Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions

Physicochemical control of solvation and molecular assembly of charged amphiphilic oligomers at air-aqueous interfaces

HYPOTHESIS

Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures.

EXPERIMENTS

Three representative salts - (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM+) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations.

FINDINGS

Langmuir trough surface pressure - area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies.

Solubilization of fish myofibrillar proteins in NaCl and KCl solutions: A DIA-based proteomics analysis

Understanding the basic solubilization of fish myofibrillar proteins (MPs) in common monovalent chloride solutions is crucial for muscle food processing. In this study, the differential proteomic profiles of MPs during extraction and solubilization in NaCl and KCl solutions were investigated by using advanced four-dimensional data-independent acquisition (4D DIA) quantitative proteomics for the first time. Compared to routine biochemical analysis, this could provide insights into the solubilization of muscle proteins. We ensure the consistency of the effective ionic strength of NaCl and KCl buffers by adjusting the conductivity. The results showed that NaCl extractor mainly facilitated the solubilization of cytoskeletal proteins, biochemical enzymes, and stromal proteins compared to KCl, such as tubulin, myosin-9, collagen, plectin, protein phosphatase, and cathepsin D. However, no significant difference was observed in the extraction of major sarcomeric proteins, including myosin, actin, troponin C, myosin-binding protein C, M-Protein, α-actinin-3, and tropomyosin.

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.

Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor

TDP-43 is a ubiquitously expressed, multidomain functional protein that is distinctively known to form aggregates in many fatal neurodegenerative disorders. However, the information for arresting TDP-43 aggregation is missing due to a lack of understanding of the molecular mechanism of the aggregation and structural properties of TDP-43. TDP-43 is inherently prone to aggregation and has minimal protein solubility. Multiple studies have been performed on the smaller parts of TDP-43 or the full-length protein attached to a large solubilization tag. However, the presence of co-solutes or solubilization tags is observed to interfere with the molecular properties and aggregation mechanism of full-length TDP-43. Notably, this study populated and characterized the native, dimeric state of TDP-43 without the interference of co-solutes or protein modifications. We observed that the electrostatics of the local environment is capable of the partial unfolding and monomerization of the native dimeric state of TDP-43 into an amyloidogenic molten globule. By employing the tools of thermodynamics and kinetics, we reveal the structural characteristics and temporal order of the early intermediates and transition states during the transition of the molten globule to β-rich, amyloid-like aggregates of TDP-43, which is governed by the electrostatics of the environment. The current advanced understanding of the nature of native and early aggregation-prone intermediates, early steps, and the influence of electrostatics in TDP-43 aggregation is essential for drug design.

Maintained particulate integrity of soy protein nanoparticles during gastrointestinal digestion via genipin crosslinking enhancing stability and bioavailability of curcumin

Poor stability during gastrointestinal digestion is a major challenge for the applications of protein-based nanoparticles as oral delivery systems. In this work, genipin was used to crosslink the partially enzymatic hydrolyzed soy protein nanoparticles, aiming to improve their performance in gastrointestinal tract as delivery carrier. Results showed that the obtained genipin-crosslinked soy protein nanoparticles (GSPNPs) were still spherically monodisperse with a diameter around 60 nm. Encapsulation with GSPNPs significantly improved the solubility of curcumin (Cur) and its stability against UV light as well as long-term storage. Compared to those un-crosslinked nanoparticles, particles crosslinked by genipin had a more compact structure less sensitive to ionic effect and digestive enzymes, showing enhanced digestion stability. The well-maintained nanoparticulate structure of GSPNPs further contributed to the enhanced bioaccessibility and facilitated absorption by epithelial cells. Furthermore, in vivo experiment on rats showed that Cur encapsulated in GSPNPs exhibited a slowed down and sustained absorption manner with an 8.11-fold improvement in its bioavailability. These suggested that GSPNPs could be a promising nanocarrier to enhance the bioavailability of functional factors.

Greasy Cations Bind to Neutral Macromolecules in Aqueous Solution

Ions influence the solution properties of macromolecules. Although much is known about anions, cationic effects are considered mostly in terms of weak interactions or exclusion from neutral interfaces. Herein, we have systematically studied the effect of quaternary tetraalkylammonium cations (NH4+, NMe4+, NEt4+, NPr4+, NBu4+) on the phase transition of poly(N-isopropylacrylamide) (PNIPAM) in aqueous solution. Solubility measurements were coupled to 1H NMR and ATR-FTIR spectroscopic measurements. The solubility and NMR measurements revealed a direct binding between the greasiest cations and the isopropyl group of the macromolecule, evidenced from the nonlinear, Langmuir-type chemical shift response only at the isopropyl NMR signals with increasing salt concentrations. The ATR-FTIR measurements focusing on the amide oxygen showed that it is not the main direct-binding site. Additionally, the salting-out effects of the greasier cations correlate with their hydration entropies. These results demonstrate that the most weakly hydrated cations can bind to macromolecules as strongly as the weakly hydrated Hofmeister anions.

Cation-Binding of Glutamate in Aqueous Solution

Interactions of the cations Li+, Na+, Mg2+, and Ca2+ with L-glutamate (Glu-) in aqueous solution were studied at room temperature with dielectric relaxation spectroscopy in the gigahertz region. Spectra of ∼0.4 M NaGlu with added LiCl, NaCl, MgCl2, or CaCl2 (c(MCln) ≤ 1.5 M) were evaluated and experiments supplemented by density functional theory and 3D reference interaction site model (3D-RISM) calculations. In addition to the modes found for aqueous NaGlu, namely, the reorientation of free Glu- ions (peaking at ∼1.6 GHz), of moderately retarded H2O molecules hydrating the carboxylate moieties of Glu- (∼8.4 GHz), of the cooperative resettling of the H-bond network of bulk water (∼20 GHz), and its preceding fast H-bond flip (∼400 GHz), an additional low-frequency relaxation at ∼0.4 GHz was detected upon the addition of the four salts. In the case of NaGlu + MgCl2(aq) and NaGlu + CaCl2(aq), this mode could be unequivocally assigned to an ion pair formed by the cation and the side-chain carboxylate moiety of Glu-. For NaGlu + LiCl(aq), either this species or a backbone-[Li+-H2O-Cl--Glu-] triple ion is formed. Binding constants increase in the order Li+ Collapse

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Grants

• Fonds der Chemischen Industrie
• G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences

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Affiliation(s)

Sergej Friesen Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
Sergey E. Kruchinin G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
Marina V. Fedotova G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
Richard Buchner Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany

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Impact of Peptide Length and Solution Conditions on Tetrameric Coiled Coil Formation

Unlike naturally derived peptides, computationally designed sequences offer programmed self-assembly and charge display. Herein, new tetrameric, coiled coil-forming peptides were computationally designed ranging from 8 to 29 amino acids in length. Experimental investigations revealed that only the sequences having three or more heptads (i.e., 21 or more amino acids) exhibited coiled coil behavior. The shortest stable coiled coil sequence had a melting temperature (Tm) of approximately 58 ± 1 °C, making it ideal for thermoreversible assembly over moderate temperatures. Effects of pH and monovalent salt were examined, revealing structural stability over a pH range of 4 to 11 and an enhancement in Tm with the addition of salt. The incorporation of the coiled coil as a hydrogel cross-linker results in a thermally and mechanically reversible hydrogel. A subsequent demonstration of the hydrogel printed through a syringe illustrated one of many potential uses from 3D printing to injectable hydrogel drug delivery.

Deciphering the guanidinium cation: Insights into thermal diffusion

Thermophoresis, or thermodiffusion, is becoming a more popular method for investigating the interactions between proteins and ligands due to its high sensitivity to the interactions between solutes and water. Despite its growing use, the intricate mechanisms behind thermodiffusion remain unclear. This gap in knowledge stems from the complexities of thermodiffusion in solvents that have specific interactions as well as the intricate nature of systems that include many components with both non-ionic and ionic groups. To deepen our understanding, we reduce complexity by conducting systematic studies on aqueous salt solutions. In this work, we focused on how guanidinium salt solutions behave in a temperature gradient, using thermal diffusion forced Rayleigh scattering experiments at temperatures ranging from 15 to 35 °C. We looked at the thermodiffusive behavior of four guanidinium salts (thiocyanate, iodide, chloride, and carbonate) in solutions with concentrations ranging from 1 to 3 mol/kg. The guanidinium cation is disk-shaped and is characterized by flat hydrophobic surfaces and three amine groups, which enable directional hydrogen bonding along the edges. We compare our results to the behavior of salts with spherical cations, such as sodium, potassium, and lithium. Our discussions are framed around how different salts are solvated, specifically in the context of the Hofmeister series, which ranks ions based on their effects on the solvation of proteins.

Direct prediction of intermolecular interactions driven by disordered regions

Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.

Specific ions effect on aggregation behaviors and structural changes of amyloid fibrils from rice glutelin

Metal ions have been considered as an important factor on fibrils assembly. Herein, a comprehensive analysis of specific ions effect on fibril formation and structural changes was investigated. The addition of ions (except Zn2+) accelerated the aggregation kinetics of rice glutelin fibrils (RGFs) from 0.93 to 1.28-2.19 h-1. In addition, the fibrillization rate followed the order of NH4+ > Li+ > Na+ > K+ > Cu2+ > Mg2+ > Ca2+ > Zn2+. The highest yield and length of fibrils were observed with Ca2+, probably due to the ionic bridging effect and hydrated capacity of Ca2+. However, Cu2+ reduced the fibrils yield, which was attributable to the fact that Cu2+ disrupted β-sheet structure and inhibited the transition of monomer to fibrils. The polymorphism of fibrils was observed with different salts, and the light metals presented a superior effect on fibrils formation than heavy metals. Overall, this work will provide a further information into how to tune the structure of RGFs using various ions.

Removal of empty capsids from high-dose adeno-associated virus 9 gene therapies

Recombinant adeno-associated virus, serotype 9 (rAAV9) has shown promise as a gene therapy vector for muscle and central nervous diseases. High-dose requirements of these therapies present critical safety considerations and biomanufacturing challenges. Notably, the reduction of empty capsids (ECs), which lack therapeutic transgene, from rAAV9 products is critical to maximize efficacy. Removal of rAAV ECs from full capsids is a major downstream challenge because of their highly similar biophysical characteristics. Ultracentrifugation (UC) reduces ECs but is laborious and difficult to scale. In this paper, to replace a poorly scalable UC process, we developed an anion exchange (AEX) chromatography for rAAV9 EC reduction from full capsids. AEX load preparation by dilution incurred major product loss. The addition of histidine and surfactants to dilution buffers increased yield and reduced aggregation. Elution salts were screened and sodium acetate was found to maximize yield and EC reduction. The most promising load dilution buffer and elution salt were used in combination to form an optimized AEX method. The process reduced ECs three-fold, demonstrated robustness to a broad range of EC load challenges, and was scaled for large-scale manufacture. Compared to UC, the AEX method simplified scale-up, reduced ECs to comparable levels (20%), afforded similar purity and product quality, and increased yield by 14%.

Analysis of the effect of cations on protein conformational stability using solid-state nanopores

The conformation of proteins is closely related to their biological functions, and it is affected by many factors, including the type of cations in solution. However, it is difficult to detect the conformational changes of a protein in situ. As a single-molecule sensing technology, nanopores can convert molecular structural information into analyzable current signals within a reasonable time range. Herein, we detect and analyze the effects of two different types of monovalent cations (Na+ and Li+) on a model protein bovine serum albumin (BSA) conformation using SiNx nanopores with different diameters. The quantitative analysis results show that the excluded volume of BSA in LiCl salt solutions is larger than the value in NaCl solution, indicating that Li+ is more prone to unfolding the proteins and making them unstable. This study demonstrated that nanopores enable the in situ detection of the structure of proteins at the single-molecule level and provide a new approach for the quantitative analysis of proteins.

Ionic Effect on the Microenvironment of Biomolecular Condensates

Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.

Preservation of Bacillus subtilis' cellular liquid state at deep sub-zero temperatures in perchlorate brines

Although a low temperature limit for life has not been established, it is thought that there exists a physical limit imposed by the onset of intracellular vitrification, typically occurring at ~-20 °C for unicellular organisms. Here, we show, through differential scanning calorimetry, that molar concentrations of magnesium perchlorate can depress the intracellular vitrification point of Bacillus subtilis cells to temperatures much lower than those previously reported. At 2.5 M Mg(ClO4)2, the peak vitrification temperature was lowered to -83 °C. Our results show that inorganic eutectic salts can in principle maintain liquid water in cells at much lower temperatures than those previously claimed as a lower limit to life, raising the prospects of active biochemical processes in low temperature natural settings. Our results may have implications for the habitability of Mars, where perchlorate salts are pervasive and potentially other terrestrial and extraterrestrial, cryosphere environments.

Lead (II) ions enable the ion-specific effects of monovalent anions on the molecular structure and interactions at silica/aqueous interfaces

HYPOTHESIS

The adsorption of heavy metal ions such as Pb(II) onto negatively charged minerals such as silica is expected to alter the structure and the interactions at the silica/aqueous interfaces. Besides the solution pH, the inner-sphere sorption of Pb(II) is expected to regulate the surface charge/potential, hypothesized to control the actions of monovalent anions in the aqueous environment. These complex pictures can be probed directly using surface-sensitive sum-frequency generation (SFG) spectroscopy.

EXPERIMENTS

The pH-dependent water structure within the double layer at silica/aqueous interfaces under the influence of different ions was examined using SFG. The recorded SFG spectra were deconvoluted into the Stern layer (SL) and diffuse layer (DL) using the maximum entropy method in conjunction with the electrical double-layer theory.

FINDINGS

Standalone monovalent sodium salts do not exhibit ion-specific effects on the silica/aqueous interfaces. However, the mixture of Pb(II) species and each of these salts display profound ion-specific effects on the structure of silica/aqueous interfaces, indicating the role of Pb(II) as an enabler of the ion-specificity of the investigated monovalent anions. The interesting effect arises from a complex interplay between the physical processes (i.e., electrostatic interactions, screening effects, etc.) and chemical processes such as the hydrolysis of Pb(II) ions, ion complexation, protonation and deprotonation of the surface silanol group.

Catalytic Strategies for the Cycloaddition of CO2 to Epoxides in Aqueous Media to Enhance the Activity and Recyclability of Molecular Organocatalysts

The cycloaddition of CO2 to epoxides to afford versatile and useful cyclic carbonate compounds is a highly investigated method for the nonreductive upcycling of CO2. One of the main focuses of the current research in this area is the discovery of readily available, sustainable, and inexpensive catalysts, and of catalytic methodologies that allow their seamless solvent-free recycling. Water, often regarded as an undesirable pollutant in the cycloaddition process, is progressively emerging as a helpful reaction component. On the one hand, it serves as an inexpensive hydrogen bond donor (HBD) to enhance the performance of ionic compounds; on the other hand, aqueous media allow the development of diverse catalytic protocols that can boost catalytic performance or ease the recycling of molecular catalysts. An overview of the advances in the use of aqueous and biphasic aqueous systems for the cycloaddition of CO2 to epoxides is provided in this work along with recommendations for possible future developments.

Chemical bonds and hair behaviour-A review

When undertaking any review of the structure of the hair and its mechanical properties it becomes apparent that the overall behaviour of keratin fibres is commonly attributed to the presence of hydrogen, disulfide and ionic bonds. The action of physico-chemical agents used during various cosmetic treatments is viewed as the result of an interaction with these bonds. Thus, the breaking of bonds by chemical agents, or via mechanical or thermal stresses, affects the relative balance of disulfide and hydrogen bonds and the contribution of hydrophobic interactions, which are all important factors that may alter hair behaviour. Generally, these chemical bonds are considered as responding homogeneously to the environmental and cosmetic factors. This unitary image is challenged, however, by evaluating the results of chemical, nanomechanical, tensile and thermal measurements, which suggest that disulfide bonds may be grouped into several types, according to their location within the fibre and the way they respond to various agents. A compensatory effect of newly formed hydrogen bonds for broken disulfide bonds may also be seen, and additionally involves different types of hydrogen bonds. As a result, the picture of chemical bonding in hair appears to be far from a homogeneous one. In addition, it is apparent that further investigation is required for clarifying the action of ionic bonds and hydrophobic interactions within the hair fibre. The present review aims, thus, at offering a deeper background for understanding how the hair behaves under various conditions.

Protein Thermodynamic Properties, Crystallisation, and the Hofmeister Series

The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein-solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i. e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool.

Assessing Weak Anion Binding to Small Peptides

Since Hofmeister's seminal studies in the late 19th century, it has been known that salts and buffers can drastically affect the properties of peptides and proteins. These Hofmeister effects can be conceived of in terms of three distinct phenomena/mechanisms: water-salt interactions that indirectly induce the salting-out of a protein by water sequestration by the salt, and direct salt-protein interactions that can either salt-in or salt-out the protein. Unfortunately, direct salt-protein interactions responsible for Hofmeister effects are weak and difficult to quantify. As such, they are frequently construed of as being nonspecific. Nevertheless, there has been considerable effort to better specify these interactions. Here, we use pentapeptides to demonstrate the utility of the H-dimension of nuclear magnetic resonance (NMR) spectroscopy to assess anion binding using N-H signal shifts. We qualify binding using these, demonstrating the upfield shifts induced by anion association and revealing how they are much larger than the corresponding downfield shifts induced by magnetic susceptibility and other ionic strength change effects. We also qualify binding in terms of how the pattern of signal shifts changes with point mutations. In general, we find that the observed upfield shifts are small compared with those induced by anion binding to amide-based hosts, and MD simulations suggest that this is so. Thus, charge-diffuse anions associate mostly with the nonpolar regions of the peptide rather than directly interacting with the amide N-H groups. These findings reveal the utility of 1H NMR spectroscopy for qualifying affinity to peptides─even when affinity constants are very low─and serve as a benchmark for using NMR spectroscopy to study anion binding to more complex systems.

Anion Competition at Positively Charged Surfactant Monolayers

Interactions of anions with hydrophobic surfaces of proteins and water-soluble polymers depend on the ability of the ions to shed their hydration shells. At positively charged surfactant monolayers, the interactions of anions are less well understood. Due to the interplay of electrostatic surface forces, hydration effects, and ion-ion interactions in the electrostatic double layer, a comprehensive microscopic picture remains elusive. Herein, we study the interactions of chloride, bromide, and a mixture of these two anions at the aqueous interface of dihexadecyldimethylammonium (DHDA+) and dioctadecyldimethylammonium (DODA+) cationic monolayers. Using molecular dynamics simulations and three surface-sensitive X-ray scattering techniques, we demonstrate that bromide interacts preferentially over chloride with both monolayers. The structure of the two monolayers and their interfacial electron density profiles obtained from the simulations quantitatively reproduce the experimental data. We observe that chloride and bromide form contact ion pairs with the quaternary ammonium groups on both monolayers. However, ion pairing with bromide leads to a greater reduction in the number of water molecules hydrating the anion, resulting in more energetically stable ion pairs. This leads to long-range (>3 nm) lateral correlations between bromide ions on the structured DODA+ monolayer. These observations indicate that ion hydration is the dominant factor determining the interfacial electrolyte structure.

Revealing the Molecular Origin of Anisotropy around Chloride Ions in Bulk Water

A clear picture of the local solvation structure around halide anions in liquid water remains elusive. This discussion has been stimulated by pioneering simulation results that proposed a "hydrophobic cavity" around anions in the bulk, which is analogous to air at the air-water interface. However, there is also sound experimental and theoretical evidence that halide ions are rather symmetrically solvated in the bulk, leading to a different viewpoint. Using extensive ab initio molecular dynamics simulations of an aqueous Cl- solution, we indeed find an anisotropic arrangement of H-bonded versus interstitial water molecules. The latter are not H-bonded to the anions and thus do not couple much electronically to Cl-. The resulting purely electronic anisotropy of the local solvation environment correlates with that structural anisotropy, which however should not be understood as an empty cavity─as it would be at the air-water interface─but rather contains interstitial water molecules.

Elucidating the influence of electrostatic force on the re-arrangement of H-bonds of protein polymers in the presence of salts

Polyampholytes/proteins have an intriguing network of hydrogen bonds (H-bonds), especially their secondary structure, which plays a crucial role in determining the conformational stability of the polymer. The changes in protein secondary structure in the protein-salt system have been extensively deciphered by researchers, yet their pathways for breakage and recreation are unknown. Understanding the mechanism of protein conformational changes towards their biological activities, like protein folding, remains one of the main challenges and requires multiscale analysis of this strongly correlated system. Herein, salts have been used to reveal the re-arrangement behavior in the H-bond network of proteins under the influence of electrostatic interactions, as the strength of electrostatic forces is much stronger than that of H-bonds. At lower salt concentrations, there are negligible changes in the secondary structures as the electrostatic forces induced by the salt ions are less. Later, the existing H-bonds break and reconstruct new H-bonds at higher salt concentrations due to the influence of the stronger electrostatic interaction induced by the large number of salt ions. Molecular dynamics (MD) simulations and FTIR studies have been used rigorously to decipher the reason behind the re-arrangement of the H-bonds within gelatin (protein). The re-arrangement in the H-bond has also been observed with time from simulations and experiments. Thus, this study could provide a fresh perspective on the conformational changes of polyampholytes/proteins and will also influence the studies of protein folding-unfolding interaction in the presence of salt ions.

A Unified Description of Salt Effects on the Liquid-Liquid Phase Separation of Proteins

Protein aggregation via liquid-liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.

Interactions between the protein barnase and co-solutes studied by NMR

Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.

Novel Conductive AgNP-Based Adhesive Based on Novel Poly (Ionic Liquid)-Based Waterborne Polyurethane Chloride Salts for E-Textiles

The emergence of novel e-textile materials that combine the inherent qualities of the textile substrate (lightweight, soft, breathable, durable, etc.) with the functionality of micro/nano-electronic materials (conductive, dielectric, sensing, etc.) has resulted in a trend toward miniaturization, integration, and intelligence in new electronic devices. However, the formation of a conductive network by micro/nano-conductive materials on textiles necessitates high-temperature sintering, which inevitably causes substrate aging and component damage. Herein, a bis-hydroxy-imidazolium chloride salt as a hard segment to synthesize a waterborne polyurethane (WPU) adhesive is designed and prepared. When used in nano-silver-based printing coatings, it offers strong adherence for coatings, reaching 16 N cm-1; on the other hand, the introduction of chloride ions enables low-temperature (60 °C) chemical sintering to address the challenge of secondary treatment and high-temperature sintering (>150 °C). Printed into flexible circuits, the resistivity can be controlled by the content of imidazolium salts anchored in the molecular chain of the WPU from a maximum resistivity of 3.1 × 107 down to 5.8 × 10-5 Ω m, and it can conduct a Bluetooth-type finger pulse detector with such low resistivity. As a flexible circuit, it also offers high stability against washing and adhesion, which the resistivity only reduces less than 20% after washing 10 times and adhesion. Owing to the adjustability of the resistivity, we fabricated an all-textile flexible pressure sensor that accurately differentiates different external pressures (min. 10 g, ~29 Pa), recognizes forms, and detects joint motions (finger bending and wrist flexion).

From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain

Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.

Dynamics of Nanocomposite Hydrogel Alignment during 3D Printing to Develop Tissue Engineering Technology

Taking inspiration from spider silk protein spinning, we developed a method to produce tough filaments using extrusion-based 3D bioprinting and salting-out of the protein. To enhance both stiffness and ductility, we have designed a blend of partially crystalline, thermally sensitive natural polymer gelatin and viscoelastic G-polymer networks, mimicking the components of spider silk. Additionally, we have incorporated inorganic nanoparticles as a rheological modifier to fine-tune the 3D printing properties. This self-healing nanocomposite hydrogel exhibits exceptional mechanical properties, biocompatibility, shear thinning behavior, and a well-controlled gelation mechanism for 3D printing.

Elucidation of the Specific Ion Effects and Intermediate Structures of Cellulose Fibers Swollen in Inorganic Salt Solutions via In Situ X-ray Diffraction

The solubilities of many substances are significantly affected by specific ions, as demonstrated by the Hofmeister series of proteins. Cellulose has a resistant fibrillar structure that hinders its swelling and dissolution. Certain inorganic salt solutions are effective swelling agents and solvents for cellulose. However, the precise effects of these ions on cellulose are not fully understood. In this study, we studied the intermediate structures of cellulose fibers during their swelling process in ZnCl2 and LiBr solutions via in situ X-ray diffraction. Two swollen phases with characteristic morphologies were observed for both salt treatments. Only the surfaces of the fibers were swollen in ZnCl2, whereas the ions penetrated the fibers and formed complexes with cellulose while the morphology of the fibers was maintained in LiBr. Our findings clarify the reasons that ZnCl2 has been used as an excellent swelling agent, whereas LiBr has been used as a good solvent for cellulose.

Observation of a super-tetrahedral cluster of acetonitrile-solvated dodecaborate dianion via dihydrogen bonding

We launched a combined negative ion photoelectron spectroscopy and multiscale theoretical investigation on the geometric and electronic structures of a series of acetonitrile-solvated dodecaborate clusters, i.e., B12H122-·nCH3CN (n = 1-4). The electron binding energies of B12H122-·nCH3CN are observed to increase with cluster size, suggesting their enhanced electronic stability. B3LYP-D3(BJ)/ma-def2-TZVP geometry optimizations indicate each acetonitrile molecule binds to B12H122- via a threefold dihydrogen bond (DHB) B3-H3 ⁝⁝⁝ H3C-CN unit, in which three adjacent nucleophilic H atoms in B12H122- interact with the three methyl hydrogens of acetonitrile. The structural evolution from n = 1 to 4 can be rationalized by the surface charge redistributions through the restrained electrostatic potential analysis. Notably, a super-tetrahedral cluster of B12H122- solvated by four acetonitrile molecules with 12 DHBs is observed. The post-Hartree-Fock domain-based local pair natural orbital- coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)] calculated vertical detachment energies agree well with the experimental measurements, confirming the identified isomers as the most stable ones. Furthermore, the nature and strength of the intermolecular interactions between B12H122- and CH3CN are revealed by the quantum theory of atoms-in-molecules and the energy decomposition analysis. Ab initio molecular dynamics simulations are conducted at various temperatures to reveal the great kinetic and thermodynamic stabilities of the selected B12H122-·CH3CN cluster. The binding motif in B12H122-·CH3CN is largely retained for the whole halogenated series B12X122-·CH3CN (X = F-I). This study provides a molecular-level understanding of structural evolution for acetonitrile-solvated dodecaborate clusters and a fresh view by examining acetonitrile as a real hydrogen bond (HB) donor to form strong HB interactions.

pH-dependent interactions of biologically important metal ions with hen egg white lysozyme based on its hydration properties: Thermodynamic and mechanistic insights

Importance of metal ion selectivity in biomolecules and their key role in proteins are widely explored. However, understanding the thermodynamics of how hydrated metal ions alter the protein hydration and their conformation is also important. In this study, the interaction of some biologically important Ca2+, Mn2+, Co2+, Cu2+, and Zn2+ ions with hen egg white lysozyme at pH 2.1, 3.0, 4.5 and 7.4 has been investigated. Intrinsic fluorescence studies have been employed for metal ion-induced protein conformational changes analysis. Thermostability based on protein hydration has been investigated using differential scanning calorimetry (DSC). Thermodynamic parameters emphasizing on metal ion-protein binding mechanistic insights have been well discussed using isothermal titration calorimetry (ITC). Overall, these experiments have reported that their interactions are pH-dependent and entropically driven. This research also reports the strongly hydrated metal ions as water structure breaker unlike osmolytes based on DSC studies. These experimental results have highlighted higher concentrations of different metal ions effect on the protein hydration and thermostability which might be helpful in understanding their interactions in aqueous solutions.

Spectroscopically dark phosphate features revealed by chemical exchange saturation transfer

Phosphate is an essential anion in the human body, comprising approximately 1% of the total body weight, and playing a vital role in metabolism, cell membranes, and bone formation. We have recently provided spectroscopic, microscopic, and computational evidence indicating that phosphates can aggregate much more readily in solution than previously thought. This prior work provided indirect evidence through the observation of unusual31 P NMR relaxation and line-broadening effects with increasing temperature. Here, we show that, under conditions of slow exchange and selective RF saturation, additional features become visible in chemical exchange saturation transfer (CEST) experiments, which appear to be related to the previously reported phosphate clustering. In particular, CEST shows pronounced dips several ppm upfield of the main phosphate resonance at low temperatures, while direct31 P spectroscopy does not produce any signals in that range. We study the pH dependence of these new spectroscopic features and present exchange and spectroscopic parameters based on fitting the CEST data. These findings could be of importance in the investigation of phosphate dynamics, especially in the biological milieu.

Lysozyme aggregation and unfolding in ionic liquid solvents: Insights from small angle X-ray scattering and high throughput screening

Understanding protein behaviour is crucial for developing functional solvent systems. Ionic liquids (ILs) are designer salts with versatile ion combinations, where some suppress unfavourable protein behaviour. This work utilizes small angle X-ray scattering (SAXS) to investigate the size and shape changes of model protein hen egg white lysozyme (HEWL) in 137 IL and salt solutions. Guinier, Kratky, and pair distance distribution analysis were used to evaluate the protein size, shape, and aggregation changes in these solvents. At low IL and salt concentration (1 mol%), HEWL remained monodispersed and globular. Most ILs increased HEWL size compared to buffer, while the nitrate and mesylate anions induced the most significant size increases. IL cation branching, hydroxyl groups, and longer alkyl chains counteracted this size increase. Common salts exhibited specific ion effects, while the IL effect varied with concentration due to complex ion-pairing. Protein aggregation and unfolding occurred at 10 mol% IL, altering the protein shape, especially for ILs with multiple alkyl chains on the cation, or with a mesylate/nitrate anion. This study highlights the usefulness of adopting a high-throughput SAXS strategy for understanding IL effects on protein behaviour and provides insights on controlling protein aggregation and unfolding with ILs.

Selectivity and Resolving Power of Hydrophobic Interaction Chromatography Targeting the Separation of Monoclonal Antibody Variants

This study presents a comprehensive investigation of the mechanistic understanding of retention and selectivity in hydrophobic interaction chromatography. It provides valuable insights into crucial method-development parameters involved in achieving chromatographic resolution for profiling molecular variants of trastuzumab. Retention characteristics have been assessed for three column chemistries, i.e., butyl, alkylamide, and long-stranded multialkylamide ligands, while distinguishing column hydrophobicity and surface area. Salt type and specifically chloride ions proved to be the key driver for improving chromatographic selectivity, and this was attributed to the spatial distribution of ions at the protein surface, which is ion-specific. The effect was notably more pronounced on the multialkylamide column, as proteins intercalated between the multiamide polymer strands, enabling steric effects. Column coupling proved to be an effective approach for maximizing resolution between molecular variants present in the trastuzumab reference sample and trastuzumab variants induced by forced oxidation. Liquid chromatography-mass spectrometry (LC-MS)/MS peptide mapping experiments after fraction collection indicate that the presence of chloride in the mobile phase enables the selectivity of site-specific deamidation (N30) situated at the heavy chain. Moreover, site-specific oxidation of peptides (M255, W420, and M431) was observed for peptides situated at the Fc region close to the CH2-CH3 interface, previously reported to activate unfolding of trastuzumab, increasing the accessible surface area and hence resulting in an increase in chromatographic retention.

Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects

The roles of cations and anions are different in the perturbation on solvation, and thus, the analyses of the separated contributions from cations and anions are useful to establish molecular pictures of ion-specific effects. In this work, we investigate the effects of cations, anions, and water separately in the solvation of n-alcohols and n-alkanes by free-energy decomposition. By utilising energy-representation theory of solvation, we address the contributions arising from the direct solute-solvent interactions and the excluded-volume effects. It is found that the change in solvation of n-alcohols and n-alkanes upon addition of salt depends primarily on the anion species. The direct interaction between the anion and solute is in agreement with the Setschenow coefficient in terms of the ranking of salting-in and salting-out for n-alkanes, which corresponds to the extent of accumulation of the anion on the solute surface. For each of the n-alcohols and n-alkanes examined, the excluded-volume component in the Setschenow coefficient is well correlated to the (total) Setschenow coefficient when the salt effects are concerned. The ranking of the excluded-volume component in the variation of the salt species is parallel to the water contribution, which is correlated further to the change in the water density upon the addition of the salt.

Specific ion effects on lignin adsorption and transport through cellulose confinements

The presence of ions in a solution is anticipated to induce distinct effects on macromolecules. Consequently, the tuning of adsorption and mass transfer of lignin molecules can be achieved by incorporating ions with chaotropic or kosmotropic characteristics. This study examines the adsorption and mass transfer behavior of lignin molecules across model cellulose membranes in presence of ions from the Hofmeister series. Experimental investigations encompassed the use of diffusion cells to quantify lignin's mass transfer through the membranes, and quartz crystal microbalance with dissipation (QCM-D) monitoring was used for adsorption studies. Notably, at high ion concentrations, the mass transport rate of lignin was observed to be lower in the presence of highly hydrated (kosmotropic) sulfate ions, conforming to the Hofmeister series. Intriguingly, this relationship was not apparent at lower ion concentrations. Furthermore, QCM-D experiments indicated that lignin displayed higher adsorption onto the cellulose surface when exposed to less hydrated (chaotropic) nitrate anions. This behavior can be rationalized by considering the system's increased entropy gain, facilitated by the release of adsorbed ions and water molecules from the cellulose surface upon lignin adsorption. This study highlights the complexity of ion-specific effects on mass transfer and adsorption processes and their dependency on ion concentrations.

Influence of tail group length, amide functionality and added salt ion identity on the behaviour of betaine surfactants

Hypothesis The behaviour of surfactants in solution and at interfaces is governed by a combination of steric and electrostatic effects experienced by surfactant molecules as they interact with solvent, other species in solution, and each other. It would therefore be anticipated that highly interacting groups would significantly influence surfactant behaviour. The widely used amide functionality has polar H-bond donor/acceptor properties, and therefore its inclusion into a surfactant structure should have a profound effect on surface activity and self-assembly of that surfactant when compared to the equivalent molecule without an amide linker. Further, chaotropic or kosmotropic salt ions that affect water structuring and hydrogen bonding may provide opportunities for further tuning surfactant interactions in such cases. Experiments A library of betaine surfactant with tail lengths n=14-22 both with and without an amidopropyl linker were synthesised to study the effect of the amide functionality on surfactant properties. Characterisation of the molecules interfacial properties were performed using pendant drop tensiometry and their solution state formulation properties were probed using small-angle neutron scattering (SANS) and rheological measurements. Findings Presence of an amidopropyl linker had little effect on aggregation propensity (as evidenced by critical micelle concentration) and aggregate morphology of betaine surfactants, but did increase the Krafft temperature of these surfactants. SANS analysis indicated that aggregate morphology of alkyl betaine surfactants could be influenced by the addition of sodium salts with chaotropic counterions (I- and SCN-), but they were insensitive to more kosmotropic anions (SO42-, F- and Cl-), providing unique and novel solution control methods for this (supposedly salt-insensitive) class of surfactants.

Differential specificity of SARS-CoV-2 main protease variants on peptide versus protein-based substrates

The SARS-CoV-2 main protease (Mpro ) holds significant importance as a biological target in combating coronaviruses due to its importance in virus replication. Considering the emergence of novel SARS-CoV-2 variants and the mutations observed in the Mpro sequence, we hypothesized that these mutations may have a potential impact on the protease's specificity. To test this, we expressed Mpro corresponding to the original strain and variants Beta1, Beta2, and Omicron and analyzed their activity on protein-based and peptide substrates. Although we observed differential activity on the protein-based substrate, there was very little difference when analyzed on the peptide substrate. We conclude that mutations on the Mpro sequence, despite having a minor effect on a peptide substrate cleavage, did not change the catalytic site environment enough to build resistance to inhibition. Therefore, we propose that inhibitors initially designed for the Mpro of the original strain will be effective in all the variants. Thus, Mpro is likely to continue to be a target of therapeutic interest as mutations in its sequence are rare and, as we show here, have a minor effect on the protease's recognition of peptide-based molecules.

Structure, aggregation dynamics and crystallization of superfolder green fluorescent protein: Effect of long alkyl chain imidazolium ionic liquids

Green fluorescent protein (GFP) and its variants are widely used in medical and biological research, especially acting as indicators of protein structural integrity, protein-protein interactions and as biosensors. This study employs superfolder GFP (sfGFP) to investigate the impact of varying alkyl chain length of 1-Cn-3-methylimidazolium chloride ionic liquid (IL) series ([Cnmim]Cl, n = 2, 4, 6, 8, 10, 12) on the protein fluorescence, structure, hydration, aggregation dynamics and crystallization behaviour. The results revealed a concentration-dependent decrease in the sfGFP chromophore fluorescence, particularly in long alkyl chain ILs ([C10mim]Cl and [C12mim]Cl). Tryptophan (Trp) fluorescence showed the quenching rate increased with longer alkyl chains indicating a nonpolar interaction between Trp57 and the alkyl chain. Secondary structural changes were observed at the high IL concentration of 1.5 M in [C10mim]Cl and [C12mim]Cl. Small-angle X-ray scattering (SAXS) indicated relatively stable protein sizes, but with IL aggregates present in [C10mim]Cl and [C12mim]Cl solutions. Dynamic light scattering (DLS) data showed increased protein size and aggregation with longer alkyl chain ILs. Notably, ILs and salts, excluding [C2mim]Cl, promoted sfGFP crystallization. This study emphasizes the influence of the cation alkyl chain length and concentration on protein stability and aggregation, providing insights into utilizing IL solvents for protein stabilization and crystallization purposes.

Studies of DNA 'Breathing' by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3)2 Dimer-Labeled DNA Fork Constructs

Local fluctuations of the sugar-phosphate backbones and bases of DNA (often called DNA 'breathing') play a variety of critical roles in controlling the functional interactions of the DNA genome with the protein complexes that regulate it. Here, we present a single-molecule fluorescence method that we have used to measure and characterize such conformational fluctuations at and near biologically important positions in model DNA replication fork constructs labeled with exciton-coupled cyanine [(iCy3)2] dimer probes. Previous work has shown that the constructs that we tested here exhibit a broad range of spectral properties at the ensemble level, and these differences can be structurally and dynamically interpreted using our present methodology at the single-molecule level. The (iCy3)2 dimer has one symmetric (+) and one antisymmetric (-) exciton, with the respective transition dipole moments oriented perpendicular to one another. We excite single-molecule samples using a continuous-wave linearly polarized laser, with the polarization direction continuously rotated at the frequency of 1 MHz. The ensuing fluorescence signal is modulated as the laser polarization alternately excites the symmetric and antisymmetric excitons of the (iCy3)2 dimer probe. Phase-sensitive detection of the modulated signal provides information about the distribution of local conformations and the conformational interconversion dynamics of the (iCy3)2 probe. We find that at most construct positions that we examined, the (iCy3)2 dimer-labeled DNA fork constructs can adopt four topologically distinct conformational macrostates. These results suggest that in addition to observing DNA breathing at and near ss-dsDNA junctions, our new methodology should be useful to determine which of these pre-existing macrostates are recognized by, bind to, and are stabilized by various genome-regulatory proteins.

Salt Effects on Caffeine across Concentration Regimes

Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to salting-in or salting-out of aqueous proteins. Early work of Tanford led to the discovery that the solvation of molecular surface motifs is proportional to the solvent accessible surface area (SASA), and later studies have shown that the proportionality constant varies with the salt concentration and type. Using multiscale computer simulations combined with vapor-pressure osmometry on caffeine-salt solutions, we reveal that this SASA description captures a rich set of molecular driving forces in tertiary solutions at changing solute and osmolyte concentrations. Central to the theoretical work is a new potential energy function that depends on the instantaneous surface area, salt type, and concentration. Used in, e.g., Monte Carlo simulations, this allows for a highly efficient exploration of many-body interactions and the resulting thermodynamics at elevated solute and salt concentrations.

Hydrogen-Deuterium Exchange Dynamics of NISTmAb Measured by Small Angle Neutron Scattering

Understanding protein dynamics and conformational stability holds great significance in biopharmaceutical research. Hydrogen-deuterium exchange (HDX) is a quantitative methodology used to examine these fundamental properties of proteins. HDX involves measuring the exchange of solvent-accessible hydrogens with deuterium, which yields valuable insights into conformational fluctuations and conformational stability. While mass spectrometry is commonly used to measure HDX on the peptide level, we explore a different approach using small-angle neutron scattering (SANS). In this work, SANS is demonstrated as a complementary and noninvasive HDX method (HDX-SANS). By assessing subtle changes in the tertiary and quaternary structure during the exchange process in deuterated buffer, along with the influence of added electrolytes on protein stability, SANS is validated as a complementary HDX technique. The HDX of a model therapeutic antibody, NISTmAb, an IgG1κ, is monitored by HDX-SANS over many hours using several different formulations, including salts from the Hofmeister series of anions, such as sodium perchlorate, sodium thiocyanate, and sodium sulfate. The impact of these formulation conditions on the thermal stability of NISTmAb is probed by differential scanning calorimetry. The more destabilizing salts led to heightened conformational dynamics in mAb solutions even at temperatures significantly below the denaturation point. HDX-SANS is demonstrated as a sensitive and noninvasive technique for quantifying HDX kinetics directly in mAb solution, providing novel information about mAb conformational fluctuations. Therefore, HDX-SANS holds promise as a potential tool for assessing protein stability in formulation.

Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus

Recombinant core spidroin eADF4(C16) has received increasing attention due to its ability to form micro- and nano-structured scaffolds, which are based on nanofibrils with great potential for biomedical and biotechnological applications. Phosphate anions have been demonstrated to trigger the eADF4(C16) self-assembly into cross-beta fibrils. In the present work, we systematically addressed the effect of nine sodium anions, namely SO4 2- , HPO4 2- (Pi), F- , Cl- , Br- , NO3 - , I- , SCN- , and ClO4 - from the Hofmeister series on the in vitro self-assembly kinetics of eADF4(C16). We show that besides the phosphate anions, only kosmotropic anions such as sulfate and fluoride can initiate the eADF4(C16) fibril formation. Global analysis of the self-assembly kinetics, utilizing the platform AmyloFit, showed the nucleation-based mechanism with a major role of secondary nucleation, surprisingly independent of the type of the kosmotropic anion. The rate constant of the fibril elongation in mixtures of phosphate anions with other studied anions correlated with their kosmotropic or chaotropic position in the Hofmeister series. Our findings suggest an important role of anion hydration in the eADF4(C16) fibrillization process.

Exosome Precipitation by Ionic Strength Modulation: ExoPRISM

Extracellular vesicles (EVs) are emerging as crucial materials for precision theragnostic applications. However, current separation methods are time-consuming, costly, and not scalable and deliver limited yields or purity. Here, we present EV precipitation by ionic strength modulation (ExoPRISM), a simple, low-cost, user-friendly, and readily adaptable approach for separating EVs in high yields without compromising their biological functions. Adding an electrolyte solution to blood plasma in small increments generates the sequential precipitation of proteins and EVs, allowing for fractional separation of EVs using low-speed centrifugation. The coprecipitated electrolytes are easily washed away, and the entire EV separation and washing process takes less than an hour. This approach successfully separates EVs from a broad range of volumes and types of biological fluids, including culture medium, urine, plasma, and serum, showing promise as a robust tool for next-generation liquid biopsies and regenerative medicine.

Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions

The effects of CaCl2 and MgCl2 on the cloud point temperature of two different elastin-like polypeptides (ELPs) were studied using a combination of cloud point measurements, molecular dynamics simulations, and infrared spectroscopy. Changes in the cloud point for the ELPs in aqueous divalent metal cation solutions were primarily governed by two competing interactions: the cation-amide oxygen electrostatic interaction and the hydration of the cation. In particular, Ca2+ cations can more readily shed their hydration shells and directly contact two amide oxygens by the formation of ion bridges. By contrast, Mg2+ cations were more strongly hydrated and preferred to partition toward the amide oxygens along with their hydration shells. In fact, although hydrophilic ELP V5A2G3 was salted-out at low concentrations of MgCl2, it was salted-in at higher salt concentrations. By contrast, CaCl2 salted the ELP sharply out of solution at higher salt concentrations because of the bridging effect.

Regulating polystyrene glass transition temperature by varying the hydration levels of aromatic ring/Li+ interaction

Polymer properties can be altered via lithium ion doping, whereby adsorbed Li+ binds with H2O within the polymer chain. However, direct spectroscopic evidence of the tightness of Li+/H2O binding in the solid state is limited, and the impact of Li+ on polymer sidechain packing is rarely reported. Here, we investigate a polystyrene/H2O/LiCl system using solid-state NMR, from which we determined a dipolar coupling of 11.4 kHz between adsorbed Li+ and H2O protons. This coupling corroborates a model whereby Li+ interacts with the oxygen atom in H2O via charge affinity, which we believe is the main driving force of Li+ binding. We demonstrated the impact of hydrated Li+ on sidechain packing and dynamics in polystyrene using proton-detected solid-state NMR. Experimental data and density functional theory (DFT) simulations revealed that the addition of Li+ and the increase in the hydration levels of Li+, coupled with aromatic ring binding, change the energy barrier of sidechain packing and dynamics and, consequently, changes the glass transition temperature of polystyrene.

Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl - Channel

Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 chloride channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. We implement the fully polarizable forcefield AMOEBA in MD simulations of open and partially-open states of the hBest1. The AMOEBA forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion- π interactions. By including polarization we demonstrate the key role that aromatic residues play in ion permeation and the functional advantages of pore asymmetry within the highly conserved hydrophobic neck of the pore. We establish that these only arise when electronic polarization is included in the molecular models. We also show that Cl - permeation in this region can be achieved through hydrophobic solvation concomitant with partial ion dehydration, which is compensated for by the formation of contacts with the edge of the phenylalanine ring. Furthermore, we demonstrate how polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures. Crucially, neglecting polarization in simulation of these systems results in the localization of Cl - at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems.

Statement of Significance

Ion channels are nanoscale protein pores that enable the selective passage of charged ions across cell membranes. Understanding the underlying mechanisms for selective anion permeation through such pores remains a challenge. To simulate their behavior efficiently in silico , fixed charge models are typically employed. However, this approach is insufficient for the study of anions. Here, we use simulations with explicit treatment of electrostatics to investigate the interactions of chloride ions in the human bestrophin 1 channel. We find that electronic polarization tunes the state of the channel and affects the interactions of chloride ions thereby revealing a mechanism for permeation. Furthermore, these simulations can be used to resolve experimental ambiguity in ion-like densities from cryo-EM structures.

Ion Partition in Polyelectrolyte Gels and Nanogels

Polyelectrolyte gels provide a load-bearing structural framework for many macroscopic biological tissues, along with the organelles within the cells composing tissues and the extracellular matrices linking the cells at a larger length scale than the cells. In addition, they also provide a medium for the selective transportation and sequestration of ions and molecules necessary for life. Motivated by these diverse problems, we focus on modeling ion partitioning in polyelectrolyte gels immersed in a solution with a single type of ionic valence, i.e., monovalent or divalent salts. Specifically, we investigate the distribution of ions inside the gel structure and compare it with the bulk, i.e., away from the gel structure. In this first exploratory study, we neglect solvation effects in our gel by modeling the gels without an explicit solvent description, with the understanding that such an approach may be inadequate for describing ion partitioning in real polyelectrolyte gels. We see that this type of model is nonetheless a natural reference point for considering gels with solvation. Based on our idealized polymer network model without explicit solvent, we find that the ion partition coefficients scale with the salt concentration, and the ion partition coefficient for divalent ions is higher than for monovalent ions over a wide range of Bjerrum length (lB) values. For gels having both monovalent and divalent salts, we find that divalent ions exhibit higher ion partition coefficients than monovalent salt for low divalent salt concentrations and low lB. However, we also find evidence that the neglect of an explicit solvent, and thus solvation, provides an inadequate description when compared to experimental observations. Thus, in future work, we must consider both ion and polymer solvation to obtain a more realistic description of ion partitioning in polyelectrolyte gels.

Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars

Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.

Monovalent cations have different effects on the assembly kinetics and morphology of α-synuclein amyloid fibrils

Formation of α-synuclein amyloid fibrils is a pathological hallmark of Parkinson's disease and a phenomenon that is strongly modulated by environmental factors. Here, we compared effects of different monovalent cations (Li+, Na+, K+) on the formation and properties of α-synuclein amyloid fibrils. Na+ > Li+ were found to have concentration-dependent catalytic effects on primary nucleation whereas K+ ions acted inhibitory. We discuss this discrepancy in terms of a superior affinity of Na+ and Li+ to carboxylic protein groups, resulting in reduced Columbic repulsion and by considering K+ as an ion with poor protein binding and slight chaotropic character, which could promote random coil protein structure. K+ ions, furthermore, appeared to lower the β-sheet content of the fibrils and increase their persistence lengths, the latter we interpret as a consequence of lesser ion binding and hence higher line charge of the fibrils. The finding that Na+ and K+ have opposite effects on α-synuclein aggregation is intriguing in relation to the significant transient gradients of these ions across axonal membranes, but also important for the design and interpretation of biophysical assays where buffers containing these monovalent cations have been intermixedly used.