Zn(II) ions substantially perturb Cu(II) ion coordination in amyloid-β at physiological pH

Copper(II) Can Kinetically Trap Arctic and Italian Amyloid-β40 as Toxic Oligomers, Mimicking Cu(II) Binding to Wild-Type Amyloid-β42: Implications for Familial Alzheimer's Disease

The self-association of amyloid-β (Aβ) peptide into neurotoxic oligomers is believed to be central to Alzheimer's disease (AD). Copper is known to impact Aβ assembly, while disrupted copper homeostasis impacts phenotype in Alzheimer's models. Here we show the presence of substoichiometric Cu(II) has very different impacts on the assembly of Aβ40 and Aβ42 isoforms. Globally fitting microscopic rate constants for fibril assembly indicates copper will accelerate fibril formation of Aβ40 by increasing primary nucleation, while seeding experiments confirm that elongation and secondary nucleation rates are unaffected by Cu(II). In marked contrast, Cu(II) traps Aβ42 as prefibrillar oligomers and curvilinear protofibrils. Remarkably, the Cu(II) addition to preformed Aβ42 fibrils causes the disassembly of fibrils back to protofibrils and oligomers. The very different behaviors of the two Aβ isoforms are centered around differences in their fibril structures, as highlighted by studies of C-terminally amidated Aβ42. Arctic and Italian familiar mutations also support a key role for fibril structure in the interplay of Cu(II) with Aβ40/42 isoforms. The Cu(II) dependent switch in behavior between nonpathogenic Aβ40 wild-type and Aβ40 Arctic or Italian mutants suggests heightened neurotoxicity may be linked to the impact of physiological Cu(II), which traps these familial mutants as oligomers and curvilinear protofibrils, which cause membrane permeability and Ca(II) cellular influx.

Molecular Structure of Cu(II)-Bound Amyloid-β Monomer Implicated in Inhibition of Peptide Self-Assembly in Alzheimer's Disease

Metal ions, such as copper and zinc ions, have been shown to strongly modulate the self-assembly of the amyloid-β (Aβ) peptide into insoluble fibrils, and elevated concentrations of metal ions have been found in amyloid plaques of Alzheimer's patients. Among the physiological transition metal ions, Cu(II) ions play an outstanding role since they can trigger production of neurotoxic reactive oxygen species. In contrast, structural insights into Cu(II) coordination of Aβ have been challenging due to the paramagnetic nature of Cu(II). Here, we employed specifically tailored paramagnetic NMR experiments to determine NMR structures of Cu(II) bound to monomeric Aβ. We found that monomeric Aβ binds Cu(II) in the N-terminus and combined with molecular dynamics simulations, we could identify two prevalent coordination modes of Cu(II). For these, we report here the NMR structures of the Cu(II)-bound Aβ complex, exhibiting heavy backbone RMSD values of 1.9 and 2.1 Å, respectively. Further, applying aggregation kinetics assays, we identified the specific effect of Cu(II) binding on the Aβ nucleation process. Our results show that Cu(II) efficiently retards Aβ fibrillization by predominately reducing the rate of fibril-end elongation at substoichiometric ratios. A detailed kinetic analysis suggests that this specific effect results in enhanced Aβ oligomer generation promoted by Cu(II). These results can quantitatively be understood by Cu(II) interaction with the Aβ monomer, forming an aggregation inert complex. In fact, this mechanism is strikingly similar to other transition metal ions, suggesting a common mechanism of action of retarding Aβ self-assembly, where the metal ion binding to monomeric Aβ is a key determinant.

Going the dHis-tance: Site-Directed Cu2+ Labeling of Proteins and Nucleic Acids

In this Account, we showcase site-directed Cu²⁺ labeling in proteins and DNA, which has opened new avenues for the measurement of the structure and dynamics of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the spin label is assembled in situ from natural amino acid residues and a metal complex and requires no post-expression synthetic modification or purification procedures. The labeling scheme exploits a double histidine (dHis) motif, which utilizes endogenous or site-specifically mutated histidine residues to coordinate a Cu²⁺ complex. Pulsed EPR measurements on such Cu²⁺-labeled proteins potentially yield distance distributions that are up to 5 times narrower than the common protein spin label-the approach, thus, overcomes the inherent limitation of the current technology, which relies on a spin label with a highly flexible side chain. This labeling scheme provides a straightforward method that elucidates biophysical information that is costly, complicated, or simply inaccessible by traditional EPR labels. Examples include the direct measurement of protein backbone dynamics at β-sheet sites, which are largely inaccessible through traditional spin labels, and rigid Cu²⁺-Cu²⁺ distance measurements that enable higher precision in the analysis of protein conformations, conformational changes, interactions with other biomolecules, and the relative orientations of two labeled protein subunits. Likewise, a Cu²⁺ label has been developed for use in DNA, which is small, is nucleotide independent, and is positioned within the DNA helix. The placement of the Cu²⁺ label directly reports on the biologically relevant backbone distance. Additionally, for both of these labeling techniques, we have developed models for interpretation of the EPR distance information, primarily utilizing molecular dynamics (MD) simulations. Initial results using force fields developed for both protein and DNA labels have agreed with experimental results, which has been a major bottleneck for traditional spin labels. Looking ahead, we anticipate new combinations of MD and EPR to further our understanding of protein and DNA conformational changes, as well as working synergistically to investigate protein-DNA interactions.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Amyloid Beta Hypothesis in Alzheimer's Disease: Major Culprits and Recent Therapeutic Strategies

Alzheimer's disease (AD) is one of the most common forms of dementia and has been a global concern for several years. Due to the multi-factorial nature of the disease, AD has become irreversible, fatal and imposes a tremendous socio-economic burden. Even though experimental medicines suggested moderate benefits, AD still lacks an effective treatment strategy for the management of symptoms or cure. Among the various hypotheses that describe development and progression of AD, the amyloid hypothesis has been a long-term adherent to the AD due to the involvement of various forms of Amyloid beta (Aβ) peptides in the impairment of neuronal and cognitive functions. Hence, majority of the drug discovery approaches in the past have focused on the prevention of the accumulation of Aβ peptides. Currently, there are several agents in the phase III clinical trials that target Aβ or the various macromolecules triggering Aβ deposition. In this review, we present the state of the art knowledge on the functional aspects of the key players involved in the amyloid hypothesis. Furthermore, we also discuss anti-amyloid agents present in the Phase III clinical trials.

Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution

Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2'dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules.

Role of PTA in the prevention of Cu(amyloid-β) induced ROS formation and amyloid-β oligomerisation in the presence of Zn

Metal-targeting drugs are being widely explored as a possible treatment for Alzheimer's disease, but most of these ligands are developed to coordinate Cu(ii). In a previous communication (E. Atrián-Blasco, E. Cerrada, A. Conte-Daban, D. Testemale, P. Faller, M. Laguna and C. Hureau, Metallomics, 2015, 7, 1229-1232) we showed another strategy where Cu(i) was targeted with the PTA (1,3,5-triaza-7-phosphaadamantane) ligand that is able to target Cu(ii) as well, reduce it and keep it in a safe complexed species. Removal of Cu(ii) from the amyloid-β peptide prevents the stabilization of oligomers and protofibrils and the complexation of Cu(i) also stops the formation of reactive oxygen species. Besides, zinc, which is found in the synaptic cleft at a higher concentration than copper, can hamper the ability of metal-targeting drug candidates, an issue that is still poorly considered and studied. Here we show that PTA fully retains the above described properties even in the presence of zinc, thus fulfilling an additional pre-requisite for its use as a model of Cu(i)-targeting drug candidates in the Alzheimer's disease context.

High fidelity visualization of multiscale dynamics of laser-induced bubbles in liquids containing gold nanoparticles

Cavitation in pure liquids and in liquids containing nanoparticles enables applications in mechanics, bio-medicine, and energy. Its evolution carries a significant interest. We describe the multiscale dynamic evolution of ultrafast-laser-induced cavitation in pure and gold-nanoparticles-doped liquids in one-dimensional geometries induced by non-diffractive ultrashort Bessel-Gauss laser beams. Covering the complete electronic and thermomechanical cycle, from the early plasma phase to bubble cavitation and collapse on ms timescales, we reconstitute, using time-resolved imaging with amplitude and phase sensitivity, the hydrodynamic phenomena concurring to bubble evolution. We indicate geometry-specific instabilities accompanying the collapse. The insertion of gold nanoparticles of 200 nm size has subtle effects in the process energetics. Albeit a moderate field enhancement minimizing the contribution to breakdown, the nanoparticles play a role in the overall relaxation dynamics of bubbles. The evolving bubble border in nanoparticles-containing liquids create a snow-plough effect that sweeps the nanoparticles at the gas liquid interface. This indicates that during the macroscopic cavity development, the nanoparticles were removed from the interaction region and dragged by the hydrodynamic movement. We thus shed light on the evolution of cavitation bubbles not triggered but perturbed by the presence of nanoparticles.

Mutual interference of Cu and Zn ions in Alzheimer's disease: perspectives at the molecular level

While metal ions such as copper and zinc are essential in biology, they are also linked to several amyloid-related diseases, including Alzheimer's disease (AD). Zinc and copper can indeed modify the aggregation pathways of the amyloid-β (Aβ) peptide, the key component encountered in AD. In addition, the redox active copper ions do produce Reactive Oxygen Species (ROS) when bound to the Aβ peptide. While Cu(i) or Cu(ii) or Zn(ii) coordination to the Aβ has been extensively studied in the last ten years, characterization of hetero-bimetallic Aβ complexes is still scarce. This is also true for the metal induced Aβ aggregation and ROS production, for which studies on the mutual influence of the copper and zinc ions are currently appearing. Last but not least, zinc can strongly interfere in therapeutic approaches relying on copper detoxification. This will be exemplified with a biological lead, namely metallothioneins, and with synthetic ligands.

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 Rapid Exchange of Zinc(2+) Enables Trace Levels to Profoundly Influence Amyloid-β Misfolding and Dominates Assembly Outcomes in Cu(2+)/Zn(2+) Mixtures

The misfolding and self-assembly of amyloid-β (Aβ) into oligomers and fibres is fundamental to Alzheimer's disease pathology. Alzheimer's disease is a multifaceted disease. One factor that is thought to have a significant role in disease aetiology is Zn(2+) homeostasis, which is disrupted in the brains of Alzheimer's disease sufferers and has been shown to modulate Alzheimer's symptoms in animal models. Here, we investigate how the kinetics of Aβ fibre growth are affected at a range of Zn(2+) concentrations and we use transmission electron microscopy to characterise the aggregate assemblies formed. We demonstrate that for Aβ(1-40), and Aβ(1-42), as little as 0.01mol equivalent of Zn(2+) (100nM) is sufficient to greatly perturb the formation of amyloid fibres irreversibly. Instead, Aβ(1-40) assembles into short, rod-like structures that pack tightly together into ordered stacks, whereas Aβ(1-42) forms short, crooked assemblies that knit together to form a mesh of disordered tangles. Our data suggest that a small number of Zn(2+) ions are able to influence a great many Aβ molecules through the rapid exchange of Zn(2+) between Aβ peptides. Surprisingly, although Cu(2+) binds to Aβ 10,000 times tighter than Zn(2+), the effect of Zn(2+) on Aβ assembly dominates in Cu(2+)/Zn(2+) mixtures, suggesting that trace levels of Zn(2+) must have a profound effect on extracellular Aβ accumulation. Trace Zn(2+) levels profoundly influence Aβ assembly even at concentrations weaker than its affinity for Aβ. These observations indicate that inhibitors of fibre assembly do not necessarily have to be at high concentration and affinity to have a profound impact.

Characterization of periodic cavitation in optical tweezers

Microscopic vapor explosions or cavitation bubbles can be generated repeatedly in optical tweezers with a microparticle that partially absorbs at the trapping laser wavelength. In this work we measure the size distribution and the production rate of cavitation bubbles for microparticles with a diameter of 3 μm using high-speed video recording and a fast photodiode. We find that there is a lower bound for the maximum bubble radius R(max)∼2  μm which can be explained in terms of the microparticle size. More than 94% of the measured R(max) are in the range between 2 and 6 μm, while the same percentage of the measured individual frequencies f(i) or production rates are between 10 and 200 Hz. The photodiode signal yields an upper bound for the lifetime of the bubbles, which is at most twice the value predicted by the Rayleigh equation. We also report empirical relations between R(max), f(i), and the bubble lifetimes.

Cu(II)-Zn(II) Cross-Modulation in Amyloid-Beta Peptide Binding: An X-ray Absorption Spectroscopy Study

In this work we analyze at a structural level the mechanism by which Cu(II) and Zn(II) ions compete for binding to the Aβ peptides that is involved in the etiology of Alzheimer's disease. We collected X-ray absorption spectroscopy data on samples containing Aβ with Cu and Zn at different concentration ratios. We show that the order in which metals are added to the peptide solution matters and that, when Zn is added first, it prevents Cu from binding. On the contrary, when Cu is added first, it does not (completely) prevent Zn binding to Aβ peptides. Our analysis suggests that Cu and Zn ions are coordinated to different numbers of histidine residues depending on the [ion]:[peptide] concentration ratio.

Study of early stages of amyloid Aβ13-23 formation using molecular dynamics simulation in implicit environments

β-amyloid aggregation and formation of senile plaques is one of the hallmarks of Alzheimer's disease (AD). It leads to degeneration of neurons and decline of cognitive functions. The most aggregative and toxic form of β-amyloid is Aβ1-42 but in experiments, the shorter forms able to form aggregates are also used. The early stages of amyloid formation are of special interest due to the influence of this peptide on progression of AD. Here, we employed nine helices of undecapeptide Aβ13-23 and studied progress of amyloid formation using 500ns molecular dynamics simulation and implicit membrane environment. The small β-sheets emerged very early during simulation as separated two-strand structures and a presence of the membrane facilitated this process. Later, the larger β-sheets were formed. However, the ninth helix which did not form paired structure stayed unchanged till the end of MD simulation. Paired helix-helix interactions seemed to be a driving force of β-sheet formation at early stages of amyloid formation. Contrary, the specific interactions between α-helix and β-sheet can be very stable and be stabilized by the membrane.

Metal ion mediated transition from random coil to β-sheet and aggregation of Bri2-23, a natural inhibitor of Aβ aggregation

Soft metal ion binding enforces critical rearrangement of the structure of Bri2-23, a natural inhibitor of Aβ aggregation, thus shifting its solution behavior to a self aggregating system.

Nanopore investigation of the stereoselective interactions between Cu(2+) and D,L-histidine amino acids engineered into an amyloidic fragment analogue

Stereochemistry is an essential theme for a number of industries and applications, constructed around discriminating various chiral enantiomers, including amino acids, chiral metal complexes, and drugs. In this work, we designed a set of peptide mutants of the human amyloidic Aβ1-16 sequence, known to display an effective Cu(2+) coordinating pocket provided mainly by the intramolecular His-6, His-13, and His-14 residues, that were engineered to contain L- and D-His enantiomers in positions 6 and 13 and provide a local coordination environment with distinct Cu(2+) binding geometries and affinities. We examined the mechanism of selective chiral recognition of Cu(2+) by such mutant peptides, by quantifying their stochastic sensing in real time with a single α-hemolysin (α-HL) protein immobilized in a planar lipid membrane, while incubated in various concentrations of Cu(2+). Our data reveal that the Cu(2+)-binding affinity lies within the micromolar range, and decreases by orders of magnitude as L-His is replaced with its Denantiomer, with the effect being prevalent when such changes were inflicted on the His-6 residue. The presented results demonstrate the feasibility of tuning the metal selectivity in a relatively simple peptide substrate by enantiomeric replacement of key metal binding residues and illustrates the potential of the protein nanopores as a promising approach to quantify the chiral recognition of l/d amino acids by metals.

Copper-zinc cross-modulation in prion protein binding

In this paper we report a systematic XAS study of a set of samples in which Cu(II) was progressively added to complexes in which Zn(II) was bound to the tetra-octarepeat portion of the prion protein. This work extends previous EPR and XAS analysis in which, in contrast, the effect of adding Zn(II) to Cu(II)-tetra-octarepeat complexes was investigated. Detailed structural analysis of the XAS spectra taken at both the Cu and Zn K-edge when the two metals are present at different relative concentrations revealed that Zn(II) and Cu(II) ions compete for binding to the tetra-octarepeat peptide by cross-regulating their relative binding modes. We show that the specific metal-peptide coordination mode depends not only, as expected, on the relative metal concentrations, but also on whether Zn(II) or Cu(II) was first bound to the peptide. In particular, it seems that the Zn(II) binding mode in the absence of Cu(II) is able to promote the formation of small peptide clusters in which triplets of tetra-octarepeats are bridged by pairs of Zn ions. When Cu(II) is added, it starts competing with Zn(II) for binding, disrupting the existing peptide cluster arrangement, despite the fact that Cu(II) is unable to completely displace Zn(II). These results may have a bearing on our understanding of peptide-aggregation processes and, with the delicate cross-regulation balancing we have revealed, seem to suggest the existence of an interesting, finely tuned interplay among metal ions affecting protein binding, capable of providing a mechanism for regulation of metal concentration in cells.

ESEEM analysis of multi-histidine Cu(II)-coordination in model complexes, peptides, and amyloid-β

We validate the use of ESEEM to predict the number of (14)N nuclei coupled to a Cu(II) ion by the use of model complexes and two small peptides with well-known Cu(II) coordination. We apply this method to gain new insight into less explored aspects of Cu(II) coordination in amyloid-β (Aβ). Aβ has two coordination modes of Cu(II) at physiological pH. A controversy has existed regarding the number of histidine residues coordinated to the Cu(II) ion in component II, which is dominant at high pH (∼8.7) values. Importantly, with an excess amount of Zn(II) ions, as is the case in brain tissues affected by Alzheimer's disease, component II becomes the dominant coordination mode, as Zn(II) selectively substitutes component I bound to Cu(II). We confirm that component II only contains single histidine coordination, using ESEEM and set of model complexes. The ESEEM experiments carried out on systematically (15)N-labeled peptides reveal that, in component II, His 13 and His 14 are more favored as equatorial ligands compared to His 6. Revealing molecular level details of subcomponents in metal ion coordination is critical in understanding the role of metal ions in Alzheimer's disease etiology.