Multivariate effects of pH, salt, and Zn(2+) ions on Aβ(40) fibrillation

Exploration of the influence of environmental changes on the conformational and amyloidogenic landscapes of the zinc finger protein DPF3a by combining biophysical and molecular dynamics approaches

In the past few years, the double PHD fingers 3 (DPF3) protein isoforms (DPF3b and DPF3a) have been identified as new amyloidogenic intrinsically disordered proteins (IDPs). Although such discovery is coherent and promising in light of their involvement in proteinopathies, their amyloidogenic pathway remains largely unexplored. As environmental variations in pH and ionic strength are relevant to DPF3 pathophysiological landscape, we therefore enquired the effect of these physicochemical parameters on the protein structural and prone-to-aggregation properties, by focusing on the more disordered DPF3a isoform. In the present study, we exploited in vitro and in silico strategies by combining spectroscopy, microscopy, and all-atom molecular dynamics methods. Very good consistency and complementary information were found between the experiments and the simulations. Acidification unequivocally abrogated DPF3a fibrillation upon maintaining the protein in highly hydrated and expanded conformers due to extensive repulsion between positively charged regions. In contrast, alkaline pH delayed the aggregation process due to loss in intramolecular contacts and chain decompaction, the extent of which was partly reduced thanks to the compensation of negative charge by arginine side chains. Through screening attractive electrostatic interactions, high ionic strength conditions (300 and 500 mM NaCl) shifted the conformational ensemble towards more swollen, heterogeneous, and less H-bonded structures, which were responsible for slowing down the conversion into β-sheeted species and restricting the fibril elongation. For defining the self-assembly pathway of DPF3a, we unveiled that the protein amyloidogenicity intimately communicates with its conformational landscape, which is particularly sensitive to modification of its physicochemical environment. As such, understanding how to modulate DPF3a conformational ensemble will help designing novel protein-specific strategies for targeting neurodegeneration.

Clinical Importance of Amyloid Beta Implication in the Detection and Treatment of Alzheimer's Disease

The role of amyloid beta peptide (Aβ) in memory regulation has been a subject of substantial interest and debate in neuroscience, because of both physiological and clinical issues. Understanding the dual nature of Aβ in memory regulation is crucial for developing effective treatments for Alzheimer's disease (AD). Moreover, accurate detection and quantification methods of Aβ isoforms have been tested for diagnostic purposes and therapeutic interventions. This review provides insight into the current knowledge about the methods of amyloid beta detection in vivo and in vitro by fluid tests and brain imaging methods (PET), which allow for preclinical recognition of the disease. Currently, the priority in the development of new therapies for Alzheimer's disease has been given to potential changes in the progression of the disease. In light of increasing amounts of data, this review was focused on the diagnostic and therapeutic employment of amyloid beta in Alzheimer's disease.

Solid-State Nanopore Real-Time Assay for Monitoring Cas9 Endonuclease Reactivity

The field of nanopore sensing is now moving beyond nucleic acid sequencing. An exciting avenue is the use of nanopore platforms for the monitoring of biochemical reactions. Biological nanopores have been used for this application, but solid-state nanopore approaches have lagged. This is due to the necessity of using higher salt conditions (e.g., 4 M LiCl) to improve the signal-to-noise ratio which completely abolish the activities of many biochemical reactions. We pioneered a polymer electrolyte solid-state nanopore approach that maintains a high signal-to-noise ratio even at a physiologically relevant salt concentration. Here, we report the monitoring of the restriction enzyme SwaI and CRISPR-Cas9 endonuclease activities under physiological salt conditions and in real time. We investigated the dsDNA cleavage activity of these enzymes in a range of digestion buffers and elucidated the off-target activity of CRISPR-Cas9 ribonucleoprotein endonuclease in the presence of single base pair mismatches. This approach enables the application of solid-state nanopores for the dynamic monitoring of biochemical reactions under physiological salt conditions.

Reinforcing Nrf2 Signaling: Help in the Alzheimer's Disease Context

Oxidative stress plays a role in various pathophysiological diseases, including neurogenerative diseases, such as Alzheimer's disease (AD), which is the most prevalent neuro-pathology in the aging population. Oxidative stress has been reported to be one of the earliest pathological alterations in AD. Additionally, it was demonstrated that in older adults, there is a loss of free radical scavenging ability. The Nrf2 transcription factor is a key regulator in antioxidant defense systems, but, with aging, both the amount and the transcriptional activity of Nrf2 decrease. With the available treatments for AD being poorly effective, reinforcing the antioxidant defense systems via the Nrf2 pathway may be a way to prevent and treat AD. To highlight the predominant role of Nrf2 signaling in defending against oxidative stress and, therefore, against neurotoxicity, we present an overview of the natural compounds that exert their own neuroprotective roles through the activation of the Nrf2 pathway. This review is an opportunity to promote a holistic approach in the treatment of AD and to highlight the need to further refine the development of new potential Nrf2-targeting drugs.

How Salt and Temperature Drive Reentrant Condensation of Aβ40

Within the framework of liquid-liquid phase separation (LLPS), biomolecular condensation orchestrates vital cellular processes, and its dysregulation is implicated in severe pathological conditions. Recent studies highlight the role of intrinsically disordered proteins (IDPs) in LLPS, yet the influence of microenvironmental factors has remained a puzzling factor. Here, via computational simulation of the impact of solution conditions on LLPS behavior of neurologically pathogenic IDP Aβ40, we chanced upon a salt-driven reentrant condensation phenomenon, wherein Aβ40 aggregation increases with low salt concentrations (25-50 mM), followed by a decline with further salt increments. An exploration of the thermodynamic and kinetic signatures of reentrant condensation unveils a nuanced interplay between protein electrostatics and ionic strength as potential drivers. Notably, the charged residues of the N-terminus exhibit a nonmonotonic response to salt screening, intricately linked to the recurrence of reentrant behavior in hydrophobic core-induced condensation. Intriguingly, our findings also unveil the reappearance of similar reentrant condensation phenomena under varying temperature conditions. Collectively, our study illuminates the profoundly context-dependent nature of Aβ40s liquid-liquid phase separation behavior, extending beyond its intrinsic molecular framework, where microenvironmental cues wield significant influence over its aberrant functionality.

Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions

The coacervation of alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is central to amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work shows that factors promoting or inhibiting aggregation have similar effects on LLPS. This study provides a detailed scanning of a wide range of parameters, including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and LLPS. The influence of salt on aggregation under crowding conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, this study finds a monotonic salt dependence of LLPS due to intermolecular interactions. Furthermore, it observes time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving aggregates through heterotypic interactions, thus preventing αSyn from its dynamically arrested state.

pH regulating mechanisms of astrocytes: A critical component in physiology and disease of the brain

Strict homeostatic control of pH in both intra- and extracellular compartments of the brain is fundamentally important, primarily due to the profound impact of free protons ([H+]) on neuronal activity and overall brain function. Astrocytes, crucial players in the homeostasis of various ions in the brain, actively regulate their intracellular [H+] (pHi) through multiple membrane transporters and carbonic anhydrases. The activation of astroglial pHi regulating mechanisms also leads to corresponding alterations in the acid-base status of the extracellular fluid. Notably, astrocyte pH regulators are modulated by various neuronal signals, suggesting their pivotal role in regulating brain acid-base balance in both health and disease. This review presents the mechanisms involved in pH regulation in astrocytes and discusses their potential impact on extracellular pH under physiological conditions and in brain disorders. Targeting astrocytic pH regulatory mechanisms represents a promising therapeutic approach for modulating brain acid-base balance in diseases, offering a potential critical contribution to neuroprotection.

Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions

The coacervation and structural rearrangement of the protein alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is recognized as the key element of amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work showed that factors promoting or inhibiting amyloid formation have similar effects on phase separation. Here, we provide a detailed scanning of a wide range of parameters including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and phase separation. The influence of salt on aggregation under crowded conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, we find a monotonic salt dependence of phase separation due to the intermolecular interaction. Furthermore, we observe the time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving the aggregates through a variety of heterotypic interactions, thus preventing αSyn from its dynamically arrested state.

Transition Networks Unveil Disorder-to-Order Transformations in Aβ Caused by Glycosaminoglycans or Lipids

The aggregation of amyloid-β (Aβ) peptides, particularly of Aβ1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aβ1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids using molecular dynamics simulations. We analyze the conformational changes that occur in Aβ by extracting the key structural features that are then used to generate transition networks. Using the same three features per network highlights the transitions from intrinsically disordered states ubiquitous in Aβ1-42 in solution to more compact states arising from stable β-hairpin formation when Aβ1-42 is in the vicinity of a GAG molecule, and even more compact states characterized by a α-helix or β-sheet structures when Aβ1-42 interacts with a POPC lipid cluster. We show that the molecular mechanisms underlying these transitions from disorder to order are different for the Aβ1-42/GAG and Aβ1-42/POPC systems. While in the latter the hydrophobicity provided by the lipid tails facilitates the folding of Aβ1-42, in the case of GAG there are hardly any intermolecular Aβ1-42-GAG interactions. Instead, GAG removes sodium ions from the peptide, allowing stronger electrostatic interactions within the peptide that stabilize a β-hairpin. Our results contribute to the growing knowledge of the role of GAGs and lipids in the conformational preferences of the Aβ peptide, which in turn influences its aggregation into toxic oligomers and amyloid fibrils.

Manganese Ion-Induced Amyloid Fibrillation Kinetics of Hen Egg White-Lysozyme in Thermal and Acidic Conditions

As manganese ions (Mn²⁺) are identified as an environmental risk factor for neurodegenerative diseases, uncovering their action mechanism on protein amyloid fibril formation is crucial for related disease treatments. Herein, we performed a combined study of Raman spectroscopy, atomic force microscopy (AFM), thioflavin T (ThT) fluorescence, and UV-vis absorption spectroscopy assays, in which the distinctive effect of Mn²⁺ on the amyloid fibrillation kinetics of hen egg white-lysozyme (HEWL) was clarified at the molecular level. With thermal and acid treatments, the unfolding of protein tertiary structures is efficiently accelerated by Mn²⁺ to form oligomers, as indicated by two Raman markers for the Trp residues on protein side chains: the FWHM at 759 cm^-1 and the I₁₃₄₀/I₁₃₆₀ ratio. Meanwhile, the inconsistent evolutionary kinetics of the two indicators, as well as AFM images and UV-vis absorption spectroscopy assays, validate the tendency of Mn²⁺ toward the formation of amorphous aggregates instead of amyloid fibrils. Moreover, Mn²⁺ plays an accelerator role in the secondary structure transition from α-helix to organized β-sheet structures, as indicated by the N-C_α-C intensity at 933 cm^-1 and the amide I position of Raman spectroscopy and ThT fluorescence assays. Notably, the more significant promotion effect of Mn²⁺ on the formation of amorphous aggregates provides credible clues to understand the fact that excess exposure to manganese is associated with neurological diseases^.

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.