Spectroscopic and Microscopic Studies of Aggregation and Fibrillation of Lysozyme in Water/Ethanol Solutions

Interaction, inhibition and disruption of lysozyme fibrillar aggregates by the plant alkaloid berberine

This study investigated the interaction and impact of berberine, a pharmacologically important natural alkaloid, on lysozyme amyloidosis with the aim to develop effective anti-amyloidogenic agents. Interaction between berberine and lysozyme was analyzed using both theoretical and experimental tools to unleash its anti-amyloidogenic potency. The intrinsic fluorescence of lysozyme was quenched by berberine through static mechanism, indicating the presence of single binding site predominantly involving TRP residues. Complexation with berberine caused microenvironmental and conformational changes in lysozyme as shown by synchronous and 3D fluorescence spectroscopic analysis. Molecular docking and dynamic simulation study revealed the probable binding site and pharmacokinetics involved in lysozyme-berberine complexation. Berberine significantly inhibited lysozyme fibrillation which was confirmed by Thioflavin T, Congo red, Nile red and ANS assays. FTIR and circular dichroism studies revealed that berberine reduced β-sheet content of lysozyme fibrillar samples, indicating inhibition of fibril formation. Additionally, berberine can degrade pathogenic mature fibril as well. Amyloid inhibition and defibrillation was visualised by atomic force microscopy.

From Self-Assembly to Drug Delivery: Understanding and Exploring Protein Fibrils

It is crucial to comprehend protein misfolding and aggregation in the domains of biomedicine, pharmaceuticals, and proteins. Amyloid fibrils are formed when proteins misfold and assemble, resulting in the debilitating illness known as "amyloidosis". This work investigates lysozyme fibrillation with pluronics (F68 and F127). The effect of pluronics on protein aggregation and fibrillation has been studied mechanistically using a combination of calorimetric and spectroscopic techniques. TEM images and the ThT binding experiment were used to analyze the conformation of protein fibrils, and the results showed that pluronics accelerated the fibrillation process. When pluronics interact with protein at different stages of fibrillation, their pre- and postmicellar concentrations show a decrease in ΔHm° value as the time of incubation increases. This indicates the formation of amorphous aggregates due to which endothermic enthalpy is observed. As a consequence, it was investigated if these generated aggregates can also act as drug delivery vehicle; therefore, the work was carried out with 5-fluorouracil and cytarabine. The endothermic enthalpy of interaction suggests that hydrophobic interaction is more prevalent when cytarabine is employed with protein fibrils, whereas the electrostatic interaction is more prevalent when 5-fluorouracil is combined with it. The former drug, however, showed a greater adsorption than the latter on the surface of protein fibrils. It is therefore determined that 5-fluorouracil has relatively significant adsorption on fibril surfaces, whereas cytarabine has weak adsorption and is easily desorbed in cells. Consequently, the combination of LFF127 and 5-FU is lethal to malignant cells. The drug encapsulation and delivery aspect of protein fibrils/aggregates needs further exploration.

Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates

Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.

Insights into the interaction and inhibitory action of palmatine on lysozyme fibrillogenesis: Spectroscopic and computational studies

Interaction under amyloidogenic condition between naturally occurring protoberberine alkaloid palmatine and hen egg white lysozyme was executed by adopting spectrofluorometric and theoretical molecular docking and dynamic simulation analysis. In spetrofluorometric method, different types of experiments were performed to explore the overall mode and mechanism of interaction. Intrinsic fluorescence quenching of lysozyme (Trp residues) by palmatine showed effective binding interaction and also yielded different binding parameters like binding constant, quenching constant and number of binding sites. Synchronous fluorescence quenching and 3D fluorescence map revealed that palmatine was able to change the microenvironment of the interacting site. Fluorescence life time measurements strongly suggested that this interaction was basically static in nature. Molecular docking result matched with fluorimetric experimental data. Efficient drug like interaction of palmatine with lysozyme at low pH and high salt concentration prompted us to analyze its antifibrillation potential. Different assays and microscopic techniques were employed for detailed analysis of lysozyme amyloidosis.Thioflavin T(ThT) assay, Congo Red (CR) assay, 8-anilino-1-naphthalenesulfonic acid (ANS) assay, Nile Red (NR) assay, anisotropy and intrinsic fluorescence measurements confirmed that palmatine successfully retarded and reduced lysozyme fibrillation. Dynamic light scattering (DLS) and atomic force microscopy (AFM) further reiterated the excellent antiamyloidogenic potency of palmatine.

Probing the Role of Cu(II) Ions on Protein Aggregation Using Two Model Proteins

Copper is an essential trace element for human biology where its metal dyshomeostasis accounts for an increased level of serum copper, which accelerates protein aggregation. Protein aggregation is a notable feature for many neurodegenerative disorders. Herein, we report an experimental study using two model proteins, bovine serum albumin (BSA) and human serum albumin (HSA), to elucidate the mechanistic pathway by which serum albumins get converted from a fully folded globular protein to a fibril and an amorphous aggregate upon interaction with copper. Steady-state fluorescence, time-resolved fluorescence studies, and Raman spectroscopy were used to monitor the unfolding of serum albumin with increasing copper concentrations. Steady-state fluorescence studies have revealed that the fluorescence quenching of BSA/HSA by Cu(II) has occurred through a static quenching mechanism, and we have evaluated both the quenching constants individually. The binding constants of BSA-Cu(II) and HSA-Cu(II) were found to be 2.42 × 104 and 0.05 × 104 M-1, respectively. Further nanoscale morphological changes of BSA mediated by oligomers to fibril and HSA to amorphous aggregate formation were studied using atomic force microscopy. This aggregation process correlates with the Stern-Volmer plots in the absence of discernible lag phase. Raman spectroscopy results obtained are in good agreement with the increase in antiparallel β-sheet structures formed during the aggregation of BSA in the presence of Cu(II) ions. However, an increase in α-helical fractions is observed for the amorphous aggregate formed from HSA.

Interactions in protein solutions close to liquid-liquid phase separation: ethanol reduces attractions via changes of the dielectric solution properties

Ethanol is a common protein crystallization agent, precipitant, and denaturant, but also alters the dielectric properties of solutions. While ethanol-induced unfolding is largely ascribed to its hydrophobic parts, its effect on protein phase separation and inter-protein interactions remains poorly understood. Here, the effects of ethanol and NaCl on the phase behavior and interactions of protein solutions are studied in terms of the metastable liquid-liquid phase separation (LLPS) and the second virial coefficient B₂ using lysozyme solutions. Determination of the phase diagrams shows that the cloud-point temperatures are reduced and raised by the addition of ethanol and salt, respectively. The observed trends can be explained using the extended law of corresponding states as changes of B₂. The results for B₂ agree quantitatively with those of static light scattering and small-angle X-ray scattering experiments. Furthermore, B₂ values calculated based on inter-protein interactions described by the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential and considering the dielectric solution properties and electrostatic screening due to the ethanol and salt content quantitatively agree with the experimentally observed B₂ values.

Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel

A method is designed to quickly form protein hydrogels, based on the self-assembly of highly concentrated lysozyme solutions in acidic conditions. Their properties can be easily modulated by selecting the curing temperature. Molecular insights on the gelation pathway, derived by in situ FTIR spectroscopy, are related to calorimetric and rheological results, providing a consistent picture on structure–property correlations. In these self-crowded samples, the thermal unfolding induces the rapid formation of amyloid aggregates, leading to temperature-dependent quasi-stationary levels of antiparallel cross β-sheet links, attributed to kinetically trapped oligomers. Upon subsequent cooling, thermoreversible hydrogels develop by the formation of interoligomer contacts. Through heating/cooling cycles, the starting solutions can be largely recovered back, due to oligomer-to-monomer dissociation and refolding. Overall, transparent protein hydrogels can be easily formed in self-crowding conditions and their properties explained, considering the formation of interconnected amyloid oligomers. This type of biomaterial might be relevant in different fields, along with analogous systems of a fibrillar nature more commonly considered.

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.

Probing Globular Protein Self-Assembling Dynamics by Heterodyne Transient Grating Experiments

In this work, we studied the propagation of ultrasonic waves of lysozyme solutions characterized by different degrees of aggregation and networking. The experimental investigation was performed by means of the transient grating (TG) spectroscopy as a function of temperature, which enabled measurement of the ultrasonic acoustic proprieties over a wide time window, ranging from nanoseconds to milliseconds. The fitting of the measured TG signal allowed the extraction of several dynamic properties, here we focused on the speed and the damping rate of sound. The temperature variation induced a series of processes in the lysozyme solutions: Protein folding-unfolding, aggregation and sol–gel transition. Our TG investigation showed how these self-assembling phenomena modulate the sound propagation, affecting both the velocity and the damping rate of the ultrasonic waves. In particular, the damping of ultrasonic acoustic waves proved to be a dynamic property very sensitive to the protein conformational rearrangements and aggregation processes.

Fluorimetric Studies of a Transmembrane Protein and Its Interactions with Differently Functionalized Silver Nanoparticles

Transmembrane proteins play important roles in intercellular signaling to regulate interactions among the adjacent cells and influence cell fate. The study of interactions between membrane proteins and nanomaterials is paramount for the design of nanomaterial-based therapies. In the present work, the fluorescence properties of the transmembrane receptor Notch2 have been investigated. In particular, the steady-state and time-resolved fluorescence methods have been used to characterize the emission of tryptophan residues of Notch2 and then this emission is used to monitor the effect of silver colloids on protein behavior. To this aim, silver colloids are prepared with two different methods to make sure that they bear hydrophilic (citrate ions, C-AgNPs) or hydrophobic (dodecanethiol molecules, D-AgNPs) capping agents. The preparation procedures are tightly controlled to obtain metal cores with similar size distributions (7.4 ± 2.5 and 5.0 ± 0.8 nm, respectively), thus, making the comparison of the results easier. The occurrence of strong interactions between Notch2 and D-AgNPs is suggested by the efficient and statistically relevant quenching of the stationary protein emission already at low nanoparticle (NP) concentrations (ca. 12% quenching with [D-AgNPs] = 0.6 nM). The quenching becomes even more pronounced (ca. 60%) when [D-AgNPs] is raised to 8.72 nM. On the other hand, the addition of increasing concentrations of C-AgNPs to Notch2 does not affect the protein fluorescence (intensity variations below 5%) indicating that negligible interactions are taking place. The fluorescence data, recorded in the presence of increasing concentrations of silver nanoparticles, are then analyzed through the Stern-Volmer equation and the sphere of action model to discuss the nature of interactions. The effect of D-AgNPs on the fluorescence decay times of Notch2 is also investigated and a decrease in the average decay time is observed (from 4.64 to 3.42 ns). The observed variations of the stationary and time-resolved fluorescence behavior of the protein are discussed in terms of static and collisional interactions. These results document that the capping shell is able to drive the protein-particle interactions, which likely have a hydrophobic nature.

Laboratory exercise for studying the morphology of heat-denatured and amyloid aggregates of lysozyme by atomic force microscopy

To facilitate learning advanced instrumental techniques, essential tools for visualizing biomaterials, a simple and versatile laboratory exercise demonstrating the use of Atomic Force Microscopy (AFM) in biomedical applications was developed. In this experiment, the morphology of heat-denatured and amyloid-type aggregates formed from a low-cost and well-characterized model protein, hen egg white lysozyme (HEWL), are compared. Structural differences between the amorphous and ordered particles are quantified using ImageJ for the analysis of AFM images as a postlaboratory assignment. The laboratory exercise allows the direct observation of changes in the protein structure and helps students to understand the operation of AFM, as well as protein folding and misfolding related to many physiological and pathological processes. The described protocol stands alone, but also fits well into a larger module on protein structure and function or microscopic techniques as it can be linked easily to existing laboratory exercises on these topics. It can be easily adapted to the upper level undergraduate laboratory courses with limited lab hours as well as graduate level courses to improve students' research skills. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):162-171, 2018.

Study of conformational changes and protein aggregation of bovine serum albumin in presence of Sb(III) and Sb(V)

Antimony is a metalloid that affects biological functions in humans due to a mechanism still not understood. There is no doubt that the toxicity and physicochemical properties of Sb are strongly related with its chemical state. In this paper, the interaction between Sb(III) and Sb(V) with bovine serum albumin (BSA) was investigated in vitro by fluorescence spectroscopy, and circular dichroism (CD) under simulated physiological conditions. Moreover, the coupling of the separation technique, asymmetric flow field-flow fractionation, with elemental mass spectrometry to understand the interaction of Sb(V) and Sb(III) with the BSA was also used. Our results showed a different behaviour of Sb(III) vs. Sb(V) regarding their effects on the interaction with the BSA. The effects in terms of protein aggregates and conformational changes were higher in the presence of Sb(III) compared to Sb(V) which may explain the differences in toxicity between both Sb species in vivo. Obtained results demonstrated the protective effect of GSH that modifies the degree of interaction between the Sb species with BSA. Interestingly, in our experiments it was possible to detect an interaction between BSA and Sb species, which may be related with the presence of labile complex between the Sb and a protein for the first time.