Aggregation-Prone Amyloid-β⋅CuIISpecies Formed on the Millisecond Timescale under Mildly Acidic Conditions

Evaluation of Copper(II) Transfer between Amyloid-beta Peptides by Relaxation-Induced Dipolar Modulation Enhancement (RIDME)

In the brains of Alzheimer's disease patients, fibrillar aggregates containing amyloid-beta (Aβ) peptides are found, along with elevated concentrations of Cu(II) ions. The aggregation pathways of Aβ peptides can be modulated by Cu(II) ions and is determined by the formation and nature of the Cu(II)-Aβ complex. If spin-labeled, the Cu(II)-Aβ complex contains two dipolar coupled paramagnetic centers, the spin label and the Cu(II) ion. Measurement of the dipolar coupling between these paramagnetic centers by relaxation-induced dipolar modulation enhancement (RIDME) allows to monitor the complex formation and thus opens a way to follow the Cu(II) transfer between peptides if a mixture of wild-type and spin-labeled ones is used. We evaluate this approach for a specific Cu(II)-Aβ complex, the aggregation-inert Component II. The kinetics of the Cu(II) transfer can be resolved by performing RIDME in a time-dependent manner. A temporal resolution of seconds has been achieved, with the potential to reach milliseconds, using a rapid-freeze quench device to stop the Cu(II) transfer in solution after defined incubation times.

Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods

The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.

On the specificity of protein-protein interactions in the context of disorder

With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.

Molecular Insight into Cu2+-Induced Conformational Transitions of Amyloid β-Protein from Fast Kinetic Analysis and Molecular Dynamics Simulations

Cu²⁺-mediated amyloid β-protein (Aβ) aggregation is implicated in the pathogenesis of Alzheimer's disease, so it is of significance to understand Cu²⁺-mediated conformational transitions of Aβ. Herein, four Aβ mutants were created by using the environment-sensitive cyanophenylalanine to respectively substitute F4, Y10, F19, and F20 residues of Aβ₄₀. By using stopped-flow fluorescence spectroscopy and molecular dynamics (MD) simulations, the early stage conformational transitions of the mutants mediated by Cu²⁺ binding were investigated. The fast kinetics unveils that Cu²⁺ has more significant influence on the conformational changes of N-terminal (F4 and Y10) than on the central hydrophobic core (CHC, F19, and F20) under different pH conditions (pH 6.6-8.0), especially Y10. Interestingly, lag periods of the conformational transitions are observed for the F19 and F20 mutants at pH 8.0, indicating the slow response of the two mutation sites on the conformational transitions. More importantly, significantly longer lag periods for F20 than for F19 indicate the conduction of the transition from F19 to F20. The conduction time (difference in lag period) decreases from 4.5 s at Cu²⁺ = 0 to undetectable (<1 ms) at Cu²⁺ = 10 μM. The significant difference in the response time of F19 and F20 and the fast local conformational changes of Y10 imply that the conformational transitions of Aβ start around Y10. MD simulations support the observation of hydrophobicity increase at N-terminal during the conformational transitions of Aβ-Cu²⁺. It also reveals that Y10 is immediately approached by Cu²⁺, supporting the speculation that the starting point of conformational transitions of Aβ is near Y10. The work has provided molecular insight into the early stage conformational transitions of Aβ₄₀ mediated by Cu²⁺.

Normal brain aging and Alzheimer's disease are associated with lower cerebral pH: an in vivo histidine 1H-MR spectroscopy study

It is unclear whether alterations in cerebral pH underlie Alzheimer's disease (AD) and other dementias. We performed proton spectroscopy after oral administration of histidine in healthy young and elderly persons and in patients with mild cognitive impairment and dementia (total N = 147). We measured cerebral tissue pH and ratios of common brain metabolites in relation to phosphocreatine and creatine (Cr) in spectra acquired from the hippocampus, the white matter (WM) of the centrum semiovale, and the cerebellum. Hippocampal pH was inversely associated with age in healthy participants but did not differ between patients and controls. WM pH was low in AD and, to a lesser extent, mild cognitive impairment but not in frontotemporal dementia spectrum disorders and pure vascular dementia. Furthermore, WM pH provided incremental diagnostic value in addition to N-acetylaspartate to Cr ratio. Our study suggests that in vivo assessment of pH may be a useful marker for the differentiation between AD and other types of dementia.

Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer's disease therapy

Alzheimer's disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported that amyloid hypothesis-based treatments can be developed as a new approach to overcome the limitations and challenges associated with conventional AD therapeutics. In this review, we will provide a comprehensive view of the challenges in AD therapy and pathophysiology. We also discuss currently known compounds that can inhibit amyloid-β (Aβ) aggregation and their potential role in advancing current AD treatments. We have specifically focused on Aβ aggregation inhibitors including metal chelators, nanostructures, organic molecules, peptides (or peptide mimics), and antibodies. To date, these molecules have been the subject of numerous in vitro and in vivo assays as well as molecular dynamics simulations to explore their mechanism of action and the fundamental structural groups involved in Aβ aggregation. Ultimately, the aim of these studies (and current review) is to achieve a rational design for effective therapeutic agents for AD treatment and diagnostics.

Effects of Cu(II) on the aggregation of amyloid-β

Aberrant aggregation of the Aβ protein is a hallmark of Alzheimer's disease (AD), but no complete characterization of the molecular level pathogenesis has been achieved. A promising hypothesis is that dysfunction of metal ion homeostasis, and consequently, the undesired interaction of metal ions with Aβ, may be central to the development of AD. Qualitatively, most data indicate that Cu(II) induces rapid self-assembly of both Aβ40 and Aβ42 during the initial phase of the aggregation, while at longer time scales fibrillation may occur, depending on the experimental conditions. For Aβ40 and Cu(II):Aβ ≤ 1, most data imply that low concentration of Aβ40 favors nucleation and rapid fibril elongation, while high concentration of Aβ40 favors formation of amorphous aggregates. However, there are conflicting reports on this issue. For Aβ42 and Cu(II):Aβ ≤ 1, there is consensus that the lag time is extended upon addition of Cu(II). For Cu(II):Aβ > 1, the lag time is increased upon interaction with Cu(II), and in most cases fibrillation is not observed, presumably because Cu(II) occupies a second more solvent-exposed binding site, which is more prone to form metal ion-bridged species and cause rapid formation of non-fibrillar aggregates. The interesting N-terminally truncated Aβ11-40 with high affinity for Cu(II), exhibits delay of fibrillation upon addition of 0.4 eq. Cu(II). In our view, there are still problems achieving reproducible results in this field, and we provide a shortlist of some of the pitfalls. Finally, we propose a consensus model for the effects of Cu(II) on the aggregation kinetics of Aβ.

CuII Binding Properties of N-Truncated Aβ Peptides: In Search of Biological Function

As life expectancy increases, the number of people affected by progressive and irreversible dementia, Alzheimer's Disease (AD), is predicted to grow. No drug designs seem to be working in humans, apparently because the origins of AD have not been identified. Invoking amyloid cascade, metal ions, and ROS production hypothesis of AD, herein we share our point of view on Cu(II) binding properties of Aβ_4-x, the most prevalent N-truncated Aβ peptide, currently known as the main constituent of amyloid plaques. The capability of Aβ_4-x to rapidly take over copper from previously tested Aβ_1-x peptides and form highly stable complexes, redox unreactive and resistant to copper exchange reactions, prompted us to propose physiological roles for these peptides. We discuss the new findings on the reactivity of Cu(II)Aβ_4-x with coexisting biomolecules in the context of synaptic cleft; we suggest that the role of Aβ_4-x peptides is to quench Cu(II) toxicity in the brain and maintain neurotransmission.

His6, His13, and His14 residues in Aβ 1-40 peptide significantly and specifically affect oligomeric equilibria

Oligomers of Aβ peptide are implicated as the most probable causative agent in Alzheimer’s disease. However, their structural properties remain elusive due to the dynamic and heterogeneous character of oligomeric species coexisting in solution. Nevertheless, new approaches, mainly based on mass spectrometry, provide unique access to these different structural forms. Using these methods, we previously showed that the N-terminal, non-amyloidogenic region of Aβ is involved in the network of interactions specifically stabilizing oligomers. In the present study, we identified three histidine residues as active participants in this network. Detailed knowledge of the structural features that are potentially important for oligomer-mediated neurotoxicity is a prerequisite for the rational design of oligomerization modifiers.

Ion Specificity and Nonmonotonic Protein Solubility from Salt Entropy

The addition of salt to protein solutions can either increase or decrease the protein solubility, and the magnitude of this effect depends on the salt used. We show that these effects can be captured using a theory that includes attractive and repulsive electrostatic interactions, nonelectrostatic protein-ion interactions, and ion-solvent interactions via an effective solvated ion radius. We find that the ion radius has significant effects on the translational entropy of the salt, which leads to salt specificity in the protein solubility. At low salt, the dominant effect comes from the entropic cost of confining ions within the aggregate, whereas at high concentrations, the salt drives a depletion attraction that favors aggregation. Our theory explains the reversal in the Hofmeister series observed in lysozyme cloud point measurements and semi-quantitatively describes the solubility of lysozyme and chymosin crystals. We present a comparison of the contributions to the free energy and give guidelines for when salting in or salting out should be expected.

X-ray Absorption Spectroscopy Investigations of Copper(II) Coordination in the Human Amyloid β Peptide

Alzheimer's disease (AD) is the main cause of age-related dementia and currently affects approximately 5.7 million Americans. Major brain changes associated with AD pathology include accumulation of amyloid beta (Aβ) protein fragments and formation of extracellular amyloid plaques. Redox-active metals mediate oligomerization of Aβ, and the resultant metal-bound oligomers have been implicated in the putative formation of harmful, reactive species that could contribute to observed oxidative damage. In isolated plaque cores, Cu(II) is bound to Aβ via histidine residues. Despite numerous structural studies of Cu(II) binding to synthetic Aβ in vitro, there is still uncertainty surrounding Cu(II) coordination in Aβ. In this study, we used X-ray absorption spectroscopy (XAS) and high energy resolution fluorescence detected (HERFD) XAS to investigate Cu(II) coordination in Aβ(1-42) under various solution conditions. We found that the average coordination environment in Cu(II)Aβ(1-42) is sensitive to X-ray photoreduction, changes in buffer composition, peptide concentration, and solution pH. Fitting of the extended X-ray absorption fine structure (EXAFS) suggests Cu(II) is bound in a mixture of coordination environments in monomeric Aβ(1-42) under all conditions studied. However, it was evident that on average only a single histidine residue coordinates Cu(II) in monomeric Aβ(1-42) at pH 6.1, in addition to 3 other oxygen or nitrogen ligands. Cu(II) coordination in Aβ(1-42) at pH 7.4 is similarly 4-coordinate with oxygen and nitrogen ligands, although an average of 2 histidine residues appear to coordinate at this pH. At pH 9.0, the average Cu(II) coordination environment in Aβ(1-42) appears to be 5-coordinate with oxygen and nitrogen ligands, including two histidine residues.

Metal-dependent interactions of metallothionein-3 β-domain with amyloid-β peptide and related physiological implications

Aberrant interactions of metal ions with amyloid-β peptide (Aβ) can potentiate Alzheimer's disease (AD) by participating in the aggregation process of Aβ and in the generation of reactive oxygen species (ROS). Metallothionein-3 (MT3), which is aberrantly expressed in AD brains, is believed to play an important role in the AD progression due to its ability of maintaining metal homeostasis and scavenging ROS. However, the related molecular mechanism is not clear. In this work, the metal-dependent interactions of MT3 β-domain (βMT3) with amyloid-β peptide (Aβ) were systematically studied. The results showed that Zn₃-βMT3 has a higher affinity to Aβ (K_d: ~0.7 μM) than Cu₄-βMT3 (K_d: ~22 μM). In Zn₃-βMT3, both Pro⁷ and Pro⁹ face outwards with their five-member rings in parallel, favoring their binding with aromatic residues via CH/π interactions. Two aromatic residues (Phe⁴ and Tyr¹⁰) in Aβ were identified as the specific binding sites for βMT3. Based on these, we posit a characteristic in-situ protection role of Zn-MT3 in inhibiting the Cu²⁺-induced Aβ neurotoxicity, in which stable Zn-MT3/Aβ complex forms via the Zn₃-βMT3/Aβ interaction and effectively prevents the formation of Cu-Aβ in high viscosity physiological fluids. Our results provide the mechanistic pathway and the specific roles of βMT3 in its protective bioactivity against AD progression, which means significant for elucidating the function of MT3 in AD neuropathology and for designing a MT3-related therapeutic strategy for AD.

Identifying Cu(ii)-amyloid peptide binding intermediates in the early stages of aggregation by resonance Raman spectroscopy: a simulation study

The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(ii)-Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(ii) binding are not well understood. Two Cu(ii)-Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Raman and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. These signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu-Aβ binding and interconversion processes.

Cu(II) binding to various forms of amyloid-β peptides. Are they friends or foes?

In the present micro-review, we describe the Cu(II) binding to several forms of amyloid-β peptides, the peptides involved in Alzheimer's disease. It has indeed been shown that in addition to the "full-length" peptide originating from the precursor protein after cleavage at position 1, several other shorter peptides do exist in large proportion and may be involved in the disease as well. Cu(II) binding to amyloid-β peptides is one of the key interactions that impact both the aggregating properties of the amyloid peptides and the Reactive Oxygen Species (ROS) production, two events linked to the etiology of the disease. Binding sites and affinity are described in correlation with Cu(II) induced ROS formation and Cu(II) altered aggregation, for amyloid peptides starting at position 1, 3, 4, 11 and for the corresponding pyroglutamate forms when they could be obtained (i.e. for peptides cleaved at positions 3 and 11). It appears that the current paradigm which points out a toxic role of the Cu(II) - amyloid-β interaction might well be shifted towards a possible protective role when the peptides considered are the N-terminally truncated ones.

Kinetic Analysis Reveals the Identity of Aβ-Metal Complex Responsible for the Initial Aggregation of Aβ in the Synapse

The mechanism of Aβ aggregation in the absence of metal ions is well established, yet the role that Zn²⁺ and Cu²⁺, the two most studied metal ions, released during neurotransmission, paly in promoting Aβ aggregation in the vicinity of neuronal synapses remains elusive. Here we report the kinetics of Zn²⁺ binding to Aβ and Zn²⁺/Cu²⁺ binding to Aβ-Cu to form ternary complexes under near physiological conditions (nM Aβ, μM metal ions). We find that these reactions are several orders of magnitude slower than Cu²⁺ binding to Aβ. Coupled reaction-diffusion simulations of the interactions of synaptically released metal ions with Aβ show that up to a third of Aβ is Cu²⁺-bound under repetitive metal ion release, while any other Aβ-metal complexes (including Aβ-Zn) are insignificant. We therefore conclude that Zn²⁺ is unlikely to play an important role in the very early stages (i.e., dimer formation) of Aβ aggregation, contrary to a widely held view in the subject. We propose that targeting the specific interactions between Cu²⁺ and Aβ may be a viable option in drug development efforts for early stages of AD.

The Pathogenic A2V Mutant Exhibits Distinct Aggregation Kinetics, Metal Site Structure, and Metal Exchange of the Cu2+ -Aβ Complex

A prominent current hypothesis is that impaired metal ion homeostasis may contribute to Alzheimer's disease (AD). We elucidate the interaction of Cu²⁺ with wild-type (WT) Aβ_1-40 and the genetic variants A2T and A2V which display increasing pathogenicity as A2T<WT<A2V. Cu²⁺ significantly extends the lag phase in aggregation kinetics, in particular for the pathogenic A2V variant. Additionally, a rapid, initial, low intensity ThT response is observed, possibly reflecting formation of Cu²⁺ induced amorphous aggregates, as supported by atomic force microscopy (AFM) and circular dichroism (CD) spectroscopy, again most notably for the A2V variant. Electron paramagnetic resonance (EPR) spectroscopy gives pK_a values for transition between two Cu²⁺ coordination geometries (component I and II) of 7.4 (A2T), 7.9 (WT), and 8.4 (A2V), that is, component I is stabilized at physiological pH in the order A2T<WT<A2V. ¹ H NMR relaxation exhibits the same trend for the non-coordinating aromatic residues (A2T<WT<A2V), and implies markedly faster inter-peptide Cu²⁺ exchange for the A2V variant than for WT and A2T. We therefore hypothesize that component I of the Cu-Aβ complex is related to pathogenicity, accounting for both the pathogenic nature of the A2V variant and the protective nature of the A2T variant.

Amyloid plaques beyond Aβ: a survey of the diverse modulators of amyloid aggregation

Aggregation of the amyloid-β (Aβ) peptide is strongly correlated with Alzheimer's disease (AD). Recent research has improved our understanding of the kinetics of amyloid fibril assembly and revealed new details regarding different stages in plaque formation. Presently, interest is turning toward studying this process in a holistic context, focusing on cellular components which interact with the Aβ peptide at various junctures during aggregation, from monomer to cross-β amyloid fibrils. However, even in isolation, a multitude of factors including protein purity, pH, salt content, and agitation affect Aβ fibril formation and deposition, often producing complicated and conflicting results. The failure of numerous inhibitors in clinical trials for AD suggests that a detailed examination of the complex interactions that occur during plaque formation, including binding of carbohydrates, lipids, nucleic acids, and metal ions, is important for understanding the diversity of manifestations of the disease. Unraveling how a variety of key macromolecular modulators interact with the Aβ peptide and change its aggregation properties may provide opportunities for developing therapies. Since no protein acts in isolation, the interplay of these diverse molecules may differentiate disease onset, progression, and severity, and thus are worth careful consideration.

Kinetics of the Interactions between Copper and Amyloid-β with FAD Mutations and Phosphorylation at the N terminus

Mutations and post‐translational modifications of amyloid‐β (Aβ) peptide in its N terminus have been shown to increase fibril formation, yet the molecular mechanism is not clear. Here we investigated the kinetics of the interactions of copper with two Aβ peptides containing Familial Alzheimer's disease (FAD) mutations (English (H6R) and Tottori (D7N)), as well as with Aβ peptide phosphorylated at serine 8 (pS8). All three peptides bind to copper with a similar rate as the wild‐type (wt). The dissociation rates follow the order pS8>H6R>wt>D7N; the interconversion between the two coordinating species occurs 50 % faster for H6R and pS8, whereas D7N had only a negligible effect. Interestingly, the rate of ternary complex (copper‐bridged heterodimer) formation for the modified peptides was significantly faster than that for wt, thus leading us to propose that FAD and sporadic AD might share a kinetic origin for the enhanced oligomerisation of Aβ.