and improve muscle strength in patients.

Unexplored Excipients in Biotherapeutic Formulations: Natural Osmolytes as Potential Stabilizers Against Thermally Induced Aggregation of IgG1 Biotherapeutics

Monoclonal antibodies (mAbs), while incredibly successful, are prone to a variety of degradation pathways, the most significant of which is aggregation. One of the most commonly used strategy to overcome protein aggregation is addition of excipients to the formulation. Osmolytes such as trehalose, sucrose, and glycine are widely used. In this paper, we explore potential use of naturally occurring osmolytes such as betaine, sarcosine, ectoine, and hydroxyectoine for reducing aggregation of mAb therapeutics. Experimentation has been performed on two IgG1 mAbs via accelerated stability studies. A variety of analytical tools have been used for monitoring the impact, dynamic light scattering (DLS) for colloidal stability, Fourier transform infrared (FTIR) spectroscopy and fluorescence spectroscopy for conformational stability and the higher order structure (HOS), and differential scanning calorimetry (DSC) for thermal stability. No significant impact of osmolyte addition was observed on protein structure, on comparative Fc receptor (FcRn) binding, and on biocompatibility as per our hemolytic assay. Our results rank the osmolytes’ stabilizing trend to be sarcosine > betaine > hydroxyectoine > ectoine. Sarcosine emerged as the most successful osmolyte rendering highest degree of protection against aggregation. Our data support the prospect of using these osmolytes as successful excipients for mAb formulations.

Effects of amino acid additives on protein solubility - insights from desorption and direct electrospray ionization mass spectrometry

Naturally occurring amino acids have been broadly used as additives to improve protein solubility and inhibit aggregation. In this study, improvements in protein signal intensity obtained with the addition of L-serine, and structural analogs, to the desorption electrospray ionization mass spectrometry (DESI-MS) spray solvent were measured. The results were interpreted at the hand of proposed mechanisms of solution additive effects on protein solubility and dissolution. DESI-MS allows for these processes to be studied efficiently using dilute concentrations of additives and small amounts of proteins, advantages that represent real benefits compared to classical methods of studying protein stability and aggregation. We show that serine significantly increases the protein signal in DESI-MS when native proteins are undergoing unfolding during the dissolution process with an acidic solvent system (p-value = 0.0001), or with ammonium bicarbonate under denaturing conditions for proteins with high isoelectric points (p-value = 0.001). We establish that a similar increase in the protein signal cannot be observed with direct ESI-MS, and the observed increase is therefore not related to ionization processes or changes in the physical properties of the bulk solution. The importance of the presence of serine during protein conformational changes while undergoing dissolution is demonstrated through comparisons between the analyses of proteins deposited in native or unfolded states and by using native state-preserving and denaturing desorption solvents. We hypothesize that direct, non-covalent interactions involving all three functional groups of serine are involved in the beneficial effect on protein solubility and dissolution. Supporting evidence for a direct interaction include a reduction in efficacy with D-serine or the racemic mixture, indicating a non-bulk-solution physical property effect; insensitivity to the sample surface type or relative placement of serine addition; and a reduction in efficacy with any modifications to the serine structure, most notably the carboxyl functional group. An alternative hypothesis, also supported by some of our observations, could involve the role of serine clusters in the mechanism of solubility enhancement. Our study demonstrates the capability of DESI-MS together with complementary ESI-MS experiments as a novel tool for understanding protein solubility and dissolution and investigating the mechanism of action for solubility-enhancing additives.

Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine-N-oxide on the Peptide Solvation Shell

The osmolyte trimethylamine-N-oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA, 2017, 114, 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.

Entrapment of enzyme in the presence of proline: effective approach to enhance activity and stability of horseradish peroxidase

In this report, activity and stability of horseradish peroxidase (HRP) entrapped in polyacrylamide gel in the presence of proline (HEP) are compared with that of enzyme entrapped in absence of proline (HE). Within polyacrylamide (8%) beads, 80% entrapment yield for peroxidase was observed in the presence as well as absence of proline. The HEP (1.5 M proline) showed 170% higher activity compared to HE. HEP also showed significant increase in K _M, V _max and K _cat. At 8th cycle of use, HEP retained 40% of its activity, whereas HE retained only 10% of activity. In addition, in comparison with HE, HEP showed increased storage stability and thermo-stability. HEP showed higher activity compared to HE over an extensive range of pH (4-8), temperature (30-80 °C) and inhibitors such as NaN₃, Cd²⁺ and Pb²⁺. Our results suggest that peroxidase entrapment in polyacrylamide gel in the presence of proline can be a useful approach for increasing activity and stability of horseradish peroxidase.

Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell

We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine.

A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways

An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.

Hydration Dynamics in Solutions of Cyclic Polyhydroxyl Osmolytes

Simple sugars are remarkably effective at preserving protein and enzymatic structures against thermal and hydrostatic stress. Here, we investigate the hydrodynamic and biopreservative properties of three small cyclic molecules: glucose, myo-inositol, and methyl-α-d-glucopyranoside using circular dichroism spectroscopy and isothermal calorimetry. Using ultrafast fluorescence frequency upconversion spectroscopy, we measure the dynamical retardation of hydration dynamics in cosolute solutions. We find that all three molecules are effective modifiers of hydration dynamics in solution and all are also effective at protecting model protein systems against thermal denaturation. Methyl-α-d-glucopyranoside is found to be the most effective dynamic reducer displaying an approximately 30% increase in solvation relaxation time as compared to water in a cosolute free solution. myo-Inositol and glucose both exhibit a smaller reduction in dynamics with similar magnitudes of concentration dependence. Using these cosolute models, we demonstrate that the thermal enhancement of protein structure does not correlate strongly with either the dynamical reduction of the bulk solution nor with the number of hydrogen bonds a cosolute makes with the solvent. Furthermore, solutions of glucose at twice the concentration of trehalose are shown to have similar magnitudes of dynamical impact. This implies that regulation of hydration dynamics is not a distinguishing characteristic of successful osmolytes. This work highlights the need for further studies and computational analysis to understand the phenomena of preferential exclusion and the contribution of hydration dynamics to protein structural stability.

Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions

Although osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage by enthalpically-driven association with the protein, acting synergistically with temperature to induce unfolding. In contrast, betaine is sterically excluded from the protein surface thereby exerting entropic depletion forces that contribute to the stabilization of the native state. In fact, we find that while at low temperatures betaine slightly increases the folding free energy of Trp-cage by promoting another near-native conformation, it protects the protein against temperature-induced denaturation. This, in turn, can be attributed to enhanced exclusion of betaine at higher temperatures that arises from less attractive interactions with the protein surface.

Surface Behavior of BSA/Water/Carbohydrate Systems from Molecular Polarizability Measurements

The effect of the presence of glucose and sucrose on the nonintrinsic contribution to partial molar volume ⟨Θ⟩_ni of bovine serum albumin (BSA) is determined by means of static and dynamic electronic polarizability measurements. For that aim, a combined strategy based on high-resolution refractometry, high exactitude densitometry, and synchronous fluorescence spectroscopy is applied. Both static and dynamic mean electronic molecular polarizability values are found to be sensitive to the presence of glucose. In the case of sucrose, the polarizability of BSA is not appreciably affected. In fact, our results revealed that the electronic changes observed occurred without a modification of the native conformation of BSA. On the contrary, a nonmonotonous behavior with the concentration is observed in presence of glucose. These results advocate the influence of the electronic polarization on the repulsive and attractive protein-carbohydrate interactions. An analysis using the scaled particle theory indicates that the accumulation of glucose on the protein surface promotes dehydration. Inversely, hydration and preferential exclusion occur in the vicinity of the protein surface for sucrose-enriched systems.

Changing relations between proteins and osmolytes: a choice of nature

The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.

Taurine as a water structure breaker and protein stabilizer

The enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as "structure breaking" solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between osmolytes and two proteins: lysozyme and ubiquitin. Despite high structural similarity, both osmolytes exert different influence on protein stability: taurine is a stabilizer, TMT is a denaturant. We show also that taurine amino group interacts directly with the side chains of proteins, whereas TMT does not interact with proteins at all. Although two solutes weaken on average the structure of the surrounding water, their hydration spheres are different. Taurine is surrounded by two populations of water molecules: bonded with weak H-bonds around sulfonate group, and strongly bonded around amino group. The strong hydrogen-bonded network of water molecules around the amino group of taurine further improves properties of enhanced protein hydration sphere and stabilizes the native protein form. Direct interactions of this group with surface side chains provide a proper orientation of taurine and prevents the [Formula: see text] group from negative influence. The weakened [Formula: see text] hydration sphere of TMT breaks up the hydrogen-bonded network of water around the protein and destabilizes it. However, TMT at low concentration stabilize both proteins to a small extent. This effect can be attributed to an actual osmophobic effect which is overcome if the concentration increases.

Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline

Strongly hydrated l-proline cooperatively binds Na⁺ and Cl⁻ ions in aqueous solution.

Differential influence of additives on the various stages of insulin aggregation

The different species in the aggregation pathway of insulin are stabilized/destabilized to different extent in the presence of various additives.