H/D Isotope Effects in Protein Thermal Denaturation: The Case of Bovine Serum Albumin

Induced Circular Dichroism Analysis of Thermally Induced Conformational Changes on Protein Binding Sites Under a Crowding Environment

Protein-ligand interactions in crowded cellular environments play a crucial role in biological functions. The crowded environment can perturb the overall protein structure and local conformation, thereby influencing the binding pathway of protein-ligand reactions within the cellular milieu. Therefore, a detailed understanding of the local conformation is crucial for elucidating the intricacies of protein-ligand interactions in crowded cellular environments. In this study, we investigated the feasibility of induced circular dichroism (ICD) using 8-anilinonaphthalene-1-sulfonic acid (ANS) for local conformational analysis at the binding site in a crowding environment. Bovine serum albumin (BSA) concentration-dependent measurements were performed to assess the feasibility of ANS-ICD for analyzing protein interior binding sites. The results showed distinct changes in the ANS-ICD spectra of BSA solutions, indicating their potential for analyzing the internal conformation of proteins. Moreover, temperature-dependent measurements were performed in dilute and crowding environments, revealing distinct denaturation pathways of BSA binding sites. Principal component analysis of ANS-ICD spectral changes revealed lower temperature pre-denaturation in the crowded solution than that in the diluted solution, suggesting destabilization of binding sites owing to self-crowding repulsive interactions. The established ANS-ICD method can provide valuable conformational insights into protein-ligand interactions in crowded cellular environments.

D2O as an Imperfect Replacement for H2O: Problem or Opportunity for Protein Research?

D2O is commonly used as a solvent instead of H2O in spectroscopic studies of proteins, in particular, in infrared and nuclear-magnetic-resonance spectroscopy. D2O is chemically equivalent to H2O, and the differences, particularly in hydrogen-bond strength, are often ignored. However, replacing solvent water with D2O can affect not only the kinetics but also the structure and stability of biomolecules. Recent experiments have shown that even the mesoscopic structures and the elastic properties of biomolecular assemblies, such as amyloids and protein networks, can be very different in D2O and H2O. We discuss these findings, which probably are just the tip of the iceberg, and which seem to call for obtaining a better understanding of the H2O/D2O-isotope effect on water-water and water-protein interactions. Such improved understanding may change the differences between H2O and D2O as biomolecular solvents from an elephant in the room to an opportunity for protein research.

Heat-induced self-assembling of BSA at the isoelectric point

Materials based on ordered protein aggregates have recently received a lot of attention for their application as drug carriers, due to their biocompatibility and their ability to sequester many biological fluids. Bovine serum albumin (BSA) is a good candidate for this use due to its high availability and tendency to aggregate and gel under acidic conditions. In the present work, we employ spectroscopic techniques to investigate the heat-induced BSA aggregation at the molecular scale, in the 12-84 °C temperature range, at pH = 5 where two different isoforms of the protein are stable. Samples at low and high protein concentration are examined. With the advantage of the combined use of FTIR and CD, we recognize the aggregation-prone species and the different distribution of secondary structures, conformational rearrangements and types of aggregates, of millimolar compared to micromolar BSA solutions. Further, as a new tool, we use the Maximum Entropy Method to fit the kinetic curves to investigate the distribution of kinetic constants of the complex hierarchical aggregation process. Finally, we characterize the activation energy of the initial self-assembling step to observe that the formation of both small and large aggregates is driven by the same interactions.

Bovine Serum Albumin Catalysed Hydrogen and Deuterium Evolution at Mercury Electrodes

The hydrogen evolution reaction (HER), catalysed by proteins at mercury electrodes and reflected in chronopotentiometric stripping peak H, provides a label-free and reagentless analytical technique that is sensitive to protein structure. Here we show how the kinetic isotope effect affected the HER catalysed by the protein bovine serum albumin (BSA). We found that the deuteron bond, which is stronger than that of a proton, contributed to less effective transport of deuterons mediated by BSA at the Hg|D₂ O interface, and enhanced structural stability of the surface-attached native BSA in D₂ O solution. A structural transition was also observed in the surface-attached urea-denatured BSA, and is probably due to the destabilisation of some secondary structural remnants retained by the 17 SS-bonds. Because the catalytically active groups involved in proton or deuteron transfer in native proteins are often exposed towards solutions and their protons exchange almost instantly, no signs of H/D exchange were observed in native BSA using peak H under the given conditions.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.

Enthalpic stabilization of an SH3 domain by D2 O

The stability of a protein is vital for its biological function, and proper folding is partially driven by intermolecular interactions between protein and water. In many studies, H2 O is replaced by D2 O because H2 O interferes with the protein signal. Even this small perturbation, however, affects protein stability. Studies in isotopic waters also might provide insight into the role of solvation and hydrogen bonding in protein folding. Here, we report a complete thermodynamic analysis of the reversible, two-state, thermal unfolding of the metastable, 7-kDa N-terminal src-homology 3 domain of the Drosophila signal transduction protein drk in H2 O and D2 O using one-dimensional 19 F NMR spectroscopy. The stabilizing effect of D2 O compared with H2 O is enthalpic and has a small to insignificant effect on the temperature of maximum stability, the entropy, and the heat capacity of unfolding. We also provide a concise summary of the literature about the effects of D2 O on protein stability and integrate our results into this body of data.

Effect of heavy water on the conformational stability of globular proteins

It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. The latter has to be due to the strength of protein-water van der Waals attractions which are weaker in heavy water due to the smaller molecular polarizability of D₂ O compared with that of H₂ O molecules. Since protein-water van der Waals attractions occur more in the denatured than in the native state, this contribution leads to a stabilization of the latter through a destabilization of the former.

Deciphering the binding behaviours of BSA using ionic AIE-active fluorescent probes

The binding behaviours of a transport protein, bovine serum albumin (BSA), in its native, unfolding and refolding states have been probed by monitoring the emission changes of two exogenous AIE-active fluorescent probes, M2 and M3, which are designed to be anionic and cationic, respectively. Due to their AIE properties, both M2 and M3 display emission enhancement when bound to the hydrophobic cavity of BSA. The binding site of M2 and M3 is found to be subdomain IIA. Then, the BSA + M2 and BSA + M3 systems are utilized to fluorescently signal the conformation changes of BSA caused by various external stimuli, including thermally or chemically induced denaturation. The data confirmed the multi-step unfolding process and the existence of a molten-globule intermediate state. The unfolding process consists of the rearrangement of subdomain IIA, the exposure of a negatively charged binding site in domain I that prefers interacting with cationic species, and the transformation of the molten-globule intermediate into the final random coil. The anionic and cationic modifications of the probes enable us to observe that electrostatic interactions play a role in the folding and unfolding of BSA.

Extended Law of Corresponding States Applied to Solvent Isotope Effect on a Globular Protein

Investigating proteins with techniques such as NMR or neutron scattering frequently requires the partial or complete substitution of D2O for H2O as a solvent, often tacitly assuming that such a solvent substitution does not significantly alter the properties of the protein. Here, we report a systematic investigation of the solvent isotope effect on the phase diagram of the lens protein γB-crystallin in aqueous solution as a model system exhibiting liquid-liquid phase separation. We demonstrate that the observed strong variation of the critical temperature Tc can be described by the extended law of corresponding states for all H2O/D2O ratios, where scaling of the temperature by Tc or the reduced second virial coefficient accurately reproduces the binodal, spinodal, and osmotic compressibility. These findings highlight the impact of H2O/D2O substitution on γB-crystallin properties and warrant further investigations into the universality of this phenomenon and its underlying mechanisms.

Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation

The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.

Effect of grafted PEG chain conformation on albumin and lysozyme adsorption: A combined study using QCM-D and DPI

In this study, elucidation of protein adsorption mechanism is performed using dual polarization interferometry (DPI) and quartz crystal microbalance with dissipation (QCM-D) to study adsorption behaviors of bovine serum albumin (BSA) and lysozyme (LYZ) on poly (ethylene glycol) (PEG) layers. From the analysis of DPI, PEG2000 and PEG5000 show tight and loose mushroom conformations, respectively. Small amount of LYZ could displace the interfacial water surrounding the tight mushroomed PEG2000 chains by hydrogen bond attraction, leading to protein adsorption. The loose mushroomed PEG5000 chains exhibit a more flexible conformation and high elastic repulsion energy that could prevent protein adsorption of all BSA and most of LYZ. From the analysis of QCM, PEG2000 and PEG5000 show tight and extended brush conformations. The LYZ adsorbed mass has critical regions of PEG2000 (0.19 chain/nm(2)) and PEG5000 (0.16 chain/nm(2)) graft density. When graft density of PEG is higher than the critical region (brush conformations), the attraction of hydrogen bonds between PEG and LYZ is the dominant factor. When graft density of PEG is lower than the critical region (mushroom conformations), elastic repulsion between PEG and proteins is driven by the high conformation entropy of PEG chains, which is the dominant force of steric repulsion in PEG-protein systems. Therefore, the adsorption of BSA is suppressed by the high elastic repulsion energy of PEG chains, whereas the adsorption of LYZ is balanced by the interactions between the repulsion of entropy elasticity and the attraction of hydrogen bonds.

Mechanical properties of protein adsorption layers at the air/water and oil/water interface: a comparison in light of the thermodynamical stability of proteins

Over the last decades numerous studies on the interfacial rheological response of protein adsorption layers have been published. The comparison of these studies and the retrieval of a common parameter to compare protein interfacial activity are hampered by the fact that different boundary conditions (e.g. physico-chemical, instrumental, interfacial) were used. In the present work we review previous studies and attempt a unifying approach for the comparison between bulk protein properties and their adsorption films. Among many common food grade proteins we chose bovine serum albumin, β-lactoglobulin and lysozyme for their difference in thermodynamic stability and studied their adsorption at the air/water and limonene/water interface. In order to achieve this we have i) systematically analyzed protein adsorption kinetics in terms of surface pressure rise using a drop profile analysis tensiometer and ii) we addressed the interfacial layer properties under shear stress using an interfacial shear rheometer under the same experimental conditions. We could show that thermodynamically less stable proteins adsorb generally faster and yield films with higher shear rheological properties at air/water interface. The same proteins showed an analog behavior when adsorbing at the limonene/water interface but at slower rates.

Isolation of a highly reactive β-sheet-rich intermediate of lysozyme in a solvent-free liquid phase

The thermal denaturation of solvent-free liquid lysozyme at temperatures in excess of 200 °C was studied by synchrotron radiation circular dichroism spectroscopy. Temperature-dependent changes in the secondary structure were used to map the equilibrium denaturation pathway and characterize a reactive β-sheet-rich unfolding intermediate that was stable in the solvent-free liquid phase under anhydrous conditions but which underwent irreversible aggregation in the presence of water. The unfolding intermediate had a transition temperature of 78 °C and was extremely stable to temperature, eventually reaching the fully denatured state at 178 °C. We propose that the three-stage denaturation pathway arises from the decreased stability of the native state due to the absence of any appreciable hydrophobic effect, along with an entropically derived stabilization of the reactive intermediate associated with molecular crowding in the solvent-free liquid.

Promoting crystallisation of the Salmonella enteritidis fimbriae 14 pilin SefD using deuterium oxide

The use of heavy water (D(2)O) as a solvent is commonplace in many spectroscopic techniques for the study of biological macromolecules. A significant deuterium isotope effect exists where hydrogen-bonding is important, such as in protein stability, dynamics and assembly. Here we illustrate the use of D(2)O in additive screening for the production of reproducible diffraction-quality crystals for the Salmonella enteritidis fimbriae 14 (SEF14) putative tip adhesin, SefD.