Identifying Chaotropic and Kosmotropic Agents by Nanorheology

On the free energy of protein folding in optical tweezers experiments

Free energy is a critical parameter in understanding the equilibrium in chemical reactions. It enables us to determine the equilibrium proportion between the different species in the reaction and to predict in which direction the reaction will proceed if a change is performed in the system. Historically, to calculate this value, bulk experiments were performed where a parameter was altered at a gradual rate to change the population until a new equilibrium was established. In protein folding studies, it is common to vary the temperature or chaotropic agents in order to change the population and then to extrapolate to physiological conditions. Such experiments were time-consuming due to the necessity of ensuring equilibrium and reversibility. Techniques of single-molecule manipulation, such as optical/magnetic tweezers and atomic force microscopy, permit the direct measurement of the work performed by a protein undergoing unfolding/refolding at particular forces. Also, with the development of non-equilibrium free energy theorems (Jarzynski equality, Crooks fluctuation theorem, Bennett acceptance ratio, and overlapping method), it is possible to obtain free energy values in experiments far from equilibrium. This review compares different methodologies and their application in optical tweezers. Interestingly, in many proteins, discrepancies in free energy values obtained through different methods suggest additional complexities in the folding pathway, possibly involving intermediate states such as the molten globule. Further studies are needed to confirm their presence and significance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-025-01310-0.

Bovine serum albumin under the influence of alkali metal halides

The hydration shell of a protein is so important and an integral part of it, that protein's structure, stability and functionality cannot be conceived in its absence. This layer has unique properties not found in bulk water. However, ions, always present in the protein environment, disturb the hydration shell depending on their nature and concentration. In this work, we study the effect of four alkali metal halides (LiCl, NaCl, KCl and CsCl) on a Bovine Serum Albumin (BSA) suspension. In order to investigate the influence of such ions on this protein, we use several experimental methods: dynamic light scattering, differential scanning calorimetry, thermogravimetry, Fourier transform infrared spectroscopy and image analysis. We found that Li+ and Na+ prevent protein aggregation. Moreover, the ion size affects the interaction with the secondary structure of the protein (Amide III band). Notably, for the smallest ion (Li+), the water-ion interaction dominates over the Amide A band signature, contrasting with the other ions. We also differentiate between bulk and hydration water through the evaporation of protein suspensions.

Ultrasonic Sensor: A Fast and Non-Destructive System to Measure the Viscosity and Density of Molecular Fluids

This study presents the design and development of an ultrasonic sensor as a fundamental tool for characterizing the properties of fluids and biofluids. The analysis primarily focuses on measuring the electrical parameters of the system, which correlate with the density and viscosity of the solutions, in sample volumes of microliters and with high temporal resolution (up to 1 data point per second). The use of this sensor allows the fast and non-destructive evaluation of the viscosity and density of fluids deposited on its free surface. The measurements are based on obtaining the impedance versus frequency curve and the phase difference curve (between current and voltage) versus frequency. In this way, characteristic parameters of the transducer, such as the resonance frequency, phase, minimum impedance, and the quality factor of the resonant system, can characterize variations in density and viscosity in the fluid under study. The results obtained revealed the sensor's ability to identify two parameters sensitive to viscosity and two parameters sensitive to density. As a proof of concept, the unfolding of the bovine albumin protein was studied, resulting in a curve that reflects its unfolding kinetics in the presence of urea.

Towards the understanding of molecular motors and its relationship with local unfolding

Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical-structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane-Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as 'cracking'. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme's integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.

Determination of protein-protein interactions at the single-molecule level using optical tweezers

Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (k_off, k_on), affinity values (K_D), energy to the transition state ΔG^≠, distance to the transition state Δx^≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

Injectable oxygenation therapeutics: evaluating the oxygen delivery efficacy of artificial oxygen carriers and kosmotropes in vitro

The aim of this paper was to utilise an existing in vitro setup to quantify the oxygen offloading capabilities of two different subsets of injectable oxygenation therapeutics: (1) artificial oxygen carriers (AOCs), which bind or dissolve oxygen and act as transport vectors, and (2) kosmotropes, which increase water hydrogen bonding and thereby decrease the resistance to oxygen movement caused by the blood plasma. Dodecafluoropentane emulsion (DDFPe) was chosen to represent the AOC subset while trans sodium crocetinate (TSC) was selected to represent the kosmotrope subset. PEG-Telomer-B (PTB), the surfactant utilised to encapsulate DDFP in emulsion form, was also tested to determine whether it affected the oxygen transport ability of DDFPe. The in vitro set-up was used to simulate a semi closed-loop circulatory system, in which oxygen could be delivered from the lungs to hypoxic tissues. Results of this study showed that (1) 0.5 ml of a PFC outperformed 6.25 ml of a kosmotrope in a controlled, in vitro setting and (2) that PTB and sucrose do not contribute to the overall oxygen transportation efficacy of DDFPe. These results could be therapeutically beneficial to ongoing and future pre-clinical and clinical studies involving various oxygenation agents.

Influence of medium structure on the physicochemical properties of aging colloidal dispersions investigated using the synthetic clay LAPONITE®

Physical aging in colloidal dispersions manifests as a reduction in kinetic freedom of the colloids. In aqueous dispersions of charged clay colloids, the role of interparticle electrostatic interactions in determining the aging dynamics has been evaluated extensively. Despite water being the dispersion medium, the influence of water structure on the physicochemical properties of aging clay dispersions has, however, not been considered before. In this work, we use LAPONITE®, a model hectorite clay mineral that acquires surface charges when dispersed in water, to study the relative contributions of dispersion medium structure and interparticle electrostatic interactions on the physicochemical properties of aging hectorite clay dispersions. The structure of the dispersion medium is modified either by incorporating dissociating/non-dissociating kosmotropic (structure-inducing) or chaotropic (structure-disrupting) molecules or by changing dispersion temperature. Photon correlation spectroscopy, rheological measurements and particle-scale imaging are employed to evaluate the physicochemical properties of the dispersions. Our experiments involving incorporation of external additives demonstrate a strong influence of dispersion medium structure on the dispersion properties when the interparticle electrostatic interactions are weak. We introduce a new temperature dependent measurement protocol, wherein the temperature of the medium is fixed before adding the clay particles, to manipulate the hydrogen bonds in the aqueous medium in the absence of external additives. Accelerated aging, observed upon raising the temperature regardless of the experimental thermal histories, is attributed to increased interparticle electrostatic interactions as in the room temperature experiments with ionic additives. Our study identifies that in the presence of weak interparticle electrostatic interactions, changes in the physicochemical properties of charged clay dispersions can be driven by manipulating hydrogen bond populations in aqueous medium.

A comprehensive review of the factors influencing the formation of retrograded starch

The retrogradation of starch is an inevitable change that occurs in starchy food during processing and storage, in which gelatinized starch rearranges into an ordered state. The chain length, proportion and structure of amylose and amylopectin vary in different types of starch granules, and the process is affected by the genes and growth environment of plants. The internal factors play a significant role in the formation of retrograded starch, while the external factors have a direct impact on its structural rearrangement, and the creation of suitable conditions enables food components to affect the rearrangement of starch. Interestingly, water not only directly affects the gelatinization and retrogradation of starch, but also serves as a bridge to deliver the influence of other components that influence retrogradation. Moreover, there are three mechanisms responsible for forming retrograded starch: the migration of starch molecular chains in the starch-water mixed system, the redistribution of water molecules, and the recrystallization kinetics of gelatinized starch. In this paper, the effects of internal factors (amylose, amylopectin, food ingredients) and external factors (processing conditions) on the formation of retrograded starch and the mechanism controlling these effects are reviewed.

Destressing Yeast for Higher Biofuel Yields: Can Excess Chaotropicity Be Mitigated?

Biofuels have the capacity to contribute to carbon dioxide emission reduction and to energy security as oil reserves diminish and/or become concentrated in politically unstable regions. However, challenges exist in obtaining the maximum yield from industrial fermentations. One challenge arises from the nature of alcohols. These compounds are chaotropic (i.e. causes disorder in the system) which causes stress in the microbes producing the biofuel. Brewer's yeast (Saccharomyces cerevisiae) typically cannot grow at ethanol concentration much above 17% (v/v). Mitigation of these properties has the potential to increase yield. Previously, we have explored the effects of chaotropes on model enzyme systems and attempted (largely unsuccessfully) to offset these effects by kosmotropes (compounds which increase the order of the system, i.e. the "opposite" of chaotropes). Here we present some theoretical results which suggest that high molecular mass polyethylene glycols may be the most effective kosmotropic additives in terms of both efficacy and cost. The assumptions and limitations of these calculations are also presented. A deeper understanding of the effects of chaotropes on biofuel-producing microbes is likely to inform improvements in bioethanol yields and enable more rational approaches to the "neutralisation" of chaotropicity.

Promising insights into the kosmotropic effect of magnetic nanoparticles on proteins: The pivotal role of protein corona formation

Increasing concerns about biosafety of nanoparticles (NPs) has raised the need for detailed knowledge of NP interactions with biological molecules especially proteins. Herein, the concentration-dependent effect of magnetic NPs (MNPs) on bovine serum albumin and hen egg white lysozyme was explored. The X-ray diffraction patterns, zeta potential, and dynamic light scattering measurements together with scanning electron microscopy images were employed to characterize MNPs synthesized through coprecipitation method. Then, we studied the behavior of two model proteins with different surface charges and structural properties on interaction with Fe₃ O₄ . A thorough investigation of protein-MNP interaction by the help of intrinsic fluorescence at different experimental conditions revealed that affinity of proteins for MNPs is strongly affected by the similarity of protein and MNP surface charges. MNPs exerted structure-making kosmotropic effect on both proteins under a concentration threshold; however, binding strength was found to determine the extent of stabilizing effect as well as magnitude of the concentration threshold. Circular dichroism spectra showed that proteins with less resistance to conformational deformations are more prone to secondary structure changes upon adsorption on MNPs. By screening thermal aggregation of proteins in the presence of Fe₃ O₄ , it was also found that like chemical stability, thermal stability is influenced to a higher extent in more strongly bound proteins. Overall, this report not only provides an integrated picture of protein-MNP interaction but also sheds light on the molecular mechanism underling this process.

The roles and applications of chaotropes and kosmotropes in industrial fermentation processes

Chaotropicity has long been recognised as a property of some compounds. Chaotropes tend to disrupt non-covalent interactions in biological macromolecules (e.g. proteins and nucleic acids) and supramolecular assemblies (e.g. phospholipid membranes). This results in the destabilisation and unfolding of these macromolecules and assemblies. Unsurprisingly, these compounds are typically harmful to living cells since they act against multiple targets, comprising cellular integrity and function. Kosmotropes are the opposite of chaotropes and these compounds promote the ordering and rigidification of biological macromolecules and assemblies. Since many biological macromolecules have optimum levels of flexibility, kosmotropes can also inhibit their activity and can be harmful to cells. Some products of industrial fermentations, most notably alcohols, are chaotropic. This property can be a limiting factor on rates of production and yields. It has been hypothesised that the addition of kosmotropes may mitigate the chaotropicity of some fermentation products. Some microbes naturally adapt to chaotropic environments by producing kosmotropic compatible solutes. Exploitation of this in industrial fermentations has been hampered by scientific and economic issues. The cost of the kosmotropes and their removal during purification needs to be considered. We lack a complete understanding of the chemistry of chaotropicity and a robust, quantitative framework for estimating overall chaotropicities of mixtures. This makes it difficult to predict the amount of kosmotrope required to neutralise the chaotropicity. This review considers examples of industrial fermentations where chaotropicity is an issue and suggests possible mitigations.

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

Peptide Mediated Antimicrobial Dental Adhesive System

The most common cause for dental composite failures is secondary caries due to invasive bacterial colonization of the adhesive/dentin (a/d) interface. Innate material weakness often lead to an insufficient seal between the adhesive and dentin. Consequently, bacterial by-products invade the porous a/d interface leading to material degradation and dental caries. Current approaches to achieve antibacterial properties in these materials continue to raise concerns regarding hypersensitivity and antibiotic resistance. Herein, we have developed a multi-faceted, bio-functionalized approach to overcome the vulnerability of such interfaces. An antimicrobial adhesive formulation was designed using a combination of antimicrobial peptide and a ε-polylysine resin system. Effector molecules boasting innate immunity are brought together with a biopolymer offering a two-fold biomimetic design approach. The selection of ε-polylysine was inspired due to its non-toxic nature and common use as food preservative. Biomolecular characterization and functional activity of our engineered dental adhesive formulation were assessed and the combinatorial formulation demonstrated significant antimicrobial activity against Streptococcus mutans. Our antimicrobial peptide-hydrophilic adhesive hybrid system design offers advanced, biofunctional properties at the critical a/d interface.

Molecular Architecture of the Inositol Phosphatase Siw14

Siw14 is a recently discovered inositol phosphatase implicated in suppressing prion propagation in Saccharomyces cerevisiae. In this paper, we used hybrid structural methods to decipher Siw14 molecular architecture. We found the protein exists in solution as an elongated monomer that is ∼140 Å in length, containing an acidic N-terminal domain and a basic C-terminal dual-specificity phosphatase (DSP) domain, structurally similar to the glycogen phosphatase laforin. The two domains are connected by a protease susceptible linker and do not interact in vitro. The crystal structure of Siw14-DSP reveals a highly basic phosphate-binding loop and an ∼10 Å deep substrate-binding crevice that evolved to dephosphorylate pyro-phosphate moieties. A pseudoatomic model of the full-length phosphatase generated from solution, crystallographic, biochemical, and modeling data sheds light on the interesting zwitterionic nature of Siw14, which we hypothesized may play a role in discriminating negatively charged inositol phosphates.