Solvent Properties Governing Solute Partitioning in Polymer/Polymer Aqueous Two-Phase Systems: Nonionic Compounds

Recent advances in drug delivery applications of aqueous two-phase systems

Aqueous two-phase systems (ATPSs) are liquid-liquid equilibria between two aqueous phases that usually contain over 70% water content each, which results in a nontoxic organic solvent-free environment for biological compounds and biomolecules. ATPSs have attracted significant interest in applications for formulating carriers (microparticles, nanoparticles, hydrogels, and polymersomes) which can be prepared using the spontaneous phase separation of ATPSs as a driving force, and loaded with a wide range of bioactive materials, including small molecule drugs, proteins, and cells, for delivery applications. This review provides a detailed analysis of various ATPSs, including strategies employed for particle formation, polymerization of droplets in ATPSs, phase-guided block copolymer assemblies, and stimulus-responsive carriers. Processes for loading various bioactive payloads are discussed, and applications of these systems for drug delivery are summarized and discussed.

Arrangement of Hydrogen Bonds in Aqueous Solutions of Different Globular Proteins

This work presents the first evidence that dissolved globular proteins change the arrangement of hydrogen bonds in water, with different proteins showing quantitatively different effects. Using ATR-FTIR (attenuated total reflection—Fourier transform infrared) spectroscopic analysis of OH-stretch bands, we obtain quantitative estimates of the relative amounts of the previously reported four subpopulations of water structures coexisting in a variety of aqueous solutions. Where solvatochromic dyes can measure the properties of solutions of non-ionic polymers, the results correlate well with ATR-FTIR measurements. In protein solutions to which solvatochromic dye probes cannot be applied, NMR (nuclear magnetic resonance) spectroscopy was used for the first time to estimate the hydrogen bond donor acidity of water. We found strong correlations between the solvent acidity and arrangement of hydrogen bonds in aqueous solutions for several globular proteins. Even quite similar proteins are found to change water properties in dramatically different ways.

Hydrogen Bond Arrangement Is Shown to Differ in Coexisting Phases of Aqueous Two-Phase Systems

Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation.

Linear Relationships between Partition Coefficients of Different Organic Compounds and Proteins in Aqueous Two-Phase Systems of Various Polymer and Ionic Compositions

Analysis of the partition coefficients of small organic compounds and proteins in different aqueous two-phase systems under widely varied ionic compositions shows that logarithms of partition coefficients for any three compounds or proteins or two organic compounds and one protein are linearly interrelated, although for protein(s) there are ionic compositions when the linear fit does not hold. It is suggested that the established interrelationships are due to cooperativity of different types of solute-solvent interactions in aqueous media. This assumption is confirmed by analysis of distribution coefficients of various drugs in octanol-buffer systems with varied ionic compositions of the buffer. Analysis of the partition coefficients characterizing distribution of variety of drugs between blood and different tissues of rats in vivo reported in the literature showed that the above assumption is correct and enabled us to identify the tissues with the components of which the drug(s) may engage in presumably direct interactions. It shows that the suggested assumption is valid for even complex biological systems.

The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems

Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.

In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles

Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.

All-Aqueous Assemblies via Interfacial Complexation: Toward Artificial Cell and Microniche Development

In nature, the environment surrounding biomolecules and living cells can dictate their structure, function, and properties. Confinement is a key means to define and regulate such environments. For example, the confinement of appropriate constituents in compartments facilitates the assembly, dynamics, and function of biochemical machineries as well as subcellular organelles. Membraneless organelles, in particular, are thought to form via thermodynamic cues defined within the interior space of cells. On larger length scales, the confinement of living cells dictates cellular function for both mammalian and bacterial cells. One promising class of artificial structures that can recapitulate these multiscale confinement effects is based on aqueous two-phase systems (ATPSs). This feature article highlights recent developments in the production and stabilization of ATPS-droplet-based systems, with a focus on interfacial complexation. These systems enable structure formation, modulation, and triggered (dis)assembly, thereby allowing structures to be tailored to fit the desired function and designed for particular confinement studies. Open issues for both synthetic cells and niche studies are identified.

Protein intrinsic disorder-based liquid-liquid phase transitions in biological systems: Complex coacervates and membrane-less organelles

It is clear now that eukaryotic cells contain numerous membrane-less organelles, many of which are formed in response to changes in the cellular environment. Being typically liquid in nature, many of these organelles can be described as products of the reversible and highly controlled liquid-liquid phase transitions in biological systems. Many of these membrane-less organelles are complex coacervates containing (almost invariantly) intrinsically disordered proteins and often nucleic acids. It seems that the lack of stable structure in major proteinaceous constituents of these organelles is crucial for the formation of phase-separated droplets. This review considers several biologically relevant liquid-liquid phase transitions, introduces some general features attributed to intrinsically disordered proteins, represents several illustrative examples of intrinsic disorder-based phase separation, and provides some reasons for the abundance of intrinsically disordered proteins in organelles formed as a result of biological liquid-liquid phase transitions.

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.

Analysis of the distribution of organic compounds and drugs between biological tissues in the framework of solute partitioning in aqueous two-phase systems

Distribution of organic compounds between different biological tissues may be considered in the framework of solute partitioning in aqueous two-phase systems.

Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics

Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.

Analysis of partitioning of organic compounds and proteins in aqueous polyethylene glycol-sodium sulfate aqueous two-phase systems in terms of solute-solvent interactions

Partition behavior of nine small organic compounds and six proteins was examined in poly(ethylene glycol)-8000-sodium sulfate aqueous two-phase systems containing 0.5M osmolyte (sorbitol, sucrose, trehalose, TMAO) and poly(ethylene glycol)-10000-sodium sulfate system, all in 0.01M sodium phosphate buffer, pH 6.8. The differences between the solvent properties of the coexisting phases (solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were characterized with solvatochromic dyes using the solvatochromic comparison method. Differences between the electrostatic properties of the phases were determined by analysis of partitioning of sodium salts of dinitrophenylated (DNP-) amino acids with aliphatic alkyl side-chain. It was found out that the partition coefficient of all compounds examined (including proteins) may be described in terms of solute-solvent interactions. The results obtained in the study show that solute-solvent interactions of nonionic organic compounds and proteins in polyethylene glycol-sodium sulfate aqueous two-phase system differ from those in polyethylene glycol-dextran system.

Effects of Polymer Hydrophobicity on Protein Structure and Aggregation Kinetics in Crowded Milieu

We examined the effects of water-soluble polymers of various degrees of hydrophobicity on the folding and aggregation of proteins. The polymers we chose were polyethylene glycol (PEG) and UCON (1:1 copolymer of ethylene glycol and propylene glycol). The presence of additional methyl groups in UCON makes it more hydrophobic than PEG. Our earlier analysis revealed that similarly sized PEG and UCON produced different changes in the solvent properties of water in their solutions and induced morphologically different α-synuclein aggregates [Ferreira, L. A., et al. (2015) Role of solvent properties of aqueous media in macromolecular crowding effects. J. Biomol. Struct. Dyn., in press]. To improve our understanding of molecular mechanisms defining behavior of proteins in a crowded environment, we tested the effects of these polymers on secondary and tertiary structure and aromatic residue solvent accessibility of 10 proteins [five folded proteins, two hybrid proteins; i.e., protein containing ordered and disordered domains, and three intrinsically disordered proteins (IDPs)] and on the aggregation kinetics of insulin and α-synuclein. We found that effects of both polymers on secondary and tertiary structures of folded and hybrid proteins were rather limited with slight unfolding observed in some cases. Solvent accessibility of aromatic residues was significantly increased for the majority of the studied proteins in the presence of UCON but not PEG. PEG also accelerated the aggregation of protein into amyloid fibrils, whereas UCON promoted aggregation to amyloid oligomers instead. These results indicate that even a relatively small change in polymer structure leads to a significant change in the effect of this polymer on protein folding and aggregation. This is an indication that protein folding and especially aggregation are highly sensitive to the presence of other macromolecules, and an excluded volume effect is insufficient to describe their effect.

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.

Solvatochromism of symmetrical 2,6-distyrylpyridines. An experimental and theoretical study

Seven symmetrical 2,6-distyrylpyridines, phenyl-substituted with hydrogen-bond donors, hydrogen-bond acceptors, halogens and hydrophobic moieties were synthesized and their spectroscopic characterization was done. Solvent effects on the absorption and fluorescence spectra were analyzed and quantified using the Kamlet-Taft and Catalán approach. The obtained results were rationalized by comparison of electrostatic potentials of the molecules in the ground and in excited state and by comparison of the frontier molecular orbitals (HOMO and LUMO), derived from quantum-mechanical calculations (HF, DFT, MP2). Analysis of the results revealed an important influence of non-specific (dispersive) interactions on the solvatochromic behavior of the compounds. 1D and 2D NMR data, in silico obtained conformational assembly of the compound, and the NMR analysis of molecular flexibility in solution (NAMFIS), were used to estimate population of conformers and to deconvolute the UV-Vis spectrum of representative derivative; inferring that the conformational assembly is more complex than was assumed in so far published literature data for this class of compounds. Along with this, the emission spectra of the representative compounds were decomposed by the Multivariate Curve Resolution 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.

Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: I. Small organic compounds

Solvent properties of water in aqueous solutions of osmolytes (sorbitol, sucrose, trehalose, and trimethylamine N-oxide (TMAO)) were studied at different concentrations using the solvatochromic comparison method.

Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: II. Globular proteins

Partitioning of 11 globular proteins was examined in aqueous dextran–PEG–sodium/potassium phosphate buffer (0.01 M K/NaPB, pH 7.4) two-phase systems (ATPSs) containing 0.5 M sorbitol.

Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates

Here, we hypothesize that intrinsically disordered proteins (IDPs) serve as important drivers of the intracellular liquid-liquid phase separations that generate various membrane-less organelles. This hypothesis is supported by the overwhelming abundance of IDPs in these organelles. Assembly and disassembly of these organelles are controlled by changes in the concentrations of IDPs, their posttranslational modifications, binding of specific partners, and changes in the pH and/or temperature of the solution. Each resulting phase provides a distinct solvent environment for other solutes leading to their unequal distribution within phases. The specificity and efficiency of such partitioning is determined by the nature of the IDP(s) and defines "targeted" enrichment of specific molecules in the resulting membrane-less organelles that determines their specific activities.

Origin of salt additive effect on solute partitioning in aqueous polyethylene glycol-8000-sodium sulfate two-phase system

Partitioning of a homologous series of dinitrophenylted (DNP-) amino acids with aliphatic side chains was examined in aqueous polyethylene glycol (PEG)-8000-sodium sulfate two-phase systems (ATPS) with the additives NaSCN, NaClO4, and NaH2PO4 at concentrations varied from 0.025M up to 0.54M. The differences between the relative hydrophobicities and electrostatic properties of the two phases in all ATPS were estimated. Partitioning of adenine, adenosine mono-, di- and tri-phosphates was also examined in all ATPSs, including those with NaCl additive. Partition coefficients for these compounds and for nonionic organic compounds previously reported [L.A. Ferreira, P. Parpot, J.A. Teixeira, L.M. Mikheeva, B.Y. Zaslavsky, J. Chromatogr. A 1220 (2012) 14.] were analyzed in terms of linear solvent regression relationship. The results obtained suggest that the effects of the salts additives are related to their influence on the water structure.

Structural features important for differences in protein partitioning in aqueous dextran-polyethylene glycol two-phase systems of different ionic compositions

Partitioning of 15 proteins in dextran-70-polyethylene glycol (PEG)-8000 aqueous two-phase systems (ATPSs) in the presence of 0.01M sodium phosphate buffer, pH7.4 was studied. The effect of salt additives (NaCl, CsCl, Na2SO4, NaClO4 and NaSCN) at different concentrations on the protein partition behavior was examined. The salt effects on protein partitioning were analyzed by using the Collander solvent regression relationship between the protein partition coefficients in ATPSs with and without salt additives. The results obtained show that the presence and concentration of salt additives affect the protein partition behavior. Analysis of ATPSs in terms of the differences between the relative hydrophobicity and electrostatic properties of the phases does not explain the protein partition behavior. The differences between protein partitioning could not be explained by the protein size. The structural signatures for the proteins were constructed from partition coefficient values in four ATPSs with different salt additives, and the structural distances were calculated using cytochrome c as the reference structure. The structural distances for all the examined proteins (except lysozyme) were found to be interrelated. Analysis of about 50 different descriptors of the protein structures revealed that the partition behavior of proteins is determined by the peculiarities of their surfaces (e.g., the number of water-filled cavities and the averaged hydrophobicity of the surface residues) and by the intrinsic flexibility of the protein structure measured in terms of the B-factor (or temperature factor).

Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems

In an aqueous two-phase system (ATPS), the partitioning of a protein is defined by the differential interactions of the protein with aqueous media in the two phases. Our study shows that partitioning of proteins in a set of ATPSs of different ionic compositions can be used to quantify structural differences between α-synuclein, its variants and several globular proteins. Since application of ATPSs implies the use of high concentrations of two polymers in water when a certain threshold concentration of the polymers is exceeded, and since these levels of polymer concentrations are similar to those commonly used to mimic the effects of macromolecular crowding on proteins, we used circular dichroism spectroscopy to evaluate the structural consequences of placing proteins in solutions with high polymer concentrations and various ionic compositions.

Amino acid/water interactions study: a new amino acid scale

Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrostatic interactions with the aqueous environment of the amino acids were determined by multiple linear regression analysis using a modified linear solvation energy relationship. The solute-specific coefficients determined in this study together with the solute-specific coefficients reported previously for amino acids with non-polar side-chains where used in a Quantitative Structure/Property Relationship analysis. It is shown that linear combinations of these solute-specific coefficients are correlated well with various physicochemical, structural, and biological properties of amino acids.

Protein characterization by partitioning in aqueous two-phase systems

Protein partitioning in aqueous two-phase systems is a technique that enables one to monitor changes in the 3D structures of proteins in solution resulting from chemical modifications, conformational changes, and interactions with other proteins and ligands. The advantage of this technique is that it may be used to monitor the aforementioned changes for purified proteins as well as for proteins in biological fluids, and that it is readily adaptable to automated high-throughput mode.

Role of the Hofmeister series in the formation of ionic-liquid-based aqueous biphasic systems

Among the numerous and interesting features of ionic liquids is their ability to form aqueous biphasic systems (ABSs) when combined with inorganic or organic salts in aqueous media. In this work, a wide range of salts was studied, aiming at gathering a detailed picture on the molecular mechanisms that govern the ability of the salt ions to induce the formation of ionic-liquid-based ABSs. For that purpose, 1-butyl-3-methylimidazolium trifluoromethanesulfonate was chosen due to its facility to undergo liquid-liquid demixing in aqueous media containing conventional salts. The corresponding ternary phase diagrams, tie-lines, and tie-line lengths were determined at 298 K and atmospheric pressure. With the large body of data measured in this work, it was possible to establish a scale on the salt cation and anion abilities to induce the formation of ionic-liquid-based ABSs, which follows the Hofmeister series, and to show that the molar entropy of hydration of the salt ions is the driving force for aqueous two-phase system formation.

Solvent properties governing protein partitioning in polymer/polymer aqueous two-phase systems

Distribution coefficients of various proteins were measured in aqueous Dextran-Ficoll, Dextran-PES, and Ficoll-PES two-phase systems, containing 0.15M NaCl in 0.01 M phosphate buffer, pH 7.4. The acquired data were combined with data for the same proteins in different systems reported previously and known solvatochromic solvent properties of the systems to characterize the protein-solvent interactions. The relative susceptibilities of proteins to solvent dipolarity/polarizability, solvent hydrogen bond acidity, solvent hydrogen bond basicity, and solvent ability to participate in ion-ion and ion-dipole interactions were characterized. These parameters, which are representative of solute-solvent interactions, adequately described the partitioning of the proteins in each system. It was found that the relative susceptibilities of proteins to solvent dipolarity/polarizability are interrelated with their relative susceptibilities to solvent hydrogen bond acidity and solvent hydrogen bond basicity similarly to those established previously for small nonionic organic compounds.