Reversible folding-unfolding, aggregation protection, and multi-year stabilization, in high concentration protein solutions, using ionic liquids

An eminent approach towards next generation solvents for sustainable packaging and stability of enzymes: a comprehensive study of ionic liquid and deep eutectic solvent mixtures

Hybrid ionic fluids (HIFs) are newly emerging and fascinating sustainable solvent media, which are attracting a great deal of scientific interest in protecting the native structure of proteins. For a few decades, there has been a demand to consider ionic liquids (ILs) and deep eutectic solvents (DESs) as biocompatible solvent media for enzymes; however, in some cases, these solvent media also show limitations. Therefore, this work focuses on synthesising novel HIFs to intensify the properties of existing ILs and DESs by mixing them. Herein, HIFs have been synthesised by the amalgamation of a deep eutectic solvent (DES) and an ionic liquid (IL) with a common cation or anion. Later on, the stability and activity of hen's egg white lysozyme (Lyz) in the presence of biocompatible solvent media and HIFs were studied by various techniques such as UV-vis, steady-state fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and dynamic light scattering (DLS) measurements. This work emphasises the effect of a DES (synthesised using 1 : 2 choline chloride and malonic acid) [Maline], ILs (1-butyl-3-methylimidazolium chloride [BMIM]Cl or choline acetate [Chn][Ac]) and their corresponding HIFs on the structure and functionality of Lyz. Moreover, we also studied the secondary structure, thermal stability, enzymatic activity and thermodynamic profile of Lyz at pH = 7 in the presence of varying concentrations (0.1 to 0.5 M) of [BMIM]Cl and [Chn][Ac] ILs, Maline as a DES, and Maline [BMIM]Cl (HIF1) and Maline [Chn][Ac] (HIF2). Spectroscopic results elucidate that ILs affect the activity and structural stability of Lyz. In contrast, the stability and activity are inhibited by DES and are enhanced by HIFs at all the studied concentrations. Overall, the experimental results studied explicitly elucidate that the structure and stability of Lyz are maintained in the presence of HIF1 while these properties are intensified in HIF2. This study shows various applications in biocompatible green solvents, particularly in the stability and functionality of proteins, due to their unique combination where the properties counteract the negative effect of either DESs or ILs in HIFs.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Determination of the critical pH for unfolding water-soluble cod protein and its effect on encapsulation capacities

Hydrophobic polyphenols, with a variety of physiological activities, are often practically limited due to their low water solubility and chemical instability, among which curcumin (Cur) is a representative hydrophobic polyphenol. To improve Cur, the cod protein (CP)-Cur composite particles (CP-Cur) were successfully prepared using the pH-shift method, but this pH-shift method (7-12-7) required a higher pH, which limited application and increased cost. The critical pH of CP structure unfolding during pH-shift and its encapsulation effect on Cur were investigated in this paper. During the pH-shift process, the critical pH of the structural unfolding of CP was pH 10, and the degree of protein structure unfolding was higher, which was attributed to the increasing electrostatic repulsion, and the weakened hydrogen bond and hydrophobic interaction. The encapsulation efficiency of CP-Cur formed after pH 10-shift was higher than that formed after pH 9.8-shift, which increased by 22.17 %. At pH 9.8, the binding sites in CP reached saturation at the molar ratio of 10, while at pH 10 and 10.2, the binding sites in CP both reached saturation at the molar ratio of 14, also indicating that the protein treated with critical pH could bind more Cur. The binding between Cur and CP was mostly hydrophobic interaction, accompanied by hydrogen bonding and electrostatic interactions. The above results verified the necessity of critical pH in the experiment, indicating that critical pH could indeed improve the encapsulation effect and obtain a higher encapsulation efficiency. This work will help improve the large-scale application of hydrophobic functional substances in production.

The Potential Role of Ionic Liquid as a Multifunctional Dental Biomaterial

In craniofacial research and routine dental clinical procedures, multifunctional materials with antimicrobial properties are in constant demand. Ionic liquids (ILs) are one such multifunctional intelligent material. Over the last three decades, ILs have been explored for different biomedical applications due to their unique physical and chemical properties, high task specificity, and sustainability. Their stable physical and chemical characteristics and extremely low vapor pressure make them suitable for various applications. Their unique properties, such as density, viscosity, and hydrophilicity/hydrophobicity, may provide higher performance as a potential dental material. ILs have functionalities for optimizing dental implants, infiltrate materials, oral hygiene maintenance products, and restorative materials. They also serve as sensors for dental chairside usage to detect oral cancer, periodontal lesions, breath-based sobriety, and dental hard tissue defects. With further optimization, ILs might also make vital contributions to craniofacial regeneration, oral hygiene maintenance, oral disease prevention, and antimicrobial materials. This review explores the different advantages and properties of ILs as possible dental material.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study

Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.

Small angle X-ray scattering investigation of ionic liquid effect on the aggregation behavior of globular proteins

Globular proteins are well-folded model proteins, where ions can substantially influence their structure and aggregation. Ionic liquids (ILs) are salts in the liquid state with versatile ion combinations. Understanding the IL effect on protein behavior remains a major challenge. Here, we employed small angle X-ray scattering to investigate the effect of aqueous ILs on the structure and aggregation of globular proteins, namely, hen egg white lysozyme (Lys), human lysozyme (HLys), myoglobin (Mb), β-lactoglobulin (βLg), trypsin (Tryp) and superfolder green fluorescent protein (sfGFP). The ILs contain ammonium-based cations paired with the mesylate, acetate or nitrate anion. Results showed that only Lys was monomeric, whereas the other proteins formed small or large aggregates in buffer. Solutions with over 17 mol% IL resulted in significant changes in the protein structure and aggregation. The Lys structure was expanded at 1 mol% but compact at 17 mol% with structural changes in loop regions. HLys formed small aggregates, with the IL effect similar to Lys. Mb and βLg mostly had distinct monomer and dimer distributions depending on IL type and IL concentration. Complex aggregation was noted for Tryp and sfGFP. While the anion had the largest ion effect, changing the cation also induced the structural expansion and protein aggregation.

Current understanding and insights towards protein stabilization and activation in deep eutectic solvents as sustainable solvent media

Deep eutectic solvents (DESs) have emerged as a new class of green, designer and biocompatible solvents, an alternative to conventional organic solvents and ionic liquids (ILs) which are comparatively toxic and non-biodegradable. DESs are eutectic mixtures that are formed when a hydrogen bond acceptor (HBA) is mixed with a hydrogen bond donor (HBD) at particular molar ratios by mechanical grinding or under mild heating conditions. Very recently, these solvents have been the center of attention for researchers in biotechnology, biomedicine and various scientific applications. These environmentally benign solvents have a close analogy with ILs; however, they offer certain unique merits over traditional ILs. DESs display remarkable properties such as easy preparation, tunable composition, biodegradability, recyclability, inherently low toxicity, sustainability and biocompatibility; these special features validate DESs as new potential solvents/co-solvents for biomolecules. Mechanistically, the biocompatibility and protein friendly nature of DESs depend on various factors, which include the composition of the DES, viscosity and hydration level. Therefore, it becomes an essential task to bring together all the studies related to protein behaviour in DESs to unlock their biomolecular proficiency. This review specifically highlights recent insights into the biomacromolecular functionality in DESs, including outlines of the solubilization and stabilization of proteins, long term protein packaging, different extraction methods and enzyme activation in the presence of DESs. A literature survey reveals that DESs act as green media in which the protein structure and activity are retained. In some cases, proteins refolded and enzymatic activity was enhanced several fold in the presence of DESs. Furthermore, we have reviewed the possible mechanistic behaviour behind protein stabilization, refolding and activation in DESs. Overall, the main objective of this review is to explicate the advantages of the introduction of DESs for biomolecules and to demonstrate the versatility of these eco-friendly solvents for future bio-based applications.

Lipid Membrane Flexibility in Protic Ionic Liquids

Here, we determine by neutron spin echo spectrometry (NSE) how the flexibility of egg lecithin vesicles depends on solvent composition in two protic ionic liquids (PILs) and their aqueous mixtures. In combination with small-angle neutron scattering (SANS), dynamic light scattering (DLS), and fluorescent probe microscopy, we show that the bending modulus is up to an order of magnitude lower than in water but with no change in bilayer thickness or nonpolar chain composition. This effect is attributed to the dynamic association and exchange of the IL cation between the membrane and bulk liquid, which has the same origin as the underlying amphiphilic nanostructure of the IL solvent itself. This provides a new mechanism by which to tune and control lipid membrane behavior.

Role of ionic liquids on stabilization of therapeutic proteins and model proteins

Ionic liquids (ILs) exhibit potential as excipients to stabilize proteins in solutions. This mini-review is not a detailed reference book on ILs, rather a brief overview of the main achievements published in the literature on their effect on protein aggregation, unfolding, structural and thermal stability, and activity. The main focus of the manuscript is three widely studied groups of ionic liquids: imidazolium-, cholinium- and alkylammonium-based and their effect on the model and therapeutic proteins.

Recovery of enzyme structure and activity following rehydration from ionic liquid

Long-term preservation of proteins at room temperature continues to be a major challenge. Towards using ionic liquids (ILs) to address this challenge, here we present a combination of experiments and simulations to investigate changes in lysozyme upon rehydration from IL mixtures using two imidazolium-based ILs (1-ethyl-3-methylimidazolium ethylsulfate, [EMIM][EtSO₄] and 1-ethyl-3-methylimidazolium diethylphosphate, [EMIM][Et₂PO₄]). Various spectroscopic experiments and molecular dynamics simulations are performed to ascertain the structure and activity of lysozyme. Circular dichroism spectroscopy confirms that lysozyme maintains its secondary structure upon rehydration, even after 295 days. Increasing the IL concentration decreases the activity of lysozyme and is ultimately quenched at sufficiently high IL concentrations, but the rehydration of lysozyme from high IL concentrations completely restores its activity. Such rehydration occurs in the most common lysozyme activity assay, but without careful attention, this effect on the IL concentration can be overlooked. From simulations we observe occupation of [EMIM⁺] ions near the vicinity of the active site and the ligand-lysozyme complex is less stable in the presence of ILs, which results in the reduction of lysozyme activity. Upon rehydration, fast leaving of [EMIM⁺] is observed and the availability of active site is restored. In addition, suppression of structural fluctuations is also observed when in high IL concentrations, which also explains the decrease of activity. This structure suppression is recovered after undergoing rehydration. The return of native protein structure and activity indicates that after rehydration lysozyme returns to its original state. Our results also suggest a simple route to protein recovery following extended storage.

Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties

Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.

Protic Ionic Liquid Cation Alkyl Chain Length Effect on Lysozyme Structure

Solvents that stabilize protein structures can improve and expand their biochemical applications, particularly with the growing interest in biocatalytic-based processes. Aiming to select novel solvents for protein stabilization, we explored the effect of alkylammonium nitrate protic ionic liquids (PILs)-water mixtures with increasing cation alkyl chain length on lysozyme conformational stability. Four PILs were studied, that is, ethylammonium nitrate (EAN), butylammonium nitrate (BAN), hexylammonium nitrate (HAN), and octylammonium nitrate (OAN). The surface tension, viscosity, and density of PIL-water mixtures at low to high concentrations were firstly determined, which showed that an increasing cation alkyl chain length caused a decrease in the surface tension and density as well as an increase in viscosity for all PIL solutions. Small-angle X-ray scattering (SAXS) was used to investigate the liquid nanostructure of the PIL solutions, as well as the overall size, conformational flexibility and changes to lysozyme structure. The concentrated PILs with longer alkyl chain lengths, i.e., over 10 mol% butyl-, 5 mol% hexyl- and 1 mol% octylammonium cations, possessed liquid nanostructures. This detrimentally interfered with solvent subtraction, and the more structured PIL solutions prevented quantitative SAXS analysis of lysozyme structure. The radius of gyration (R_g) of lysozyme in the less structured aqueous PIL solutions showed little change with up to 10 mol% of PIL. Kratky plots, SREFLEX models, and FTIR data showed that the protein conformation was maintained at a low PIL concentration of 1 mol% and lower when compared with the buffer solution. However, 50 mol% EAN and 5 mol% HAN significantly increased the R_g of lysozyme, indicating unfolding and aggregation of lysozyme. The hydrophobic interaction and liquid nanostructure resulting from the increased cation alkyl chain length in HAN likely becomes critical. The impact of HAN and OAN, particularly at high concentrations, on lysozyme structure was further revealed by FTIR. This work highlights the negative effect of a long alkyl chain length and high concentration of PILs on lysozyme structural stability.

Recent Advances in Ionic Liquids in Biomedicine

The use of ionic liquids and deep eutectic solvents in biomedical applications has grown dramatically in recent years due to their unique properties and their inherent tunability. This review will introduce ionic liquids and deep eutectics and discuss their biomedical applications, namely solubilization of drugs, creation of active pharmaceutical ingredients, delivery of pharmaceuticals through biological barriers, stabilization of proteins and other nucleic acids, antibacterial agents, and development of new biosensors. Current challenges and future outlooks are discussed, including biocompatibility, the potential impact of the presence of impurities, and the importance of understanding the microscopic interactions in ionic liquids in order to design task-specific solvents.

Spontaneous Fibrillation of Bovine Serum Albumin at Physiological Temperatures Promoted by Hydrolysis-Prone Ionic Liquids

This study highlights the role of time-dependent hydrolysis of ionic liquid anion, [BF₄]^-, of ionic liquid (IL), 1-ethyl-3-methylimidazolium tetrafluoroborate, [C₂mim][BF₄], which results in ever-changing pH conditions. Such pH changes along with the ionic interactions bring conformational changes in bovine serum albumin (BSA), leading to the formation of amyloid fibers at 37 °C without external control of pH or addition of electrolyte. The fibrillation of BSA occurs spontaneously with the addition of IL; however, the highest growth rate has been observed in aqueous solution of 10% IL (v/v %) among investigated systems. Thioflavin T (ThT) fluorescence emission has been employed to monitor the growth and development of β-sheet content in amyloid fibrils. The structural alterations in BSA have also been investigated using intrinsic fluorescence measurements. Circular dichroism (CD) measurements confirmed the formation of amyloid fibrils. Transmission electron microscopy (TEM) has been explored to establish the morphologies of BSA fibrils at different intervals of time, whereas atomic force microscopy (AFM) has established the helically twisted nature of grown amyloid fibrils. The docking studies have been utilized to understand the insertion of IL ions in different domains of BSA, which along with decreased pH cause the unfolding and growth of BSA into amyloid fibrils. It is expected that the results obtained from this study would help to understand the impact of IL containing [BF₄]^- anion on protein stability and aggregation along with providing a new platform to control the formation of amyloid fibrils and other biomaterials driven via ionic interactions and alterations in pH.

Cryopreservation of mammalian cells using protic ionic liquid solutions

Cryopreservation has facilitated considerable advances in both medical technology and scientific research. However, further developments have been limited by the relatively low number of effective cryoprotective agents. Even after fifty years of research, most protocols rely on the same two toxic agents, i.e. dimethylsulfoxide or glycerol. Ionic liquids are a class of promising solvents which are known glass formers and may offer a less-toxic alternative. The research presented here investigates ten protic ionic liquids as potential cryoprotective agents. The liquids are screened for key properties including cellular toxicity, permeability and thermal behaviour. The most promising, ethylammonium acetate, was then tested as a cryoprotective agent on a model cell line and was found to be as effective as the common cryoprotectant, dimethylsulfoxide. This work reports the first use of a protic ionic liquid as an effective cryoprotective agent for a mammalian cell line. This will inform the development of a suite of potential new ionic liquid-based cryoprotectants that could potentially allow the cryopreservation of new cell types.

Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation

Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.

Computational analysis of the effect of [Tea][Ms] and [Tea][H2PO4] ionic liquids on the structure and stability of Aβ(17-42) amyloid fibrils

Experimental studies have reported the possibility of affecting the growth/dissolution of amyloid fibres by the addition of organic salts of the room-temperature ionic-liquid family, raising the tantalizing prospect of controlling these processes under physiological conditions. The effect of [Tea][Ms] and [Tea][H₂PO₄] at various concentrations on the structure and stability of a simple model of Aβ42 fibrils has been investigated by computational means. Free energy computations show that both [Tea][Ms] and [Tea][H₂PO₄] decrease the stability of fibrils with respect to isolated peptides in solution, and the effect is significantly stronger for [Tea][Ms]. The secondary structure of fibrils is not much affected, but single peptides in solution show a marked decrease in their β-strand character and an increase in α-propensity, again especially for [Tea][Ms]. These observations, consistent with the experimental picture, can be traced to two primary effects, i.e., the difference in the ionicity of the [Tea][Ms] and [Tea][H₂PO₄] water solutions and the remarkable affinity of peptides for [Ms]^- anions, due to the multiplicity of H-bonds.

Selective ion transport across a lipid bilayer in a protic ionic liquid

Ionic liquids (ILs) have exhibited enormous potential as electrolytes, designer solvents and reaction media, as well as being surprisingly effective platforms for amphiphile self-assembly and for preserving structure of complex biomolecules. This has led to their exploration as media for long-term biopreservation and in biosensors, for which their viability depends on their ability to sustain both structure and function within complex, multicomponent nanoscale compartments and assemblies. Here we show that a tethered lipid bilayer can be assembled directly in a purely IL environment that retains its structure upon exchange between IL and aqueous buffer, and that the membrane transporter valinomycin can be incorporated so as to retain its functionality and cation selectivity. This paves the way for the development of long-lived, non-aqueous microreactors and sensor assemblies, and demonstrates the potential for complex proteins to retain functionality in non-aqueous, ionic liquid solvents.

Effect of ionic liquids on the fluorescence properties and aggregation of superfolder green fluorescence protein

Proteins generally tend to aggregate with less desirable properties in numerous solvents, which is one of the major challenges in the development of solvents for functional proteins. This work aims to utilize fluorescence spectroscopy and small angle X-ray scattering (SAXS) to understand the effects of ionic liquids (ILs) on the fluorescence and aggregation behavior of superfolder green fluorescent protein (sfGFP). The studied ILs consisted of four different anions coupled with primary, tertiary and quaternary ammonium cations. The results show that the chromophore fluorescence was generally maintained in 1 mol% IL-water mixtures, then decreased with increasing IL concentration. We primarily employed the pseudo-radius of gyration (pseudo-R_g) to evaluate sfGFP aggregation. The sfGFP was less aggregated with nitrate-based ILs compared to in buffer, and more aggregated in the mesylate-based ILs. Further, we show that the polyol additives of glycerol and glucose in IL-water mixtures slightly decreased the sfGFP propensity to aggregate. Size-exclusion chromatography (SEC)-SAXS was used to characterize the monomeric sfGFP in ethylammonium nitrate (EAN) and triethylammonium mesylate (TEAMs)-water mixtures. The presence of 1 mol% TEAMs maintained the sfGFP fluorescence, promoted the compact structure, but slightly increased the amount of large aggregates, which contrasted with that of EAN.

Effects of Ionic Liquids on Metalloproteins

In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.

Use of Ionic Liquids in Protein and DNA Chemistry

Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.

Implication of Threonine-Based Ionic Liquids on the Structural Stability, Binding and Activity of Cytochrome c

Ionic liquids (ILs) are useful in pharmaceutical industries and biotechnology as alternative solvents or sources for protein extraction and purification, preservation of biomolecules and for regulating the catalytic activity of enzymes. However, the binding mechanism, the non-covalent forces responsible for protein-IL interactions and dynamics of proteins in IL need to be investigated in depth for the effective use of ILs as alternatives. Herein, we disclose the molecular level understanding of the structural intactness and reactivity of a model protein cytochrome c (Cyt c) in biocompatible threonine-based ILs with the help of experimental techniques such as isothermal titration calorimetry (ITC), fluorescence spectroscopy, transmission electron microscopy (TEM) as well as molecular docking. Hydrophobic and electrostatic forces are responsible for the structural and conformational integrity of Cyt c in IL. The ITC experiments revealed the Cyt c-IL binding free energies are in the range of 10-14 kJ/mol and the molecular docking studies demonstrated that ILs interact at the surfaces of Cyt c. The results look promising as the ILs used here are non-toxic and biocompatible, and thus may find potential applications in structural biology and biotechnology.

Lysozyme conformational changes with ionic liquids: Spectroscopic, small angle x-ray scattering and crystallographic study

Solvents that support protein functionality are important for biochemical applications, and new solvents are required. Here we employ FTIR and fluorescence spectroscopies, small angle X-ray scattering (SAXS) and X-ray crystallography to understand conformational changes of lysozyme with ionic liquids (ILs) added. Spectroscopic techniques identified that the secondary structure of lysozyme was maintained at the lower IL concentrations of 1 and 5 mol%, though the Tryptophan environment was significantly altered with nitrate-based ILs present. SAXS experiments indicated that the radius of gyration of lysozyme increased with 1 mol% IL present, and then decreased with increasing IL concentrations. The tertiary structure, particularly the loop regions, changed as a function of IL concentration, and this depended on the IL type. The crystallographic structure of lysozyme with the IL of ethylammonium nitrate present confirmed the loop region was extended, and identified three specific binding sites with nitrate ions, and that the positively charged areas were IL sensitive regions. This work provides a detailed understanding of lysozyme conformational changes in the presence of ILs. This approach can be extended to other functionally-important proteins.

On the Stability and Conformational Dynamics of Cytochrome c in Ammonium Ionic Liquids

Owing to their potential applications in the extraction, purification, and preservation of biomolecules and biocatalysis, ionic liquids (ILs) have gained great attention in biotechnology. Although it is known that the structure and dynamics of proteins in ILs depend on the nature of both proteins and ILs, the biophysical mechanism governing the protein-IL interaction, which determines the stability of proteins or the activity of an enzyme in these nonconventional media, is yet to be understood clearly. Herein, we study the effect of two ammonium ILs, triethylammonium dihydrogen phosphate (TEAP) and tributylammonium dihydrogen phosphate (TBAP), on the stability and conformational dynamics of cytochrome c (Cyt c) in its native and unfolded states, employing primarily the single molecule-based fluorescence correlation spectroscopy (FCS) technique. The results show that the native structure of Cyt c is not significantly altered by TEAP, but the tertiary structure is perturbed to a great extent by TBAP, which comprises a longer alkyl chain. Fluctuations of the fluorescence intensity of Alexa488 dye-labeled Cyt c in FCS measurements reveal conformational dynamics (67 ± 10 μs) in the native state of Cyt c that is accelerated in the presence of both ILs but not affected when Cyt c is in its unfolded state. The present findings demonstrate how the stability of this protein can be modulated by using ammonium ILs of different alkyl chain lengths.

Structural-functional integrity of lysozyme in imidazolium based surface active ionic liquids

The present study was designed to explore the hydrophobicity and concentration dependence of imidazolium based surface active ionic liquids (SAILs) effects on the structural-functional integrity of proteins. Specifically, we investigated the impact of SAILs viz. 1-octyl-3-methylimidazolium dodecylbenzenesulfonate ([OMIM][DBS]) and 1-dodecyl-3-methylimidazolium dodecylbenzenesulfonate ([DDMIM][DBS]) on activity, structure and stability of lysozyme. Activity measurements revealed that, in contrast to [DDMIM][DBS] that renders lysozyme either feebly active or inactive, [OMIM][DBS] significantly enhances the lysozyme activity in the concentration range of critical aggregation concentrations (CAC) to C_s (SAIL saturation concentration of protein backbone) i.e., 0.5 mM-1.35 mM. Tensiometric results in agreement with turbidity measurements inferred significant composition and concentration dependence of the lysozyme-SAIL interactions. Spectroscopic investigations revealed that compared to destabilizing behaviour of [DDMIM][DBS], [OMIM][DBS] significantly enhances both conformational as well as thermal stability of lysozyme in the CAC to C_s concentration regime. Altogether, results obtained do indicate that [OMIM][DBS], in the concentration regime of CAC to C_s, serves as an efficient stabiliser with an ability to appreciably enhance the activity, thermal stability and overall conformational stability of lysozyme. We firmly believe that [OMIM][DBS], at least in the CAC to C_s concentration ranges, can be exploited as a promising stabiliser and activity enhancer for numerous industrially important enzymes.

Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods

Understanding the interaction of the ionic liquid (IL) with protein is vital to find the origin of the conformational changes of proteins in these alternative solvents. Here, we performed biased molecular dynamics simulations of alanine dipeptide (ADP), a widely used model for protein backbone structure, in water and two hydrated ionic liquids (ILs): 80% (w/w) 1-ethyl-3-methylimidazolium acetate ([EMIm][Ac]) and 80% (w/w) choline dihydrogen phosphate ([Cho][DHP]). We employed three different biasing methods, metadynamics (metaD), well-tempered metadynamics (WT-metaD), and adaptive biasing force (ABF), to construct the free-energy landscapes of the ADP conformations using the backbone dihedral angles (ϕ and ψ) as the collective variables. The calculations were also performed in water; the free-energy landscapes of ADP in water obtained from three methods are similar and agree well with the previously reported results. In hydrated [EMIm][Ac], α-planar conformation emerges as a minimum, which is comparable to that of α and β conformations corresponding to α-helix and β-sheet-like conformations of proteins. Investigation of corresponding conformations suggests that the imidazolium ring of [EMIm] cation is stacked with the amide bonds of ADP. Acetate anion makes hydrogen bonds with the amide hydrogens of the ADP. The amide-π stacking interaction is the driving force for α-planar conformation to become one of the minimum energy conformations in this IL, which destabilizes the protein conformation. However, α and β conformations are more stable in hydrated [Cho][DHP] compared to α-planar and β-planar conformations; therefore, this IL stabilizes the protein conformation. These findings are in good correlation with the previous study of proteins in these ILs. Our study helps to understand the interaction of proteins with the ionic entities and their stability in ILs.

Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, R_g and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.

Dual mechanism of ionic liquid-induced protein unfolding

Ionic liquids (ILs) are gaining attention as protein stabilizers and refolding additives.

Strategic planning of proteins in ionic liquids: future solvents for the enhanced stability of proteins against multiple stresses

Ionic liquids (ILs) present a vast number of solvents capable of replacing toxic organic solvents in chemical, biotechnology and biomedical applications. ILs are inexpensive and environmentally friendly as the materials can be recycled conveniently. Chemists use a variety of cation and anion combinations to produce an IL that fits the requirements of the sustainable future through the pursuit of greener chemical processes. As such, the development of various types of ILs has been recognized as the emergence of environmentally friendly solvents to attain enhanced protein stability in vitro. The literature survey reveals that there exist a large number of scholarly articles as well as elegant reviews on protein stability in ILs. Biomolecules have adapted to antagonistic environmental stresses that normally denature proteins, and the mechanism of adaptation that protects the cellular components against denaturation involves the intracellular concentration of co-solvents. In this regard, recent experimental results distinctly demonstrated that ILs are stabilizing proteins against denaturing stresses, and their presence in the cells does not alter protein functional activities. However, a review focusing particularly on the refolding and counteracting effects of the ILs against denatured proteins by multiple stresses is still missing. This perspective unveils the studies that have been conducted to improve protein stabilities with ILs as well as the refolding and counteracting abilities of these ILs against the denatured proteins under the influence of multiple stresses. We believe that ILs can provide significant environmental and economic advantages for biochemical processes in the near future. Essentially, numerous investigations are required to allow us to further explore the stabilizing properties of ILs over proteins.

Key factor governing the physicochemical properties and extent of proton transfer in protic ionic liquids: ΔpKa or chemical structure?

A series of protic ionic liquids (PILs) are prepared by neutralisation of bis(trifluoromethanesulfonyl)amide acid (H[NTf₂]) with various amines, and the properties (especially thermal stability and ionicity) are compared with those of PILs from 1,8-diazabicyclo[5.4.0]-7-undecene (DBU) and various acids.

Does poly(ionic liquid) modulate the non-covalent interactions of chicken egg white lysozyme? Elucidation of biomolecular interactions between biomolecules and macromolecular solvents

Stabilizing and destabilizing effects of different poly(ionic liquid) (PIL) concentrations on chicken egg white lysozyme as a reason for bimolecular interactions.

Hydrated ionic liquids enable both solubilisation and refolding of aggregated concanavalin A

Dissolution and refolding of aggregated concanavalin A were demonstrated in hydrated ionic liquids.

Dynamics of Ionic Liquid-Assisted Refolding of Denatured Cytochrome c: A Study of Preferential Interactions toward Renaturation

In vitro refolding of denatured protein and the influence of the alkyl chain on the refolding of a protein were tested using long chain imidazolium chloride salts, 1-methyl-3-octylimidazolium chloride [C₈mim][Cl], and 1-decyl-3-methylimidazolium chloride [C₁₀mim][Cl]. The horse heart cytochrome c (h-cyt c) was denatured by urea and guanidinium hydrochloride (GdnHCl), as well as by base-induced denaturation at pH 13, to provide a broad overview of the overall refolding behavior. The variation in the alkyl chain of the ionic liquids (ILs) showed a profound effect on the refolding of denatured h-cyt c. The ligand-induced refolding was correlated to understand the mechanism of the conformational stability of proteins in aqueous solutions of ILs. The results showed that the long chain ILs having the [C₈mim]⁺ and [C₁₀mim]⁺ cations promote the refolding of alkali-denatured h-cyt c. The IL having the [C₁₀mim]⁺ cation efficiently refolded the alkali-denatured h-cyt c with the formation of the MG state, whereas the IL having the [C₈mim]⁺ cation, which is known to be compatible for protein stability, shows slight refolding and forms a different transition state. The lifetime results show successful refolding of alkaline-denatured h-cyt c by both of the ILs, however, more refolding was observed in the case of [C₁₀mim][Cl], and this was correlated with the fast and medium lifetimes (τ₁ and τ₂) obtained, which show an increase accompanied by an increase in secondary structure. The hydrophobic interactions plays an important role in the refolding of chemically and alkali-denatured h-cyt c by long chain imidazolium ILs. The formation of the MG state by [C₁₀mim][Cl] was also confirmed, as some regular structure exists far below the CMC of IL. The overall results suggested that the [C₁₀mim]⁺ cation bound to the unfolded h-cyt c triggers its refolding by electrostatic and hydrophobic interactions that stabilize the MG state.

Ionic liquids in protein amyloidogenesis: a brief screenshot of the state-of-the-art

Ionic liquids (ILs) are a vast class of organic non-aqueous electrolytes whose interaction with biomolecules is receiving great attention for potential applications in bio-nano-technology. Recently, it has been shown that ILs can affect protein amyloidogenesis. Whereas some ILs favour the aggregation of proteins into amyloids, others inhibit their formation. Moreover, ILs can dissolve mature fibrils and restore the protein biochemical function. In this letter, we present a brief state-of-the-art summary of this emerging field that holds the promise of important developments both in basic science and in applications from bio-medicine to material science, and bio-nano-technology. The huge variety of ILs offers a vast playground for future studies and potential applications.

Effect of water and ionic liquids on biomolecules

The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.