Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels.

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Depletion-Induced Self-Assembly of Colloidal Particles on a Solid Substrate.

We investigate the depletion contributions to the self-assembly of microcolloids on solid substrates. The assembly is driven by the exclusion of nanoparticles and nonadsorbing polymers from the depletion zone between the microcolloids in the liquid and the underlying substrate. The model system consists of 1 µm polystyrene particles that we deposit on a flat glass slab in an electrolyte solution. Using polystyrene nanoparticles and poly(acrylic acid) polymers as depleting agents, we demonstrate in our experiments that nanoparticle concentrations of 0.5% (w/v) support well-ordered packing of microcolloids on glass, while the presence of polymers leads to irregular aggregate deposition structures. A mixture of nanoparticles and polymers enhances the formation of colloidal aggregate and particulate surface coverage compared to using the polymers alone as a depletion agent. Moreover, tuning the polymer ionization state from pH 4 to 9 modifies the polymer conformational state and radius of gyration, which in turn alters the microcolloid deposition from compact multilayers to flocculated structures. Our study provides entropic strategies for manipulating particulate assembly on substrates from dispersed to continuous coatings.

Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds.

Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: ß-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.

Osmolytes and crowders regulate aggregation of the cancer-related L106R mutant of the Axin protein.

Protein aggregation is involved in a variety of diseases, including neurodegenerative diseases and cancer. The cellular environment is crowded by a plethora of cosolutes comprising small molecules and biomacromolecules at high concentrations, which may influence the aggregation of proteins in vivo. To account for the effect of cosolutes on cancer-related protein aggregation, we studied their effect on the aggregation of the cancer-related L106R mutant of the Axin protein. Axin is a key player in the Wnt signaling pathway, and the L106R mutation in its RGS domain results in a native molten globule that tends to form native-like aggregates. This results in uncontrolled activation of the Wnt signaling pathway, leading to cancer. We monitored the aggregation process of Axin RGS L106R in vitro in the presence of a wide ensemble of cosolutes including polyols, amino acids, betaine, and polyethylene glycol crowders. Except myo-inositol, all polyols decreased RGS L106R aggregation, with carbohydrates exerting the strongest inhibition. Conversely, betaine and polyethylene glycols enhanced aggregation. These results are consistent with the reported effects of osmolytes and crowders on the stability of molten globular proteins and with both amorphous and amyloid aggregation mechanisms. We suggest a model of Axin L106R aggregation in vivo, whereby molecularly small osmolytes keep the protein as a free soluble molecule but the increased crowding of the bound state by macromolecules induces its aggregation at the nanoscale. To our knowledge, this is the first systematic study on the effect of osmolytes and crowders on a process of native-like aggregation involved in pathology, as it sheds light on the contribution of cosolutes to the onset of cancer as a protein misfolding disease and on the relevance of aggregation in the molecular etiology of cancer.

Cyclodextrin solubilization in hydrated reline: Resolving the unique stabilization mechanism in a deep eutectic solvent.

By complexing with hydrophobic compounds, cyclodextrins afford increased solubility and thermodynamic stability to hardly soluble compounds, thereby underlining their invaluable applications in pharmaceutical and other industries. However, common cyclodextrins such as ß-cyclodextrin, suffer from limited solubility in water, which often leads to precipitation and formation of unfavorable aggregates, driving the search for better solvents. Here, we study the solvation of cyclodextrin in deep eutectic solvents (DESs), environmentally friendly media that possess unique properties. We focus on reline, the DES formed from choline chloride and urea, and resolve the mechanism through which its constituents elevate ß-cyclodextrin solubility in hydrated solutions compared to pure water or dry reline. Combining experiments and simulations, we determine that the remarkable solubilization of ß-cyclodextrin in hydrated reline is mostly due to the inclusion of urea inside ß-cyclodextrin's cavity and at its exterior surfaces. The role of choline chloride in further increasing solvation is twofold. First, it increases urea's solubility beyond the saturation limit in water, ultimately leading to much higher ß-cyclodextrin solubility in hydrated reline in comparison to aqueous urea solutions. Second, choline chloride increases urea's accumulation in ß-cyclodextrin's vicinity. Specifically, we find that the accumulation of urea becomes stronger at high reline concentrations, as the solution transitions from reline-in-water to water-in-reline, where water alone cannot be regarded as the solvent. Simulations further suggest that in dry DES, the mechanism of ß-cyclodextrin solvation changes so that reline acts as a quasi-single component solvent that lacks preference for the accumulation of urea or choline chloride around ß-cyclodextrin.

Bridges of Calcium Bicarbonate Tightly Couple Dipolar Lipid Membranes.

The interaction between lipid membranes and ions is associated with a range of key physiological processes. Most earlier studies have focused on the interaction of lipids with cations, while the specific effects of the anions have been largely overlooked. Owing to dissolved atmospheric carbon dioxide, bicarbonate is an important ubiquitous anion in aqueous media. In this paper, we report on the effect of bicarbonate anions on the interactions between dipolar lipid membranes in the presence of previously adsorbed calcium cations. Using a combination of solution X-ray scattering, osmotic stress, and molecular dynamics simulations, we followed the interactions between 1,2-didodecanoyl-sn-glycero-3-phosphocholine (DLPC) lipid membranes that were dialyzed against CaCl2 solutions in the presence and absence of bicarbonate anions. Calcium cations adsorbed onto DLPC membranes, charge them, and lead to their swelling. In the presence of bicarbonate anions, however, the calcium cations can tightly couple one dipolar DLPC membrane to the other and form a highly condensed and dehydrated lamellar phase with a repeat distance of 3.45 ± 0.02 nm. Similar tight condensation and dehydration has only been observed between charged membranes in the presence of multivalent counterions. Bridging between bilayers by calcium bicarbonate complexes induced this arrangement. Furthermore, in this condensed phase, lipid molecules and adsorbed ions were arranged in a two-dimensional oblique lattice.

Heterogeneous Electrofreezing of Super-Cooled Water on Surfaces of Pyroelectric Crystals is Triggered by Trigonal Planar Ions.

Electrofreezing experiments of super-cooled water (SCW) with different ions, performed directly on the charged hemihedral faces of pyroelectric LiTaO3 and AgI crystals, in the presence and in the absence of pyroelectric charge are reported. It is demonstrated that bicarbonate (HCO3 - ) ions elevate the icing temperature near the positively charged faces. In contrast, the hydronium (H3 O+ ) slightly reduces the icing temperature. Molecular dynamics simulations suggest that the hydrated trigonal planar HCO3 - ions self-assemble with water molecules near the surface of the AgI crystal as clusters of slightly different configuration from those of the ice-like hexagons. These clusters, however, have a tendency to serve as embryonic nuclei for ice crystallization. Consequently, we predicted and experimentally confirmed that the trigonal planar ions of NO3 - and guanidinium (Gdm+ ), at appropriate concentrations, elevate the icing temperature near the positive and negative charged surfaces, respectively. On the other hand, the Cl- and SO4 2- ions of different configurations reduce the icing temperature.

How Sugars Modify Caffeine Self-Association and Solubility: Resolving a Mechanism of Selective Hydrotropy.

The aggregation of drugs and nutraceuticals in aqueous media is an outstanding problem for their efficacy and bioavailability. A common solution is to add excipients or hydrotropes that increase solubility and limit aggregation. Here we study caffeine, a widely consumed drug that undergoes oligomerization and aggregation in aqueous solutions. Combining partition and solubility experiments with molecular dynamics simulations, we determined the effect of sugars (mono- and disaccharides) on caffeine self-association and solubility. We find that sugars selectively increase the concentration of caffeine in its monomeric state, but decrease its solubility in all oligomeric forms. Thus, we determine that, in contrast to common hydrotropes, sugars act as selective hydrotropes toward caffeine, since they differentially act on specific solvated forms of the drug. We furthermore unravel the molecular mechanism for this selectivity, and comment on the general design principles that should help develop targeted excipients for bioavailability and taste modification in drugs and foods.

TMAO mediates effective attraction between lipid membranes by partitioning unevenly between bulk and lipid domains.

Under environmental duress, many organisms accumulate large amounts of osmolytes - molecularly small organic solutes. Osmolytes are known to counteract stress, driving proteins to their compact native states by their exclusion from protein surfaces. In contrast, the effect of osmolytes on lipid membranes is poorly understood and widely debated. Many fully membrane-permeable osmolytes exert an apparent attractive force between lipid membranes, yet all proposed models fail to fully account for the origin of this force. We follow the quintessential osmolyte trimethylamine N-oxide (TMAO) and its interaction with dimyristoyl phosphatidylcholine (DMPC) membranes in aqueous solution. We find that by partitioning away from the inter-bilayer space, TMAO pushes adjacent membranes closer together. Experiments and simulations further show that the partitioning of TMAO away from the volume between bilayers stems from its exclusion from the lipid-water interface, similar to the mechanism of protein stabilization by osmolytes. We extend our analysis to show that the preferential interaction of other physiologically relevant solutes (including sugars and DMSO) also correlates with their effect on membrane bilayer interactions. Our study resolves a long-standing puzzle, explaining how osmolytes can increase membrane-membrane attraction or repulsion depending on their preferential interactions with lipids.

Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.

BACKGROUND: The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influence membrane reshaping and fusion processes as well as the organisation and function of membrane proteins. Determining these properties is therefore key for a mechanistic understanding of how the cell functions. RESULTS: We have developed a method to determine the bending rigidity and tilt modulus, for lipidic assemblies of arbitrary lipid composition and shape, from molecular dynamics simulations. The method extracts the elastic moduli from the distributions of microscopic tilts and splays of the lipid components. We present here an open source implementation of the method as a set of Python modules using the computational framework OpenStructure. These modules offer diverse algorithms typically used in the calculatation the elastic moduli, including routines to align MD trajectories of complex lipidic systems, to determine the water/lipid interface, to calculate lipid tilts and splays, as well as to fit the corresponding distributions to extract the elastic properties. We detail the implementation of the method and give several examples of how to use the modules in specific cases. CONCLUSIONS: The method presented here is, to our knowledge, the only available computational approach allowing to quantify the elastic properties of lipidic assemblies of arbitrary shape and composition (including lipid mixtures). The implementation as python modules offers flexibility, which has already allowed the method to be applied to diverse lipid assembly types, ranging from bilayers in the liquid ordered and disordered phases to a study of the inverted-hexagonal phase, and with different force-fields (both all-atom and coarse grained representations). The modules are freely available through GitHub at https://github.com/njohner/ost_pymodules/ while OpenStructure can be obtained at http://www.openstructure.org .

Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions.

We present the assembly of asymmetric two-layer hybrid DNA-based hydrogels revealing stimuli-triggered reversibly modulated shape transitions. Asymmetric, linear hydrogels that include layer-selective switchable stimuli-responsive elements that control the hydrogel stiffness are designed. Trigger-induced stress in one of the layers results in the bending of the linear hybrid structure, thereby minimizing the elastic free energy of the systems. The removal of the stress by a counter-trigger restores the original linear bilayer hydrogel. The stiffness of the DNA hydrogel layers is controlled by thermal, pH (i-motif), K+ ion/crown ether (G-quadruplexes), chemical (pH-doped polyaniline), or biocatalytic (glucose oxidase/urease) triggers. A theoretical model relating the experimental bending radius of curvatures of the hydrogels with the Young's moduli and geometrical parameters of the hydrogels is provided. Promising applications of shape-regulated stimuli-responsive asymmetric hydrogels include their use as valves, actuators, sensors, and drug delivery devices.

Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals.

The riddle of anomalous polar behavior of the centrosymmetric crystal of α-glycine is resolved by the discovery of a polar, several hundred nanometer thick hydrated layer, created at the {010} faces during crystal growth. This layer was detected by two independent pyroelectric analytical methods: (i) periodic temperature change technique (Chynoweth) at ambient conditions and (ii) contactless X-ray photoelectron spectroscopy under ultrahigh vacuum. The total polarization of the surface layer is extremely large, yielding ≈1 µC·cm-2, and is preserved in ultrahigh vacuum, but disappears upon heating to 100 °C. Molecular dynamics simulations corroborate the formation of polar hydrated layers at the sub-microsecond time scale, however with a thickness of only several nanometers, not several hundred. This inconsistency might be reconciled by invoking a three-step nonclassical crystal growth mechanism comprising (i) docking of clusters from the supersaturated solution onto the evolving crystal, (ii) surface recognition and polar induction, and (iii) annealing and dehydration, followed by site-selective recrystallization.

Competing processes of micellization and fibrillization in native and reduced casein proteins.

Kappa-casein (κCN) and beta-casein (ßCN) are disordered proteins present in mammalian milk. In vitro, ßCN self-assembles into core-shell micelles. κCN self assembles into similar micelles, as well as into amyloid-like fibrils. Recent studies indicate that fibrillization can be suppressed by mixing ßCN and κCN, but the mechanism of fibril inhibition has not been identified. Examining the interactions of native and reduced kappa-caseins (N-κCN and R-κCN) with ßCN, we expose a competition between two different self-assembly processes: micellization and fibrillization. Quite surprisingly, however, we find significant qualitative and quantitative differences in the self-assembly between the native and reduced κCN forms. Specifically, thermodynamic analysis reveals exothermic demicellization for ßCN and its mixtures with R-κCN, as opposed to endothermic demicellization of N-κCN and its mixtures with ßCN at the same temperature. Furthermore, with time, R-κCN/ßCN mixtures undergo phase separation into pure ßCN micelles and R-κCN fibrils, while in the N-κCN/ßCN mixtures fibril formation is considerably delayed and mixed micelles persist for longer periods of time. Fibrils formed in N-κCN/ßCN mixtures are shorter and more flexible than those formed in R-κCN/ßCN systems. Interestingly, in the N-κCN/ßCN mixtures, the sugar moieties of N-κCN oligomers seem to organize on the mixed micelles surface in a manner similar to the organization of κCN in milk casein micelles.

Properties of Polyvinylpyrrolidone in a Deep Eutectic Solvent.

Deep eutectic solvents (DES) are mixtures of two or more components with high melting temperatures, which form a liquid at room temperature. These DES hold great promise as green solvents for chemical processes, as they are inexpensive and environmentally friendly. Specifically, they present a unique solvating environment to polymers that is different from water. Here, we use small angle neutron scattering to study the polymer properties of the common, water-soluble, polyvinylpyrrolidone (PVP) in the prominent DES formed by a 1:2 molar mixture of choline chloride and urea. We find that the polymer adopts a slightly different structure in DES than in water, so that at higher concentrations the polymer favors a more expanded conformation compared to the same concentration in water. Yet, the osmotic pressure of PVP solutions in DES is very similar to that in water, indicating that both solvents are of comparable quality and that the DES components interact favorably with PVP. The osmotic pressure measurements within this novel class of promising solvents should be of value toward future technological applications as well as for osmotic stress experiments in nonaqueous environments.

Effect of capsid confinement on the chromatin organization of the SV40 minichromosome.

Using small-angle X-ray scattering, we determined the three-dimensional packing architecture of the minichromosome confined within the SV40 virus. In solution, the minichromosome, composed of closed circular dsDNA complexed in nucleosomes, was shown to be structurally similar to cellular chromatin. In contrast, we find a unique organization of the nanometrically encapsidated chromatin, whereby minichromosomal density is somewhat higher at the center of the capsid and decreases towards the walls. This organization is in excellent agreement with a coarse-grained computer model, accounting for tethered nucleosomal interactions under viral capsid confinement. With analogy to confined liquid crystals, but contrary to the solenoid structure of cellular chromatin, our simulations indicate that the nucleosomes within the capsid lack orientational order. Nucleosomes in the layer adjacent to the capsid wall, however, align with the boundary, thereby inducing a 'molten droplet' state of the chromatin. These findings indicate that nucleosomal interactions suffice to predict the genome organization in polyomavirus capsids and underscore the adaptable nature of the eukaryotic chromatin architecture to nanoscale confinement.

Capturing Lipid Nanodisc Shape and Properties Using a Continuum Elastic Theory.

Lipid nanodiscs are nanometric bilayer patches enveloped by confining structures, commonly composed of membrane scaffolding proteins (MSPs). To resolve the interplay between MSP geometry, lipid confinement, and membrane material properties on the nanodisc shape, we apply a continuum elastic theory accounting for lipid bending, tilting, and area deformations. The equilibrium nanodisc shape is then determined by minimizing the elastic free energy functional. Analytic expressions derived under simplifying assumptions demonstrate that the nanodisc shape is sensitive to its size, lipid density, and the lipid tilt and thickness imposed at the contact with the MSP. Under matching physical parameters, these expressions quantitatively reproduce the shape of nanodiscs seen in molecular dynamics simulations, but only if lipid tilt is explicitly considered. We further demonstrate how the bending rigidity can be extracted from the membrane shape profile by fitting the numerically minimized full elastic functional to the membrane shape found in simulations. This fitting procedure faithfully informs on the bending rigidity of nanodiscs larger than ca. 5 nm in radius. The fitted profiles accurately reproduce the increase in bending modulus found using real-space fluctuation analysis of simulated nanodiscs and, for large nanodiscs, also accurately resolve its spatial variations. Our study shows how deformations in lipid patches confined in nanodiscs can be well described by a continuum elastic theory and how this fit can be used to determine local material properties from shape analysis of nanodiscs in simulations. This methodology could potentially allow direct determination of lipid properties from experiments, for example cryo-electron microscopy images of lipid nanodiscs, thereby allowing to guide the development of future nanodisc formulations with desired properties.

Urea counteracts trimethylamine N-oxide (TMAO) compaction of lipid membranes by modifying van der Waals interactions.

To cope with stress induced by high salinity and hydrostatic pressure, some marine animals accumulate small organic solutes called osmolytes. Most notable among these osmolytes are the denaturant urea, and trimethylamine N-oxide (TMAO) that is known to stabilize proteins. Although their effects on proteins and nucleic acids have been extensively studied, osmolytes are less commonly studied in the context of lipids, which are a crucial component in many cellular processes. Here we resolve the mechanism for urea's action on the forces acting between lipid membranes, in the presence and absence of TMAO. We find that unlike the way urea denatures proteins, and by contrast to TMAO, urea does not preferentially interact with net-neutral lipid membranes. Instead, urea modulates the interactions between membranes mainly by weakening the van der Waals attraction between bilayers. Interestingly, regardless of concentration, the effects of urea and TMAO appear to be additive to a large extent, so that the presence of one osmolyte hardly changes the interaction of the other with lipid. Weak non-additive effects are likely due to structural changes in the lipid membrane induced by the osmolytes. Finally, we comment on the potential role of osmolytes acting together in the modification of lipid adhesion and fusion.

Deep Eutectic Solvents for Efficient Drug Solvation: Optimizing Composition and Ratio for Solubility of ß-Cyclodextrin.

Deep eutectic solvents (DESs) show promise in pharmaceutical applications, most prominently as excellent solubilizers. Yet, because DES are complex multi-component mixtures, it is challenging to dissect the contribution of each component to solvation. Moreover, deviations from the eutectic concentration lead to phase separation of the DES, making it impractical to vary the ratios of components to potentially improve solvation. Water addition alleviates this limitation as it significantly decreases the melting temperature and stabilizes the DES single-phase region. Here, we follow the solubility of ß-cyclodextrin (ß-CD) in DES formed by the eutectic 2:1 mole ratio of urea and choline chloride (CC). Upon water addition to DES, we find that at almost all hydration levels, the highest ß-CD solubility is achieved at DES compositions that are shifted from the 2:1 ratio. At higher urea to CC ratios, due to the limited solubility of urea, the optimum composition allowing the highest ß-CD solubility is reached at the DES solubility limit. For mixtures with higher CC concentration, the composition allowing optimal solvation varies with hydration. For example, ß-CD solubility at 40 wt% water is enhanced by a factor of 1.5 for a 1:2 urea to CC mole ratio compared with the 2:1 eutectic ratio. We further develop a methodology allowing us to link the preferential accumulation of urea and CC in the vicinity of ß-CD to its increased solubility. The methodology we present here allows a dissection of solute interactions with DES components that is crucial for rationally developing improved drug and excipient formulations.

Spontaneous Patterning of Binary Ligand Mixtures on CdSe Nanocrystals: From Random to Janus Packing.

Binary compositions of surface ligands are known to improve the colloidal stability and fluorescence quantum yield of nanocrystals (NCs), due to ligand-ligand interactions and surface organization. Herein, we follow the thermodynamics of a ligand exchange reaction of CdSe NCs with alkylthiol mixtures. The effects of ligand polarity and length difference on ligand packing were investigated using isothermal titration calorimetry (ITC). The thermodynamic signature of the formation of mixed ligand shells was observed. Correlating the experimental results with thermodynamic mixing models has allowed us to calculate the interchain interactions and to infer the final ligand shell configuration. Our findings demonstrate that, in contrast to macroscopic surfaces, the small dimensions of the NCs and the subsequent increased interfacial region between dissimilar ligands allow the formation of a myriad of clustering patterns, controlled by the interligand interactions. This work provides a fundamental understanding of the parameters determining the ligand shell structure and should help guide smart surface design toward NC-based applications.

Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State.

Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.