Substrate mediated reduction of copper-amyloid-beta complex in Alzheimer's disease

Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure

An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4-8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ4-8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that CuII is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ4-8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ4-16 peptide. Robust investigations of XAS provide structural details of CuII binding with a very different bis-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ4-12/16 imply that both CuII and CuIII are accommodated in an ATCUN-like binding site. Hypotheses for these CuI, CuII and CuIII geometries were proven and disproven using the novel data and statistical analysis including F tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems.

Copper-Mediated β-Amyloid Toxicity and its Chelation Therapy in Alzheimer's Disease

The link between bio-metals, Alzheimer's disease (AD), and its associated protein, amyloid-β (Aβ) is very complex and one of the most studied aspects currently. Alzheimer's disease, a progressive neurodegenerative disease, is proposed to occurs due to the misfolding and aggregation of Aβ. Dyshomeostasis of metal ions and their interaction with Aβ has largely been implicated in AD. Copper plays a crucial role in amyloid-β toxicity and AD development potentially occurs through direct interaction with the copper-binding motif of APP and different amino acid residues of Aβ. Previous reports suggest that high levels of copper accumulation in the AD brain result in modulation of toxic Aβ peptide levels, implicating the role of copper in the pathophysiology of AD. In this review, we explore the possible mode of copper ion interaction with Aβ which accelerates the kinetics of fibril formation and promote amyloid-β mediated cell toxicity in Alzheimer's disease and the potential use of various copper chelators in the prevention of copper-mediated Aβ toxicity.

Structural Insight into Redox Dynamics of Copper Bound N-Truncated Amyloid-β Peptides from in Situ X-ray Absorption Spectroscopy

X-ray absorption spectroscopy of Cu^II amyloid-β peptide (Aβ) under in situ electrochemical control (XAS-EC) has allowed elucidation of the redox properties of Cu^II bound to truncated peptide forms. The Cu binding environment is significantly different for the Aβ_1-16 and the N-truncated Aβ_4-9, Aβ_4-12, and Aβ_4-16 (Aβ_4-9/12/16) peptides, where the N-truncated sequence (F₄R₅H₆) provides the high-affinity amino-terminal copper nickel (ATCUN) binding motif. Low temperature (ca. 10 K) XAS measurements show the adoption of identical Cu^II ATCUN-type binding sites (Cu^II_ATCUN) by the first three amino acids (FRH) and a longer-range interaction modeled as an oxygen donor ligand, most likely water, to give a tetragonal pyramid geometry in the Aβ_4-9/12/16 peptides not previously reported. Both XAS-EC and EPR measurements show that Cu^II:Aβ_4-16 can be reduced at mildly reducing potentials, similar to that of Cu^II:Aβ_1-16. Reduction of peptides lacking the H₁₃H₁₄ residues, Cu^II:Aβ_4-9/12, require far more forcing conditions, with metallic copper the only metal-based reduction product. The observations suggest that reduction of Cu^II_ATCUN species at mild potentials is possible, although the rate of reduction is significantly enhanced by involvement of H₁₃H₁₄. XAS-EC analysis reveals that, following reduction, the peptide acts as a terdentate ligand to Cu^I (H₁₃, H₁₄ together with the linking amide oxygen atom). Modeling of the EXAFS is most consistent with coordination of an additional water oxygen atom to give a quasi-tetrahedral geometry. XAS-EC analysis of oxidized Cu^II:Aβ_4-12/16 gives structural parameters consistent with crystallographic data for a five-coordinate Cu^III complex and the Cu^II_ATCUN complex. The structural results suggest that Cu^II and the oxidation product are both accommodated in an ATCUN-like binding site.

Structural insights into the interaction of platinum-based inhibitors with the Alzheimer's disease amyloid-β peptide

Extended X-ray absorption fine structure spectroscopy, mass spectrometry, dynamic light scattering and density functional theory are combined to derive structural models for the interaction of neurotoxicity-ablating platinum-based compounds with the amyloid-β peptide.

Alkemio: association of chemicals with biomedical topics by text and data mining

The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have implemented the Alkemio text mining web tool and SOAP web service to help in this task. The tool uses biomedical articles discussing chemicals (including drugs), predicts their relatedness to the query topic with a naïve Bayesian classifier and ranks all chemicals by P-values computed from random simulations. Benchmarks on seven human pathways showed good retrieval performance (areas under the receiver operating characteristic curves ranged from 73.6 to 94.5%). Comparison with existing tools to retrieve chemicals associated to eight diseases showed the higher precision and recall of Alkemio when considering the top 10 candidate chemicals. Alkemio is a high performing web tool ranking chemicals for any biomedical topics and it is free to non-commercial users.

AVAILABILITY

http://cbdm.mdc-berlin.de/∼medlineranker/cms/alkemio.

Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-β peptide

Alzheimer's disease is the most common form of dementia in humans and is related to the accumulation of the amyloid-β (Aβ) peptide and its interaction with metals (Cu, Fe, and Zn) in the brain. Crystallographic structural information about Aβ peptide deposits and the details of the metal-binding site is limited owing to the heterogeneous nature of aggregation states formed by the peptide. Here, we present a crystal structure of Aβ residues 1-16 fused to the N-terminus of the Escherichia coli immunity protein Im7, and stabilized with the fragment antigen binding fragment of the anti-Aβ N-terminal antibody WO2. The structure demonstrates that Aβ residues 10-16, which are not in complex with the antibody, adopt a mixture of local polyproline II-helix and turn type conformations, enhancing cooperativity between the two adjacent histidine residues His13 and His14. Furthermore, this relatively rigid region of Aβ (residues, 10-16) appear as an almost independent unit available for trapping metal ions and provides a rationale for the His13-metal-His14 coordination in the Aβ1-16 fragment implicated in Aβ metal binding. This novel structure, therefore, has the potential to provide a foundation for investigating the effect of metal ion binding to Aβ and illustrates a potential target for the development of future Alzheimer's disease therapeutics aimed at stabilizing the N-terminal monomer structure, in particular residues His13 and His14, and preventing Aβ metal-binding-induced neurotoxicity.

Copper(I) and copper(II) binding to β-amyloid 16 (Aβ16) studied by electrospray ionization mass spectrometry

Copper-β-amyloid 16 (Aβ16) complexes were investigated by electrospray ionization mass spectrometry (ESI-MS). Copper(i) and (ii) complexes were formed on-line in a microchip electrospray emitter by using a sacrificial copper electrode as the anode in positive ionization mode. In the presence of ascorbic acid in the peptide solution, the amount of Cu(i)-Aβ16 generated electrochemically was even higher. A kinetic model is proposed to account for the generation of copper complexes. The structure of Cu(i)-Aβ16 was investigated by tandem mass spectrometry (MS/MS), and the binding site of Cu(i) to Aβ16 was identified at the His13, His14 residues. Cu(ii)-Aβ16 was also investigated by MS/MS and, based on the unusual observations of a-ions, the two binding residues of His13 and His14 of Aβ16 to Cu(ii) were also confirmed. This approach provides direct information on Cu(i)-Aβ16 complexes generated in solution from metallic copper and gives evidence that both His13 and His14 are involved in the coordination of both Cu(i)- and Cu(ii)-Aβ16 complexes.

Modelling Copper Binding to the Amyloid-β Peptide in Alzheimer

Oxidative modification due to reactive oxygen species generated by Cu2+ bound to the amyloid-β peptide may be one of the sources of neurodegeneration observed in Alzheimer’s disease. Understanding the structure and function of the copper binding site can assist in the design of effective therapeutics. This paper highlights some of the most significant recent developments in computational modelling studies of the structure of the binding site and reaction mechanisms of reactive oxygen species generation.

Mixed monolayers of ferrocenylalkanethiol and encapsulated horseradish peroxidase for sensitive and durable electrochemical detection of hydrogen peroxide

This paper describes the construction of a mixed monolayer of ferrocenylalkanethiol and encapsulated horseradish peroxidase (HRP) at a gold electrode for amperometric detection of H(2)O(2) at trace levels. By tuning the alkanethiol chain lengths that tether the HRP enzyme and the ferrocenylalkanethiol (FcC(11)SH) mediator, facile electron transfer between FcC(11)SH and HRP can be achieved. Unlike most HRP-based electrochemical sensors, which rely on HRP-facilitated H(2)O(2) reduction (to H(2)O), the electrocatalytic current is resulted from an HRP-catalyzed oxidation reaction of H(2)O(2) (to O(2)). Upon optimizing other experimental conditions (surface coverage ratio, pH, and flow rate), the electrocatalytic reaction proceeding at the electrode was used to attain a low amperometric detection level (0.64 nM) and a dynamic range spanning over 3 orders of magnitude. Not only does the thin hydrophilic porous HRP capsule allow facile electron transfer, it also enables H(2)O(2) to permeate. More significantly, the enzymatic activity of the encapsulated HRP is retained for a considerably longer period (>3 weeks) than naked HRP molecules attached to an electrode or those wired to a redox polymer thin film. By comparing to electrodes modified with denatured HRP that are subsequently encapsulated or embedded in a poly-L-lysine matrix, it is concluded that the encapsulation has significantly preserved the native structure of HRP and therefore its enzymatic activity. The electrode covered with FcC(11)SH and encapsulated HRP is shown to be capable of rapidly and reproducibly detecting H(2)O(2) present in complex sample media.

Importance of dynamical processes in the coordination chemistry and redox conversion of copper amyloid-beta complexes

Interaction of Cu ions with the amyloid-beta (Abeta) peptide is linked to the development of Alzheimer's disease; hence, determining the coordination of Cu(I) and Cu(II) ions to Abeta and the pathway of the Cu(I)(Abeta)/Cu(II)(Abeta) redox conversion is of great interest. In the present report, we use the room temperature X-ray absorption near edge structure to show that the binding sites of the Cu(I) and Cu(II) complexes are similar to those previously determined from frozen-solution studies. More precisely, the Cu(I) is coordinated by the imidazole groups of two histidine residues in a linear fashion. However, an NMR study unravels the involvement of all three histidine residues in the Cu(I) binding due to dynamical exchange between several set of ligands. The presence of an equilibrium is also responsible for the complex redox process observed by cyclic voltammetry and evidenced by a concentration-dependent electrochemical response.

The amyloid-beta peptide of Alzheimer's disease binds Cu(I) in a linear bis-his coordination environment: insight into a possible neuroprotective mechanism for the amyloid-beta peptide

Oxidative stress has been suggested to contribute to neuronal apoptosis associated with Alzheimer's disease (AD). Copper may participate in oxidative stress through redox-cycling between its +2 and +1 oxidation states to generate reactive oxygen species (ROS). In vitro, copper binds to the amyloid-beta peptide of AD, and in vivo, copper is associated with amyloid plaques characteristic of AD. As a result, the AbetaCu(I) complex may be a critical reactant involved in ROS associated with AD etiology. To characterize the AbetaCu(I) complex, we have pursued X-ray absorption (XAS) and electron paramagnetic resonance (EPR) spectroscopy of AbetaCu(II) and AbetaCu(I) (produced by ascorbate reduction of AbetaCu(II)). The AbetaCu(II) complex Cu K-edge XAS spectrum is indicative of a square-planar Cu(II) center with mixed N/O ligation. Multiple scattering analysis of the extended X-ray absorption fine structure (EXAFS) data for AbetaCu(II) indicates that two of the ligands are imidazole groups of histidine ligands, indicating a (N(Im))(2)(N/O)(2) Cu(II) ligation sphere for AbetaCu(II). After reduction of the AbetaCu(II) complex with ascorbate, the edge region decreases in energy by approximately 4 eV. The X-ray absorption near-edge spectrum region of AbetaCu(I) displays an intense pre-edge feature at 8984.1(2) eV. EXAFS data fitting yielded a two-coordinate geometry, with two imidazole ligands coordinated to Cu(I) at 1.877(2) A in a linear geometry. Ascorbate reduction of AbetaCu(II) under inert atmosphere and subsequent air oxidation of AbetaCu(I) to regenerate AbetaCu(II) was monitored by low-temperature EPR spectroscopy. Slow reappearance of the AbetaCu(II) EPR signal indicates that O(2) oxidation of the AbetaCu(I) complex is kinetically sluggish and Abeta damage is occurring following reoxidation of AbetaCu(I) by O(2). Together, these results lead us to hypothesize that Cu(I) is ligated by His13 and His14 in a linear coordination environment in Alphabeta, that Abeta may be playing a neuroprotective role, and that metal-mediated oxidative damage of Abeta occurs over multiple redox cycles.

The structure of the amyloid-beta peptide high-affinity copper II binding site in Alzheimer disease

Neurodegeneration observed in Alzheimer disease (AD) is believed to be related to the toxicity from reactive oxygen species (ROS) produced in the brain by the amyloid-beta (Abeta) protein bound primarily to copper ions. The evidence for an oxidative stress role of Abeta-Cu redox chemistry is still incomplete. Details of the copper binding site in Abeta may be critical to the etiology of AD. Here we present the structure determined by combining x-ray absorption spectroscopy (XAS) and density functional theory analysis of Abeta peptides complexed with Cu(2+) in solution under a range of buffer conditions. Phosphate-buffered saline buffer salt (NaCl) concentration does not affect the high-affinity copper binding mode but alters the second coordination sphere. The XAS spectra for truncated and full-length Abeta-Cu(2+) peptides are similar. The novel distorted six-coordinated (3N3O) geometry around copper in the Abeta-Cu(2+) complexes include three histidines: glutamic, or/and aspartic acid, and axial water. The structure of the high-affinity Cu(2+) binding site is consistent with the hypothesis that the redox activity of the metal ion bound to Abeta can lead to the formation of dityrosine-linked dimers found in AD.