Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins

Protein misfolding and amyloid nucleation through liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.

Biomimetic Sol-Gel Chemistry to Tailor Structure, Properties, and Functionality of Bionanocomposites by Biopolymers and Cells

Biosilica, synthesized annually only by diatoms, is almost 1000 times more abundant than industrial silica. Biosilicification occurs at a high rate, although the concentration of silicic acid in natural waters is ~100 μM. It occurs in neutral aqueous solutions, at ambient temperature, and under the control of proteins that determine the formation of hierarchically organized structures. Using diatoms as an example, the fundamental differences between biosilicification and traditional sol-gel technology, which is performed with the addition of acid/alkali, organic solvents and heating, have been identified. The conditions are harsh for the biomaterial, as they cause protein denaturation and cell death. Numerous attempts are being made to bring sol-gel technology closer to biomineralization processes. Biomimetic synthesis must be conducted at physiological pH, room temperature, and without the addition of organic solvents. To date, significant progress has been made in approaching these requirements. The review presents a critical analysis of the approaches proposed to date for the silicification of biomacromolecules and cells, the formation of bionanocomposites with controlled structure, porosity, and functionality determined by the biomaterial. They demonstrated the broad capabilities and prospects of biomimetic methods for creating optical and photonic materials, adsorbents, catalysts and biocatalysts, sensors and biosensors, and biomaterials for biomedicine.

The role of water in reactions catalysed by hydrolases under conditions of molecular crowding

Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.

Hofmeister Series: From Aqueous Solution of Biomolecules to Single Cells and Nanovesicles

Hofmeister effects play a critical role in numerous physicochemical and biological phenomena, including the solubility and/or accumulation of proteins, the activities of enzymes, ion transport in biochannels, the structure of lipid bilayers, and the dynamics of vesicle opening and exocytosis. This minireview focuses on how ionic specificity affects the physicochemical properties of biomolecules to regulate cellular exocytosis, vesicular content, and nanovesicle opening. We summarize recent progress in further understanding Hofmeister effects on biomacromolecules and their applications in biological systems. These important steps have increased our understanding of the Hofmeister effects on cellular exocytosis, vesicular content, and nanovesicle opening. Increasing evidence is firmly establishing that the ions along the Hofmeister series play an important role in living organisms that has often been ignored.

Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis

Aberrant aggregation of the misfolded presynaptic protein, α-Synuclein (α-Syn) into Lewy body (LB) and Lewy neuritis (LN) is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Numerous studies have suggested that prefibrillar and fibrillar species of the misfolded α-Syn aggregates are responsible for cell death in PD pathogenesis. However, the precise molecular events during α-Syn aggregation, especially in the early stages, remain elusive. Emerging evidence has demonstrated that liquid-liquid phase separation (LLPS) of α-Syn occurs in the nucleation step of α-Syn aggregation, which offers an alternate non-canonical aggregation pathway in the crowded microenvironment. The liquid-like α-Syn droplets gradually undergo an irreversible liquid-to-solid phase transition into amyloid-like hydrogel entrapping oligomers and fibrils. This new mechanism of α-Syn LLPS and gel formation might represent the molecular basis of cellular toxicity associated with PD. This review aims to demonstrate the recent development of α-Syn LLPS, the underlying mechanism along with the microscopic events of aberrant phase transition. This review further discusses how several intrinsic and extrinsic factors regulate the thermodynamics and kinetics of α-Syn LLPS and co-LLPS with other proteins, which might explain the pathophysiology of α-Syn in various neurodegenerative diseases.

Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY)

The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.

Structural Rearrangements of Carbonic Anhydrase Entrapped in Sol-Gel Magnetite Determined by ATR–FTIR Spectroscopy

Enzymatically active nanocomposites are a perspective class of bioactive materials that finds their application in numerous fields of science and technology ranging from biosensors and therapeutic agents to industrial catalysts. Key properties of such systems are their stability and activity under various conditions, the problems that are addressed in any research devoted to this class of materials. Understanding the principles that govern these properties is critical to the development of the field, especially when it comes to a new class of bioactive systems. Recently, a new class of enzymatically doped magnetite-based sol-gel systems emerged and paved the way for a variety of potent bioactive magnetic materials with improved thermal stability. Such systems already showed themself as perspective industrial and therapeutic agents, but are still under intense investigation and many aspects are still unclear. Here we made a first attempt to describe the interaction of biomolecules with magnetite-based sol-gel materials and to investigate facets of protein structure rearrangements occurring within the pores of magnetite sol-gel matrix using ATR Fourier-transform infrared spectroscopy.

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis

Cytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neurotoxic species causing neuronal cell death. However, understanding the structural and molecular insights of these oligomers are very challenging due to the heterogeneity and transient nature of the species. In this review, we discuss the recent advancements in understanding the formation and role of α-Syn oligomers in PD pathogenesis. We also summarize the different types of α-Syn oligomeric species and potential mechanisms to exert neurotoxicity. Finally, we address the possible ways to target α-Syn as a promising approach against PD and the possible future directions.

Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL

The Escherichia coli ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nanocage for a short duration. If confinement of the SPs is the mechanism by which GroEL/ES facilitates folding, it follows that the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. On the basis of our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.

All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy

The high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.

Nanoscale Surface-Induced Unfolding of Single Fibronectin Is Restricted by Serum Albumin Crowding

Understanding nanoscale protein conformational changes at solid-liquid interfaces is critical for predicting how proteins will impact the performance of biomaterials in vivo. Crowding is an important contributor to conformational stability. Here we apply single-molecule high resolution imaging with photobleaching to directly measure dye-conjugated fibronectin's unfolding in varying conditions of crowding with human serum albumin on aminosilanized glass. Using this approach, we identify serum albumin's crowding mechanism. We find that fibronectin achieves larger degrees of unfolding when not crowded by coadsorbed serum albumin. Serum albumin does not as effectively constrict fibronectin's conformation if it is sequentially, rather than simultaneously, introduced, suggesting that serum albumin's crowding mechanism is dependent on its ability to sterically block fibronectin's unfolding during the process of adsorption. Because fibronectin's conformation is dependent on interfacial macromolecular crowding under in vitro conditions, it is important to consider the role of in vivo crowding on protein activity.

Biodegradable polyethylene glycol hydrogels for sustained release and enhanced stability of rhGALNS enzyme

Mucopolysaccharidosis IVA (Morquio A disease) is a genetic disorder caused by deficiency of N-acetylgalactosamine-6-sulfate-sulfatase (GALNS), leading to accumulation of keratan sulfate and chondroitin-6-sulfate in lysosomes. Many patients become wheelchair-dependent as teens, and their life span is 20-30 years. Currently, enzyme replacement therapy (ERT) is the treatment of choice. Although it alleviates some symptoms, replacing GALNS enzyme poses several challenges including very fast clearance from circulation and instability at 37 °C. These constraints affect frequency and cost of enzyme infusion and ability to reach all tissues. In this study, we developed injectable and biodegradable polyethylene glycol (PEG) hydrogels, loaded with recombinant human GALNS (rhGALNS) to improve enzyme stability and bioavailability, and to sustain release. We established the enzyme's release profile via bulk release experiments and determined diffusivity using fluorescence correlation spectroscopy. We observed that PEG hydrogels preserved enzyme activity during sustained release for 7 days. In the hydrogel, rhGALNS diffused almost four times slower than in buffer. We further confirmed that the enzyme was active when released from the hydrogels, by measuring its uptake in patient fibroblasts. The developed hydrogel delivery device could overcome current limits of rhGALNS replacement and improve quality of life for Morquio A patients. Encapsulated GALNS enzyme in a polyethylene glycol hydrogel improves GALNS stability by preserving its activity, and provides sustained release for a period of at least 7 days.

Recombinant expression, biophysical and functional characterization of ClpS from Mycobacterium tuberculosis

Intracellular proteolysis is attracting more and more attention for its unique and important character in Mycobacterium tuberculosis (Mt). The ClpS protein from Mt (MtClpS) plays a critical role in intracellular proteolysis by recognizing N-end rule substrates, which makes it become a potential target for antibacterial drugs. However, the molecular mechanism of MtClpS recognizing N-end rule substrates remains unclear. Preparation of highly concentrated and pure MtClpS protein is a prerequisite for further structural and functional studies. In the present work, we tried several fusion tags and various expression conditions to maximize the production of MtClpS in Escherichia coli. We established an efficient approach for preparing the MtClpS protein with a high yield of 24.7 mg/l and a high purity of 98%. After buffer screening, we obtained a stable MtClpS protein sample concentrated at 0.63 mM in the presence of glycerol, l-Arginine, and l-Glutamate. Moreover, circular dichroism characterization indicated that the secondary structure of MtClpS consists of 38% α-helix and 24% β-sheet. The 2D 1H-15N HSQC nuclear magnetic resonance spectrum showed a good dispersion of resonance peaks with uniform intensity, indicating that the purified MtClpS protein was well folded and conformationally homogeneous. Isothermal titration calorimetry experiments revealed significant interactions of MtClpS with N-end rule peptides beginning with Leu, Tyr, Trp, or Phe. Furthermore, residues D34, D35, and H66 were confirmed as key residues for MtClpS recognizing the N-end rule peptide. The successful expression and biophysical characterization of MtClpS enabled us to gain insight into the molecular mechanism of MtClpS recognizing N-end rule substrates. The obtained stable and pure recombinant MtClpS will enable future inhibitor screening experiments.

The Hofmeister series: Specific ion effects in aqueous polymer solutions

Specific ion effects in aqueous polymer solutions have been under active investigation over the past few decades. The current state-of-the-art research is primarily focused on the understanding of the mechanisms through which ions interact with macromolecules and affect their solution stability. Hence, we herein first present the current opinion on the sources of ion-specific effects and review the relevant studies. This includes a summary of the molecular mechanisms through which ions can interact with polymers, quantification of the affinity of ions for the polymer surface, a thermodynamic description of the effects of salts on polymer stability, as well as a discussion on the different forces that contribute to ion-polymer interplay. Finally, we also highlight future research issues that call for further scrutiny. These include fundamental questions on the mechanisms of ion-specific effects and their correlation with polymer properties as well as a discussion on the specific ion effects in more complex systems such as mixed electrolyte solutions.

Thick Two-Dimensional Water Film Confined between the Atomically Thin Mica Nanosheet and Hydrophilic Substrate

The interesting properties of water molecules confined in a two-dimensional (2D) environment have aroused great attention. However, the study of 2D-confined water at the hydrophilic-hydrophilic interface is largely unexplored due to the lack of appropriate system. In this work, the behavior of water molecules confined between an atomically thin mica nanosheet and a hydrophilic SiO₂/Si substrate was investigated using an atomic force microscope in detail at ambient conditions. The confined water molecules aggregated as droplets when the relative humidity (RH) of the environment was 11%. A large-area 2D water film with a uniform thickness of ∼2 nm was observed when the mica flake was incubated at 33% RH for 1 h before being mechanically exfoliated on a SiO₂/Si substrate. Interestingly, the water film showed ordered edges with a predominant angle of 120°, which was the same with the lattice orientation of the mica nanosheet on top of it. The water film showed a fluidic behavior at the early stage and reached a stable state after 48 h under ambient conditions. The surface properties of the upper mica nanosheet and the underlying substrate played a crucial role in manipulating the behavior of confined water molecules. When the surface of the upper mica nanosheet was modified by Na⁺, Ni²⁺_, and aminopropyltriethoxysilane (APS), only some small water droplets were observed instead of a water film. The surface of the underlying SiO₂/Si substrate was functionalized by hydrophilic APS and hydrophobic octadecyltrimethoxysiliane (OTS). The small water droplets were imaged on a hydrophobic OTS-SiO₂/Si substrate, while the water film with regular edges was maintained on a hydrophilic APS-SiO₂/Si substrate. Our results might provide an alternative molecular view for investigating structures and properties of confined water molecules in 2D environments.

Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo

Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).

Macromolecular crowding for materials-directed controlled self-assembly

Macromolecular crowding refers to intracellular environments where various macromolecules, including proteins and nucleic acids, are present at high total concentrations. Its influence on biological processes has been investigated using a highly concentrated in vitro solution of water-soluble polymers as a model. Studies have revealed significant effects of macromolecular crowding on the thermodynamic equilibria and dynamics of biomolecular self-assembly in vivo. Recently, macromolecular crowding has attracted materials scientists, especially those in bio-related areas, as a tool to control molecular/colloidal self-assembly. Macromolecular crowding has been exploited to control the structure of supramolecular materials, assemble nanomaterials, and improve the performance of polymeric materials. Furthermore, nanostructured materials have been shown to be an interesting alternative to water-soluble polymers for creating crowded environments for controlled self-assembly. In this review article, we summarize recent progress in research on macromolecular crowding for controlled self-assembly in bio-related materials chemistry.

Interrogating the Osmotic Pressure of Self-Crowded Bovine Serum Albumin Solutions: Implications of Specific Monovalent Anion Effects Relative to the Hofmeister Series

The free-solvent-based (FSB) model and osmotic pressure were used to probe the ion binding and protein hydration for self-crowded bovine serum albumin in 0.15 M NaF, NaCl, NaI, and NaSCN solutions. All experiments were conducted with solutions at pH 7.4. The regressed results of the FSB model behavior to the measured osmotic pressure were excellent, albeit, the osmotic pressure data for NaSCN were noisy. The resulting ion binding and hydration were realistic values and the covariance of the two parameters was exceptionally low, providing substantial credibility to the FSB model. The results showed that the kosmotropic F^- and neutral Cl^- solutions generated significantly higher ion binding and protein hydration than the chaotropic solutions of I^- and SCN^-. Further, the ionic strength ratio and resulting hydration implied that the chaotropic solutions had substantially higher aggregation than the other salts investigated. Overall, the FSB model provides an additional, complementary tool to contribute to the analysis of crowded protein solutions relative to anions in the Hofmeister series as it can interrogate crowded solutions directly; something that is not possible with many measurement techniques.

Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels

Spatially confined environments are seen in biological systems and in the fields of biotechnology and nanotechnology. The confinement restricts the conformational space of polymeric molecules and increasing the degree of molecular crowding. Here, we developed preparation methods for agarose and polyacrylamide gels applicable to UV spectroscopy that can evaluate the confinement effects on DNA and protein structures. Measurements of UV absorbance and CD spectra showed no significant effect of the confinement in the porous media of agarose gels on the base-pair stability of DNA polynucleotides [poly(dA)/poly(dT)] and oligonucleotides (hairpin, duplex, and triplex structures). On the other hand, a highly confined environment created by polyacrylamide gels at high concentrations increased the stability of polynucleotides while leaving that of oligonucleotides unaffected. The changes in the base-pair stability of the polynucleotides were accompanied by the perturbation of the helical conformation. The polyacrylamide gels prepared in this study were also used for the studies on proteins (lysozyme, bovine serum albumin, and myoglobin). The effects on the proteins were different from the effects on DNA structures, suggesting different nature of interactions within the gel. The experimental methods and results are useful to understand the physical properties of nucleic acids and proteins under confined conditions.

Disorder-to-order transitions in the molten globule-like Golgi Reassembly and Stacking Protein

BACKGROUND

Golgi Reassembly and Stacking Proteins (GRASPs) are widely spread among eukaryotic cells (except plants) and are considered as key components in both the stacking of the Golgi cisternae and its lateral connection. Furthermore, GRASPs were also proved essential in the unconventional secretion pathway of several proteins, even though the mechanism remains obscure. It was previously observed that the GRASP homologue in Cryptococcus neoformans has a molten globule-like behavior in solution.

METHODS

We used circular dichroism, synchrotron radiation circular dichroism and steady-state as well as time-resolved fluorescence.

RESULTS

We report the disorder-to-order transition propensities for a native molten globule-like protein in the presence of different mimetics of cell conditions. Changes in the dielectric constant (such as those experienced close to the membrane surface) seem to be the major factor in inducing multiple disorder-to-order transitions in GRASP, which shows very distinct behavior when in conditions that mimic the vicinity of the membrane surface as compared to those found when free in solution. Other folding factors such as molecular crowding, counter ions, pH and phosphorylation exhibit lower or no effect on GRASP secondary structure and/or stability.

GENERAL SIGNIFICANCE

To the best of our knowledge, this is the first study focusing on understanding the disorder-to-order transitions of a molten globule structure without the need of any mild denaturing condition. A model is also introduced aiming at describing how the cell could manipulate the GRASP sensitivity to changes in the dielectric constant during different cell-cycle periods.

Thermal stability, storage and release of proteins with tailored fit in silica

Biological substances based on proteins, including vaccines, antibodies, and enzymes, typically degrade at room temperature over time due to denaturation, as proteins unfold with loss of secondary and tertiary structure. Their storage and distribution therefore relies on a "cold chain" of continuous refrigeration; this is costly and not always effective, as any break in the chain leads to rapid loss of effectiveness and potency. Efforts have been made to make vaccines thermally stable using treatments including freeze-drying (lyophilisation), biomineralisation, and encapsulation in sugar glass and organic polymers. Here for the first time we show that proteins can be enclosed in a deposited silica "cage", rendering them stable against denaturing thermal treatment and long-term ambient-temperature storage, and subsequently released into solution with their structure and function intact. This "ensilication" method produces a storable solid protein-loaded material without the need for desiccation or freeze-drying. Ensilication offers the prospect of a solution to the "cold chain" problem for biological materials, in particular for vaccines.

Enzymatic Synthesis of Cellulose Oligomer Hydrogels Composed of Crystalline Nanoribbon Networks under Macromolecular Crowding Conditions

Macromolecular crowding, a solution state with high macromolecular concentrations, was used to promote the crystallization-driven self-assembly of enzymatically synthesized cellulose oligomers. Cellulose oligomers were synthesized via cellodextrin phosphorylase-catalyzed enzymatic reactions in the concentrated solutions of water-soluble polymers, such as dextran, poly(ethylene glycol), and poly(N-vinylpyrrolidone). The reaction mixtures were transformed into cellulose oligomer hydrogels composed of well-grown crystalline nanoribbon networks irrespective of the polymer species. This method was successfully applied in the one-pot preparation of double network hydrogels composed of the nanoribbons and physically cross-linked gelatin molecules through the simple control of reaction temperatures, demonstrating the superior mechanical properties of the composite hydrogels. Our concept that promotes the growth of self-assembled architectures under macromolecular crowding conditions demonstrates a new avenue into developing novel hydrogel materials.

Specific Ion Effects and pH Dependence on the Interaction Forces between Polystyrene Particles

Colloidal interactions have been extensively studied due to the wide number of applications where colloids are present. In general, the electric double layer force and the van der Waals interaction dominate the net force acting between two colloids at large separation distances. However, it is well accepted that some other phenomena, especially those acting at short separation distances, might be relevant and induce substantial changes in the force profiles. Within these phenomena, those related to the surface contact angle, the hydration degree of the ions, or the pH, may dominate the force profiles features, not only at short distances. In this paper, we analyzed the effect of the pH and counterion type on the long-range as well as short-range forces between polystyrene colloidal particles by using the colloidal probe technique based on AFM. Our results confirm that the features of the force profiles between polystyrene surfaces are strongly affected by the pH and hydration degree of the counterions in solution. Additionally, we performed a study of the role of the pH on the wettability properties of hydrated and nonhydrated polystyrene sheets to scan the wettability properties of this material with pH. Contact angle measurements confirmed that the polystyrene surface is hydrophobic in aqueous solutions over the entire range of pHs investigated. These results are in good agreement with the features observed in the force profiles at low pH. At high pH, a short-range repulsion similar to the one observed for hydrophilic materials is observed. This repulsion scales with the pH, and it also depends on the hydration degree of the ions in solution. This way, the short-range forces between polystyrene surfaces may be tunable with the pH, and its origin does not seem to be related to the hydrophobicity of the material.

Environmental Topology and Water Availability Modulates the Catalytic Activity of β-Galactosidase Entrapped in a Nanosporous Silicate Matrix

In the present work we studied the catalytic activity of E. coli β-Gal confined in a nanoporous silicate matrix (E_β-Gal) at different times after the beginning of the sol-gel polymerization process. Enzyme kinetic experiments with two substrates (ONPG and PNPG) that differed in the rate-limiting steps of the reaction mechanism for their β-Gal-catalyzed hydrolysis, measurements of transverse relaxation times (T₂) of water protons through ¹H-NMR, and scanning electron microscopy analysis of the gel nanostructure, were performed. In conjunction, results provided evidence that water availability is crucial for the modulation observed in the catalytic activity of β-Gal as long as water participate in the rate limiting step of the reaction (only with ONPG). In this case, a biphasic rate vs. substrate concentration was obtained exhibiting one phase with catalytic rate constant (k_cA), similar to that observed in solution, and another phase with a higher and aging-dependent catalytic rate constant (k_cB). More structured water populations (lower T₂) correlates with higher catalytic rate constants (k_cB). The T₂-k_cB negative correlation observed along the aging of gels within the 15-days period assayed reinforces the coupling between water structure and the hydrolysis catalysis inside gels.

Pair correlations that link the hydrophobic and Hofmeister effects

The Hofmeister effect describes how different ions make solutes more or less hydrophobic. The effect is thought to occur due to structural changes in the solvent induced by the ion's presence, particularly in water. In this study, the structural changes in water due to the presence of ions are investigated by molecular dynamics simulations of various monatomic ions in the SPC/E water model. Structural analyses reveal specific orientations of solvating waters around each of the ions studied. Using a new method, these orientations are quantified by a set of pair correlation functions that describe dipole-ion correlations in structure. These correlations are shown to contribute to the potential of mean force between waters and the ion of interest, and therefore to the free energy of the system. The magnitude of this free energy is found to result in a Hofmeister series for the various ions studied, therefore demonstrating a Hofmeister effect with respect to water's structure that is quantified by pair correlation functions. Most crucially, the pair correlations that lead to this Hofmeister effect also contribute to the hydrophobic effect (the entropy of hydrophobic solvation) [Liu et al., J. Chem. Phys., 2015, 142, 114117], and those which dominate the hydrophobic effect are modulated by an ion's presence, therefore demonstrating a mechanistic link between the two effects.

Hofmeister Ion-Induced Changes in Water Structure Correlate with Changes in Solvation of an Aggregated Protein Complex

RecA is a naturally aggregating Escherichia coli protein that catalyzes the strand exchange reaction utilized in DNA repair. Previous studies have shown that the presence of salts influence RecA activity, aggregation, and stability and that salts stabilize RecA in an inverse-anionic Hofmeister series. Here we utilized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and circular dichroism (CD) to investigate how various Hofmeister salts alter the water structure and RecA solvation and aggregation. Spectroscopic studies performed in water and deuterium oxide suggest that salts alter water O-(1)H and O-(2)H stretch and bend vibrations as well as protein amide I (or I') and amide II (or II') vibrations. Anions have a much larger influence on water vibrations than cations. Water studies also show increased water-water and/or water-ion interactions in the presence of strongly hydrated SO4(2-) salts and evidence for decreased interactions with weakly hydrated Cl(-) and ClO4(-) salts. Salt-water difference infrared spectra show that kosmotropic salts are more hydrated than chaotropic salts. Interestingly, this is the opposite trend to the changes in protein solvation. Infrared spectra of RecA show that vibrations associated with protein desolvation were observed in the presence of SO4(2-) salts. Conversely, vibrations associated with protein solvation were observed in the presence of Cl(-) and ClO4(-) salts. Difference infrared studies on the dehydration of model proteins aided in identifying changes in RecA-solvent interactions. This study provides evidence that salt-induced changes in water vibrations correlate to changes in protein solvent interactions and thermal stability.

Protein unfolding in crowded milieu: what crowding can do to a protein undergoing unfolding?

The natural environment of a protein inside a cell is characterized by the almost complete lack of unoccupied space, limited amount of free water, and the tightly packed crowd of various biological macromolecules, such as proteins, nucleic acids, polysaccharides, and complexes thereof. This extremely crowded natural milieu is poorly mimicked by slightly salted aqueous solutions containing low concentrations of a protein of interest. The accepted practice is to model crowded environments by adding high concentrations of various polymers that serve as model "crowding agents" to the solution of a protein of interest. Although studies performed under these model conditions revealed that macromolecular crowding might have noticeable influence on various aspects related to the protein structure, function, folding, conformational stability, and aggregation propensity, the complete picture describing conformational behavior of a protein under these conditions is missing as of yet. Furthermore, there is an accepted belief that the conformational stability of globular proteins increases in the presence crowding agents due to the excluded volume effects. The goal of this study was to conduct a systematic analysis of the effect of high concentrations of PEG-8000 and Dextran-70 on the unfolding behavior of eleven globular proteins belonging to different structural classes.

Hydrophobicity-dependent effects of polymers on different protein conformations

Polymers can either induce or disrupt secondary and tertiary structure in partially disordered protein conformations. The balance of the forces driving these structural changes depends on the polymer hydrophobicity and protein sequence and structure. ​

Effects of macromolecular crowding on the structure of a protein complex: a small-angle scattering study of superoxide dismutase

Macromolecular crowding can alter the structure and function of biological macromolecules. We used small-angle scattering to measure the effects of macromolecular crowding on the size of a protein complex, SOD (superoxide dismutase). Crowding was induced using 400 MW PEG (polyethylene glycol),TEG (triethylene glycol), α-MG (methyl-α-glucoside), and TMAO (trimethylamine n-oxide). Parallel small-angle neutron scattering and small-angle x-ray scattering allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. Small-angle x-ray scattering done in the presence of TEG suggests that for further deformation-beyond a 9% decrease in volume-the resistance to deformation may increase dramatically.

Spectroscopic Characterization of Structural Changes in Membrane Scaffold Proteins Entrapped within Mesoporous Silica Gel Monoliths

The changes in the orientation and conformation of three different membrane scaffold proteins (MSPs) upon entrapment in sol-gel-derived mesoporous silica monoliths were investigated. MSPs were examined in either a lipid-free or a lipid-bound conformation, where the proteins were associated with lipids to form nanolipoprotein particles (NLPs). NLPs are water-soluble, disk-shaped patches of a lipid bilayer that have amphiphilic MSPs shielding the hydrophobic lipid tails. The NLPs in this work had an average thickness of 5 nm and diameters of 9.2, 9.7, and 14.8 nm. We have previously demonstrated that NLPs are more suitable lipid-based structures for silica gel entrapment than liposomes because of their size compatibility with the mesoporous network (2-50 nm) and minimally altered structure after encapsulation. Here we further elaborate on that work by using a variety of spectroscopic techniques to elucidate whether or not different MSPs maintain their protein-lipid interactions after encapsulation. Fluorescence spectroscopy and quenching of the tryptophan residues with acrylamide, 5-DOXYL-stearic acid, and 16-DOXYL-stearic acid were used to determine the MSP orientation. We also utilized fluorescence anisotropy of tryptophans to measure the relative size of the NLPs and MSP aggregates after entrapment. Finally, circular dichroism spectroscopy was used to examine the secondary structure of the MSPs. Our results showed that, after entrapment, all of the lipid-bound MSPs maintained orientations that were minimally changed and indicative of association with lipids in NLPs. The tryptophan residues appeared to remain buried within the hydrophobic core of the lipid tails in the NLPs and appropriately spaced from the bilayer center. Also, after entrapment, lipid-bound MSPs maintained a high degree of α-helical content, a secondary structure associated with protein-lipid interactions. These findings demonstrate that NLPs are capable of serving as viable hosts for functional integral membrane proteins in the synthesis of sol-gel-derived bioinorganic hybrid nanomaterials.

Role of solvent properties of aqueous media in macromolecular crowding effects

Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.

Beyond the excluded volume effects: mechanistic complexity of the crowded milieu

Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.

A comparative study of the effects of the Hofmeister series anions of the ionic salts and ionic liquids on the stability of α-chymotrypsin

Direct interactions between the anion and the catalytic amino acid residues lead to denaturation of CT.

The effect of amorphous calcium phosphate on protein protection against thermal denaturation

The amorphous calcium phosphate can maintain a stable semi-aqueous nanoscale environment for encapsulated catalase to significantly improve its thermal stability.

Entropy and enthalpy of interaction between amino acid side chains in nanopores

Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.