Advances of ionic liquids-based methods for protein analysis

Scattering approaches to unravel protein solution behaviors in ionic liquids and deep eutectic solvents: From basic principles to recent developments

Proteins in ionic liquids (ILs) and deep eutectic solvents (DESs) have gained significant attention due to their potential applications in various fields, including biocatalysis, bioseparation, biomolecular delivery, and structural biology. Scattering approaches including dynamic light scattering (DLS) and small-angle X-ray and neutron scattering (SAXS and SANS) have been used to understand the solution behavior of proteins at the nanoscale and microscale. This review provides a thorough exploration of the application of these scattering techniques to elucidate protein properties in ILs and DESs. Specifically, the review begins with the theoretical foundations of the relevant scattering approaches and describes the essential solvent properties of ILs and DESs linked to scattering such as refractive index, scattering length density, ion-pairs, liquid nanostructure, solvent aggregation, and specific ion effects. Next, a detailed introduction is provided on protein properties such as type, concentration, size, flexibility and structure as observed through scattering methodologies. This is followed by a review of the literature on the use of scattering for proteins in ILs and DESs. It is highlighted that enhanced data analysis and modeling tools are necessary for assessing protein flexibility and structure, and for understanding protein hydration, aggregation and specific ion effects. It is also noted that complementary approaches are recommended for comprehensively understanding the behavior of proteins in solution due to the complex interplay of factors, including ion-binding, dynamic hydration, intermolecular interactions, and specific ion effects. Finally, the challenges and potential research directions for this field are proposed, including experimental design, data analysis approaches, and supporting methods to obtain fundamental understandings of complex protein behavior and protein systems in solution. We envisage that this review will support further studies of protein interface science, and in particular studies on solvent and ion effects on proteins.

Protein Interface Regulating the Inserting Process of Imidazole Ionic Liquids into the Cell Membrane

Ionic liquids (ILs) have shown promising potential in membrane protein extraction; however, the underlying mechanism remains unclear. Herein, we employed GPU-accelerated molecular dynamics (MD) simulations to investigate the dynamic insertion process of ILs into cell membranes containing membrane proteins. Our findings reveal that ILs spontaneously insert into the membrane, and the presence of membrane proteins significantly decelerates the rate of IL insertion into the membrane. Specifically, the relationship between the insertion rate and inserting free energy exhibits non-monotonic changes, which can be attributed to interfacial effects. The protein-water interface acts as trap for free ions and ionic clusters, while free ions preferentially insert into the membrane from the protein-lipid interface, which limits the insertion rate due to its narrowness. Thus, the insertion rate is governed by a combination of the free energy and interfacial effects. These findings provide valuable insights into the interfacial effects of protein-lipid bilayers and have implications for various biochemical-related applications.

Concentrated ionic liquids for proteomics: Caveat emptor!

The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.

Metal organic layers enabled cell surface engineering coupling biomembrane fusion for dynamic membrane proteome profiling

Systematically dissecting the highly dynamic and tightly communicating membrane proteome of living cells is essential for the system-level understanding of fundamental cellular processes and intricate relationship between membrane-bound organelles constructed through membrane traffic. While extensive efforts have been made to enrich membrane proteins, their comprehensive analysis with high selectivity and deep coverage remains a challenge, especially at the living cell state. To address this problem, we developed the cell surface engineering coupling biomembrane fusion method to map the whole membrane proteome from the plasma membrane to various organelle membranes taking advantage of the exquisite interaction between two-dimensional metal-organic layers and phospholipid bilayers on the membrane. This approach, which bypassed conventional biochemical fractionation and ultracentrifugation, facilitated the enrichment of membrane proteins in their native phospholipid bilayer environment, helping to map the membrane proteome with a specificity of 77% and realizing the deep coverage of the HeLa membrane proteome (5087 membrane proteins). Furthermore, membrane N-phosphoproteome was profiled by integrating the N-phosphoproteome analysis strategy, and the dynamic membrane proteome during apoptosis was deciphered in combination with quantitative proteomics. The features of membrane protein N-phosphorylation modifications and many differential proteins during apoptosis associated with mitochondrial dynamics and ER homeostasis were found. The method provided a simple and robust strategy for efficient analysis of membrane proteome, offered a reliable platform for research on membrane-related cell dynamic events and expanded the application of metal-organic layers.

Ionic Liquid-Based Polymer Nanocomposites for Sensors, Energy, Biomedicine, and Environmental Applications: Roadmap to the Future

Current interest toward ionic liquids (ILs) stems from some of their novel characteristics, like low vapor pressure, thermal stability, and nonflammability, integrated through high ionic conductivity and broad range of electrochemical strength. Nowadays, ionic liquids represent a new category of chemical-based compounds for developing superior and multifunctional substances with potential in several fields. ILs can be used in solvents such as salt electrolyte and additional materials. By adding functional physiochemical characteristics, a variety of IL-based electrolytes can also be used for energy storage purposes. It is hoped that the present review will supply guidance for future research focused on IL-based polymer nanocomposites electrolytes for sensors, high performance, biomedicine, and environmental applications. Additionally, a comprehensive overview about the polymer-based composites' ILs components, including a classification of the types of polymer matrix available is provided in this review. More focus is placed upon ILs-based polymeric nanocomposites used in multiple applications such as electrochemical biosensors, energy-related materials, biomedicine, actuators, environmental, and the aviation and aerospace industries. At last, existing challenges and prospects in this field are discussed and concluding remarks are provided.

Insights into Ionic Liquids: From Z-Bonds to Quasi-Liquids

Ionic liquids (ILs) hold great promise in the fields of green chemistry, environmental science, and sustainable technology due to their unique properties, such as a tailorable structure, the various types available, and their environmentally friendly features. On the basis of multiscale simulations and experimental characterizations, two unique features of ILs are as follows: (1) strong coupling interactions between the electrostatic forces and hydrogen bonds, namely in the Z-bond, and (2) the unique semiordered structure and properties of ultrathin films, specifically regarding the quasi-liquid. In accordance with the aforementioned theoretical findings, many cutting-edge applications have been proposed: for example, CO₂ capture and conversion, biomass conversion and utilization, and energy storage materials. Although substantial progress has been made recently in the field of ILs, considerable challenges remain in understanding the nature of and devising applications for ILs, especially in terms of e.g. in situ/real-time observation and highly precise multiscale simulations of the Z-bond and quasi-liquid. In this Perspective, we review recent developments and challenges for the IL research community and provide insights into the nature and function of ILs, which will facilitate future applications.

Ionic Liquid-Based Extraction System for In-Depth Analysis of Membrane Protein Complexes

Limited by the rare efficient extraction system in extracting hydrophobic membrane protein complexes (MPCs) without compromising the stability of protein-protein interactions (PPIs), the in-depth functional study of MPCs has lagged far behind. In this study, the first systematic screening of ionic liquids (ILs) was performed and showed that triethylammonium acetate (TEAA) IL exhibited excellent performance in stabilizing PPIs, which was further confirmed by molecular docking simulations. By combining TEAA with the conventional detergent Nonidet P-40 (NP-40), a novel IL-based extraction system, i-TAN (TEAA IL with 1% NP-40), was proposed, which demonstrated superior performance in extracting and stabilizing MPCs, attributed to its larger size, more uniform distribution, and closer-to-neutral microenvironment of micelles. Extraction of MPCs with i-TAN allowed the confident identification of more hydrophobic EGFR-interacting proteins that are easily dissociated during the extraction process. Quantitative analysis of the difference in EGFR complexes between trastuzumab-sensitive and trastuzumab-resistant breast cancer cells provided comprehensive insights to understand the drug resistance mechanism, suggesting that i-TAN has great potential in interactomics and functional analysis of MPCs. This study provides a novel strategy for MPC extraction and downstream processing.

Unravelling the Interactions of Magnetic Ionic Liquids by Energy Decomposition Schemes: Towards a Transferable Polarizable Force Field

This work aims at unravelling the interactions in magnetic ionic liquids (MILs) by applying Symmetry-Adapted Perturbation Theory (SAPT) calculations, as well as based on those to set-up a polarisable force field model for these liquids. The targeted MILs comprise two different cations, namely: 1-butyl-3-methylimidazolium ([Bmim]⁺) and 1-ethyl-3-methylimidazolium ([Emim]⁺), along with several metal halides anions such as [FeCl₄]⁻, [FeBr₄]⁻, [ZnCl₃]⁻ and [SnCl₄]²⁻ To begin with, DFT geometry optimisations of such MILs were performed, which in turn revealed that the metallic anions prefer to stay close to the region of the carbon atom between the nitrogen atoms in the imidazolium fragment. Then, a SAPT study was carried out to find the optimal separation of the monomers and the different contributions for their interaction energy. It was found that the main contribution to the interaction energy is the electrostatic interaction component, followed by the dispersion one in most of the cases. The SAPT results were compared with those obtained by employing the local energy decomposition scheme based on the DLPNO-CCSD(T) method, the latter showing slightly lower values for the interaction energy as well as an increase of the distance between the minima centres of mass. Finally, the calculated SAPT interaction energies were found to correlate well with the melting points experimentally measured for these MILs.

Carbon material-immobilized ionic liquids were applied on absorption of Hg2+ from water phase

In this study, several immobilized ionic liquid adsorbents on carbon materials were synthesized with impregnation method. The carrier materials were activated carbon and three kinds of multi-walled carbon nanotubes. And the synthetic adsorbents immobilized different kinds of ionic liquids were characterized by Boehm titration, FT-IR, XPS, TG, and BET analysis, respectively. Finally, carbon materials after [C4mim]HSO₄ immobilization were selected as adsorbent to remove Hg²⁺ from water phase. The optimum conditions of adsorption test of ionic liquid immobilized by multi-walled carbon nanotubes were as follows: the initial concentration of Hg²⁺ was 400 mg/L, the adsorbent addition amount was 40 mg, the temperature was 20 °C, the reaction time was 200 min, the removal rate of Hg²⁺ peaked at 62.95%, the adsorption capacity was reached 79.00 mg/g. The optimum conditions of adsorption test of ionic liquid immobilized by activated carbon were as follows: the initial concentration of Hg²⁺ was 300 mg/L, the adsorbent addition amount was 0.2 g, the temperature was 20 °C, pH was 2.0, the reaction time was 100 min, the removal rate of Hg²⁺ was more than 99%, the adsorption capacity was 118.65 mg/g. The adsorption isotherm fitting study found that the adsorption of adsorbent on Hg²⁺ was more in line with the Langmuir model, and the adsorption kinetics study shows that the adsorption process is consistent with the pseudo-second-order kinetic equation. The results of kinetic analysis are further verified by thermodynamic analysis.

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.

New Developments in Material Preparation Using a Combination of Ionic Liquids and Microwave Irradiation

During recent years, synthetic methods combining microwaves and ionic liquids became accepted as a promising methodology for various materials preparations because of their high efficiency and low energy consumption. Ionic liquids with high polarity are heated rapidly, volumetrically and simultaneously under microwave irradiation. Hence, combination of microwave irradiation as a heating source with ionic liquids with various roles (e.g., solvent, additive, template or reactant) opened a completely new technique in the last twenty years for nanomaterials and polymers preparation for applications in various materials science fields including polymer science. This review summarizes recent developments of some common materials syntheses using microwave-assisted ionic liquid method with a focus on inorganic nanomaterials, polymers, carbon-derived composites and biomass-based composites. After that, the mechanisms involved in microwave-assisted ionic-liquid (MAIL) are discussed briefly. This review also highlights the role of ionic liquids in the reaction and crucial issues that should be addressed in future research involving this synthesis technique.