Effects of Trehalose on Thermodynamic Properties of Alpha-synuclein Revealed through Synchrotron Radiation Circular Dichroism

Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders

Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.

Effect of Trehalose and Ceftriaxone on the Stability of Aggregating-Prone Tau Peptide Containing PHF6* Sequence: An SRCD Study

The tau protein, a soluble protein associated with microtubules, which is involved in the assembly and stabilization of cytoskeletal elements, was found to form neurofibrillary tangles in different neurodegenerative diseases. Insoluble tau aggregates were observed to be organized in paired helical filaments (PHFs) and straight filaments (SFs). Recently, two small sequences (306–311 and 275–280) in the microtubule-binding region (MTBR), named PHF6 and PHF6*, respectively, were found to be essential for tau aggregation. Since a possible therapeutic approach consists of impairing amyloid formation either by stabilizing the native proteins or reducing the level of amyloid precursors, here we use synchrotron radiation circular dichroism (SRCD) at Diamond B23 beamline to evaluate the inhibitory effects of two small molecules, trehalose and ceftriaxone, against the aggregation of a small peptide containing the PHF6* sequence. Our results indicate that both these molecules, ceftriaxone and trehalose, increased the stability of the peptide toward aggregation, in particular that induced by heparin. With trehalose being present in many fruits, vegetables, algae and processed foods, these results support the need to investigate whether a diet richer in trehalose might exert a protective effect toward pathologies linked to protein misfolding.

Photoisomerization Kinetics of Photoswitchable Thin Films Based on Nanostructure/Molecular Layers of AlN-AO7

The photoisomerization kinetics of photoswitchable thin films based on nanostructure/molecular layers of AlN-AO7 have been studied, investigated and reported. The trans → cis isomerization process occurs by UV-light irradiation. The cis-isomer could be turned back to the trans-isomer by either thermal or optical relaxation. The kinetics and time-evolution of the photoisomerization and reverse isomerization mechanism of AlN-AO7 thin films are investigated by UV-Vis absorbance spectra using relevant models. All phases of AlN-AO7 thin film, initial trans-, cis-, optical trans-, thermal trans-phases, were investigated using UV-Vis absorbance spectra, FTIR spectra, XRD and SEM. Transforming AlN-AO7 thin film from the initial trans-phase into cis-phase leads to curvature in the AO7 leaves and increases in the strain inside the structure. Going back to the trans-phase by either optical or thermal relaxation leads to vanishing the curvature and decreasing the structure's strain. Finally, the energy storage capacity was calculated using DSC and was found to be 36.38 J g^-1 , simultaneously realizing the multisource solar energy storage and environmental heat.

Synthesis and Characterization of Thin Films Based on Azobenzene Derivative Anchored to CeO2 Nanoparticle for Photoswitching Applications

Azobenzene has attracted substantial attention as a photoswitchable molecule since its applications range from energy and data storage to biomedical applications. This work reports a new type of thin-film based on azobenzene derivative anchored to cerium oxide nanoparticles CeO₂ NPs for photoswitching applications. The trans-cis isomerization and reverse isomerization occur by UV-light exposure and thermal relaxation process, respectively. The photoisomerization and reverse isomerization kinetics for CeO₂ NPs-MR thin films are studied, investigated, and analyzed using UV-Vis absorbance spectra, FTIR spectroscopy, XRD, and scanning electron microscopy (SEM), in addition to differential scanning calorimetry (DSC) measurement to study the energy storage capacity. The results found that anchoring azobenzene to CeO₂ NPs is successful in multisource storage of solar energy applications.

Trehalose Restrains the Fibril Load towards α-Lactalbumin Aggregation and Halts Fibrillation in a Concentration-Dependent Manner

Protein aggregation and misfolding are some of the most challenging obstacles, customarily studied for their association with amyloid pathologies. The mechanism of amyloid fibrillation development is a dynamic phenomenon involving various factors such as the intrinsic properties of protein and the physical and chemical environmental conditions. The purpose of this study was to see the thermal aggregation profile of alpha-lactalbumin (α-LA) and to delineate the effect of trehalose on its aggregation profile. α-LA was subjected to thermal aggregation at high concentrations. UV-Vis spectroscopy, a turbidity assay, intrinsic fluorescence, Rayleigh scattering and a thioflavin T (ThT) assay explained the steady outcomes that 1 M trehalose repressed α-LA aggregation in the most effective way followed by 0.75 M and 0.5 M and to a significantly lesser degree by 0.25 M. Multi spectroscopic obser Sania Bashir ations were further entrenched by microscopy. Transmission electron microscopy confirmed that in the presence of its higher concentration, trehalose hinders fibril development in α-LA. In vitro studies were further validated by in silico studies. Molecular docking analysis indicated that trehalose occupied the binding pocket cavity of α-LA and offered several significant interactions, including H-bonds with important residues. This study provides a platform for trehalose in the therapeutic management of protein aggregation-related diseases.

Effect of Iodine Filler on Photoisomerization Kinetics of Photo-Switchable Thin Films Based on PEO-BDK-MR

We report the effect of an iodine filler on photoisomerization kinetics of photo-switchable PEO-BDK-MR thin films. The kinetics of photoisomerization and time progression of PEO-BDK-MR/I₂ nanocomposite thin films are investigated using UV-Vis, FTIR spectroscopies, and modified mathematical models developed using new analytical methods. Incorporating iodine filler into the PEO-BDK-MR polymeric matrix enhances the isomerization energy barrier and considerably increases the processing time. Our outcomes propose that enhanced photoisomerized and time processed (PEO-BDK-MR)/I₂ thin films could be potential candidates for a variety of applications involving molecular solar thermal energy storage media.

New Insight on Photoisomerization Kinetics of Photo-Switchable Thin Films Based on Azobenzene/Graphene Hybrid Additives in Polyethylene Oxide

In this work, we reported a new insight on the kinetics of photoisomerization and time evolution of hybrid thin films considering the azo-dye methyl red (MR) incorporated with graphene accommodated in polyethylene oxide (PEO). The kinetics of photoisomerization and time-evolution of hybrid thin films were investigated using UV-Vis s and FTIR spectroscopies, as well as appropriate models developed with new analytical methods. The existence of azo-dye MR in the complex is crucial for the resource action of the trans↔cis cycles through UV-illumination ↔ Visible-illumination relaxations. The results of the UV–Vis and the FTIR investigations prove the cyclical trans ↔ cis-states. Consequently, PEO-(MR-Graphene) hybrid composite thin films can be introduced as possible applicants for photochromic molecular switches, light-gated transistors, and molecular solar thermal energy storage media.

Biophysical Elucidation of Fibrillation Inhibition by Sugar Osmolytes in α-Lactalbumin: Multispectroscopic and Molecular Docking Approaches

Protein aggregation is among the most challenging new frontiers in protein chemistry as well as in molecular medicine and has direct implications in protein misfolding. This study investigated the role of sugar molecules (glucose, fructose, sucrose, and the mixture of glucose and fructose) in protecting the structural integrity of α-lactalbumin (α-LA) against aggregation. The research focused here is the inhibitory capabilities of sugars against α-LA fibril formation investigated employing diverse multispectroscopic and microscopic techniques. The aggregation was induced in α-LA thermally with a change in concentration. UV-vis spectroscopy, ThT binding assay, Trp fluorescence, Rayleigh scattering, and turbidity assay depicted synchronized results. Further, transmission electron microscopy (TEM) complemented that a mixture of glucose and fructose was the best inhibitor of α-LA fibril formation. Inhibition of α-LA aggregation by sugar osmolytes is attributed to the formation of hydrogen bonds between these osmolytes, as evidenced by the molecular docking results. This hydrogen bonding is a key player that prevents aggregation in α-LA in the presence of sugar osmolytes. This study provides an insight into the ability of naturally occurring sugar osmolytes to inhibit fibril formation and can serve as a platform to treat protein misfolding and aggregation-oriented disorders.

Kinematics of Photoisomerization Processes of PMMA-BDK-MR Polymer Composite Thin Films

We investigate and report on the kinematics of photoisomerization processes of polymer composite thin films based on azo dye methyl red (MR) hosted in polymethylmethacrylate (PMMA) incorporated with Benzyl dimethyl ketal (BDK) as a photo-initiator. Understanding photoisomerization mechanisms is crucial for several optical applications such as Read/Write/Erase (WRE) optical data storage media, UV light Read/Write heads, and UV light sensors. The as-prepared polymer composite thin films are characterized using UV–Vis spectroscopy. Furthermore, Fourier transform infrared spectroscopy (FTIR) and scanning electron microscope (SEM) are employed to investigate the optical, chemical, and morphological properties of trans- and cis-states of PMMA-BDK-MR polymer composite thin films. The presence of the azo dye MR in the composite is essential for the efficient performance of the cis ↔ trans cycles through illumination ↔ thermal relaxation for Write/Read/Erase optical data storage and UV-light sensors. Moreover, UV–Vis and FTIR results confirm the hysteresis cycle of trans- and cis-states and that PMMA-BDK-MR thin films may be regarded as potential candidates for successful Write/Read/Erase optical data storage and UV-light sensors. In addition, the morphology of the thin film surface is investigated by SEM technique. The SEM images indicate that uncured surfaces of PMMA-BDK-MR thin films are inhomogeneous compared with the corresponding surfaces after curing. The transformation from inhomogeneous surfaces to homogeneous surfaces is attributed to the polymerization of thin films by UV curing.

Lactulose and Melibiose Inhibit α-Synuclein Aggregation and Up-Regulate Autophagy to Reduce Neuronal Vulnerability

Parkinson's disease (PD) is a neurodegenerative disease characterized by selective dopaminergic (DAergic) neuronal degeneration in the substantia nigra (SN) and proteinaceous α-synuclein-positive Lewy bodies and Lewy neuritis. As a chemical chaperone to promote protein stability and an autophagy inducer to clear aggregate-prone proteins, a disaccharide trehalose has been reported to alleviate neurodegeneration in PD cells and mouse models. Its trehalase-indigestible analogs, lactulose and melibiose, also demonstrated potentials to reduce abnormal protein aggregation in spinocerebellar ataxia cell models. In this study, we showed the potential of lactulose and melibiose to inhibit α-synuclein aggregation using biochemical thioflavin T fluorescence, cryogenic transmission electron microscopy (cryo-TEM) and prokaryotic split Venus complementation assays. Lactulose and melibiose further reduced α-synuclein aggregation and associated oxidative stress, as well as protected cells against α-synuclein-induced neurotoxicity by up-regulating autophagy and nuclear factor, erythroid 2 like 2 (NRF2) pathway in DAergic neurons derived from SH-SY5Y cells over-expressing α-synuclein. Our findings strongly indicate the potential of lactulose and melibiose for mitigating PD neurodegeneration, offering new drug candidates for PD treatment.

The Secondary Structure of a Major Wine Protein is Modified upon Interaction with Polyphenols

Polyphenols are an important constituent of wines and they are largely studied due to their antioxidant properties and for their effects on wine quality and stability, which is also related to their capacity to bind to proteins. The effects of some selected polyphenols, including procyanidins B1 and B2, tannic acid, quercetin, and rutin, as well as those of a total white wine procyanidin extract on the conformational properties of the major wine protein VVTL1 (Vitis vinifera Thaumatin-Like-1) were investigated by Synchrotron Radiation Circular Dichroism (SRCD). Results showed that VVTL1 interacts with polyphenols as demonstrated by the changes in the secondary (far-UV) and tertiary (near-UV) structures, which were differently affected by different polyphenols. Additionally, polyphenols modified the two melting temperatures (TM) that were found for VVTL1 (32.2 °C and 53.9 °C for the protein alone). The circular dichroism (CD) spectra in the near-UV region revealed an involvement of the aromatic side-chains of the protein in the interaction with phenolics. The data demonstrate the existence of an interaction between polyphenols and VVTL1, which results in modification of its thermal and UV denaturation pattern. This information can be useful in understanding the behavior of wine proteins in presence of polyphenols, thus giving new insights on the phenomena that are involved in wine stability.

Influence of small molecules on the photo-stability of water soluble porcine lens proteins

The eye lens is a biconvex structure composed of lens fibres, cells that lack of blood and nerve supply and of any organelle, allowing for a high concentration of water soluble proteins that determine the lens transparency and refractive index. The lens water soluble protein pool in mammals is composed of α-, β-, and γ-crystallins, the latter being involved in calcium homeostasis and having structural importance, the first playing a crucial role in preventing protein aggregation and the consequent lens obfuscation, which leads to the clinical outcome of cataract. Among different factors, oxidative stress, free radicals, and reactive oxygen species (ROSs) generated by the exposure to UV light are widely recognized to cause cataract formation. Taking advantage of synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies, in the present study we investigate the influence of different small molecules with the potential to either quench ROS generation or to stabilize protein conformation. Therefore, ascorbic acid, an excellent antioxidant agent already present in the eye aqueous humour, has been tested along with ceftriaxone, mannitol and trehalose, which osmolyte activity was demonstrated interfering with model proteins misfolding. Our results showed that ascorbic acid strongly inhibits the ROS production without, however, preserving the native protein structure, whereas mannitol had no effect on the ROS production but retained better the secondary structure of WS proteins. Collectively, the use of a mixture of ascorbic acid and mannitol could be used to better protect eye lens proteins from ROS damage preventing the cataract onset.

Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein

We describe a strategy for experimentally-constraining computational simulations of intrinsically disordered proteins (IDPs), using α-synuclein, an IDP with a central role in Parkinson's disease pathology, as an example. Previously, data from single-molecule Förster Resonance Energy Transfer (FRET) experiments have been effectively utilized to generate experimentally constrained computational models of IDPs. However, the fluorophores required for single-molecule FRET experiments are not amenable to the study of short-range (<30 Å) interactions. Using ensemble FRET measurements allows one to acquire data from probes with multiple distance ranges, which can be used to constrain Monte Carlo simulations in PyRosetta. To appropriately employ ensemble FRET data as constraints, we optimized the shape and weight of constraining potentials to afford ensembles of structures that are consistent with experimental data. We also used this approach to examine the structure of α-synuclein in the presence of the compacting osmolyte trimethylamine-N-oxide. Despite significant compaction imparted by 2 M trimethylamine-N-oxide, the underlying ensemble of α-synuclein remains largely disordered and capable of aggregation, also in agreement with experimental data. These proof-of-concept experiments demonstrate that our modeling protocol enables one to efficiently generate experimentally constrained models of IDPs that incorporate atomic-scale detail, allowing one to study an IDP under a variety of conditions.

Trehalose as a promising therapeutic candidate for the treatment of Parkinson's disease

Parkinson's disease (PD) is a progressive movement disorder resulting primarily from loss of nigrostriatal dopaminergic neurons. PD is characterized by the accumulation of protein aggregates, and evidence suggests that aberrant protein deposition in dopaminergic neurons could be related to the dysregulation of the lysosomal autophagy pathway. The therapeutic potential of autophagy modulators has been reported in experimental models of PD. Trehalose is a natural disaccharide that has been considered as a new candidate for the treatment of neurodegenerative diseases. It has a chaperone-like activity, prevents protein misfolding or aggregation, and by promoting autophagy, contributes to the removal of accumulated proteins. In this review, we briefly summarize the role of aberrant autophagy in PD and the underlying mechanisms that lead to the development of this disease. We also discuss reports that used trehalose to counteract the neurotoxicity in PD, focusing particularly on the autophagy promoting, protein stabilization, and anti-neuroinflammatory effects of trehalose.

UV-Denaturation Assay to Assess Protein Photostability and Ligand-Binding Interactions Using the High Photon Flux of Diamond B23 Beamline for SRCD

Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host–ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD.

Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load

Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.

α-Synuclein aggregation modulation: an emerging approach for the treatment of Parkinson's disease

Parkinson's disease (PD) is a multifactorial progressive neurological disorder. Pathological hallmarks of PD are characterized by the presence of α-synuclein (αSyn) aggregates known as Lewy bodies. αSyn aggregation is one of the leading causes for the neuronal dysfunction and death in PD. It is also associated with neurotransmitter and calcium release. Current therapies of PD are limited to only symptomatic relief without addressing the underlying pathogenic factors of the disease process such as aggregation of αSyn. Consequently, the progression of the disease continues with the current therapies. Therefore, the modulation of αSyn aggregation is an emerging approach as a novel therapeutic target to treat PD. There are two major aspects that might be targeted therapeutically: first, protein is prone to aggregation, therefore, anti-aggregative or compounds that can break the pre-existing aggregates should be helpful. Second, there are number of molecular events that may be targeted to combat the disease.

Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions

This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.

Characterisation of Conformational and Ligand Binding Properties of Membrane Proteins Using Synchrotron Radiation Circular Dichroism (SRCD)

Membrane proteins are notoriously difficult to crystallise for use in X-ray crystallographic structural determination, or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour in solution. The advantage of synchrotron radiation circular dichroism (SRCD) measured with synchrotron beamlines compared to the CD from benchtop instruments is the extended spectral far-UV region that increases the accuracy of secondary structure estimations, in particular under high ionic strength conditions. Membrane proteins are often available in small quantities, and for this SRCD measured at the Diamond B23 beamline has successfully facilitated molecular recognition studies. This was done by probing the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells (1-5 cm) of small volume capacity (70 μl-350 μl). In this chapter we describe the use of SRCD to qualitatively and quantitatively screen ligand binding interactions (exemplified by Sbma, Ace1 and FsrC proteins); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by FsrC); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by inositol transporters) as well as the stability of membrane proteins (exemplified by GalP, Ace1). The importance of the in solution characterisation of the conformational behaviour and ligand binding properties of proteins in both far- andnear-UV regions and the use of high-throughput CD (HT-CD) using 96- and 384-well multiplates to study the folding effects in various protein crystallisation buffers are also discussed.