On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics

Ionic Liquid Gating Induces Anomalous Permeation through Membrane Channel Proteins

Membrane channel proteins (MCPs) play key roles in matter transport through cell membranes and act as major targets for vaccines and drugs. For emerging ionic liquid (IL) drugs, a rational understanding of how ILs affect the structure and transport function of MCP is crucial to their design. In this work, GPU-accelerated microsecond-long molecular dynamics simulations were employed to investigate the modulating mechanism of ILs on MCP. Interestingly, ILs prefer to insert into the lipid bilayer and channel of aquaporin-2 (AQP2) but adsorb on the entrance of voltage-gated sodium channels (Nav). Molecular trajectory and free energy analysis reflect that ILs have a minimal impact on the structure of MCPs but significantly influence MCP functions. It demonstrates that ILs can decrease the overall energy barrier for water through AQP2 by 1.88 kcal/mol, whereas that for Na+ through Nav is increased by 1.70 kcal/mol. Consequently, the permeation rates of water and Na+ can be enhanced and reduced by at least 1 order of magnitude, respectively. Furthermore, an abnormal IL gating mechanism was proposed by combining the hydrophobic nature of MCP and confined water/ion coordination effects. More importantly, we performed experiments to confirm the influence of ILs on AQP2 in human cells and found that treatment with ILs significantly accelerated the changes in cell volume in response to altered external osmotic pressure. Overall, these quantitative results will not only deepen the understanding of IL-cell interactions but may also shed light on the rational design of drugs and disease diagnosis.

Perspectives in the Computational Modeling of New Generation, Biocompatible Ionic Liquids

In this Perspective, I review the current state of computational simulations on ionic liquids with an emphasis on the recent biocompatible variants. These materials are used here as an example of relatively complex systems that highlights the limits of some of the approaches commonly used to study their structure and dynamics. The source of these limits consists of the coexistence of nontrivial electrostatic, many-body quantum effects, strong hydrogen bonds, and chemical processes affecting the mutual protonation state of the constituent molecular ions. I also provide examples on how it is possible to overcome these problems using suitable simulation paradigms and recently improved techniques that, I expect, will be gradually introduced in the state-of-the-art of computational simulations of ionic liquids.

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.

Exploring conformational preferences of proteins: ionic liquid effects on the energy landscape of avidin

In this work we experimentally investigate solvent and temperature induced conformational transitions of proteins and examine the role of ion–protein interactions in determining the conformational preferences of avidin, a homotetrameric glycoprotein, in choline-based ionic liquid (IL) solutions. Avidin was modified by surface cationisation and the addition of anionic surfactants, and the structural, thermal, and conformational stabilities of native and modified avidin were examined using dynamic light scattering, differential scanning calorimetry, and thermogravimetric analysis experiments. The protein-surfactant nanoconjugates showed higher thermostability behaviour compared to unmodified avidin, demonstrating distinct conformational ensembles. Small-angle X-ray scattering data showed that with increasing IL concentration, avidin became more compact, interpreted in the context of molecular confinement. To experimentally determine the detailed effects of IL on the energy landscape of avidin, differential scanning fluorimetry and variable temperature circular dichroism spectroscopy were performed. We show that different IL solutions can influence avidin conformation and thermal stability, and we provide insight into the effects of ILs on the folding pathways and thermodynamics of proteins. To further study the effects of ILs on avidin binding and correlate thermostability with conformational heterogeneity, we conducted a binding study. We found the ILs examined inhibited ligand binding in native avidin while enhancing binding in the modified protein, indicating ILs can influence the conformational stability of the distinct proteins differently. Significantly, this work presents a systematic strategy to explore protein conformational space and experimentally detect and characterise ‘invisible’ rare conformations using ILs.

Revealing solvent and temperature induced conformational transitions of proteins and the role of ion–protein interactions in determining the conformational preferences of avidin in ionic liquids.

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.

Proteins in Ionic Liquids: Reactions, Applications, and Futures

Biopolymer processing and handling is greatly facilitated by the use of ionic liquids, given the increased solubility, and in some cases, structural stability imparted to these molecules. Focussing on proteins, we highlight here not just the key drivers behind protein-ionic liquid interactions that facilitate these functionalities, but address relevant current and potential applications of protein-ionic liquid interactions, including areas of future interest.