Dynamics of Zn(II) binding as a key feature in the formation of amyloid fibrils by Aβ11-28

Supramolecular assembly of peptides and proteins into amyloid fibrils is of multifold interest, going from materials science to physiopathology. The binding of metal ions to amyloidogenic peptides is associated with several amyloid diseases, and amyloids with incorporated metal ions are of interest in nanotechnology. Understanding the mechanisms of amyloid formation and the role of metal ions can improve strategies toward the prevention of this process and enable potential applications in nanotechnology. Here, studies on Zn(II) binding to the amyloidogenic peptide Aβ11-28 are reported. Zn(II) modulates the Aβ11-28 aggregation, in terms of kinetics and fibril structures. Structural studies suggest that Aβ11-28 binds Zn(II) by amino acid residues Glu11 and His14 and that Zn(II) is rapidly exchanged between peptides. Structural and aggregation data indicate that Zn(II) binding induces the formation of the dimeric Zn(II)(1)(Aβ11-28)(2) species, which is the building block of fibrillar aggregates and explains why Zn(II) binding accelerates Aβ11-28 aggregation. Moreover, transient Zn(II) binding, even briefly, was enough to promote fibril formation, but the final structure resembled that of apo-Aβ11-28 amyloids. Also, seeding experiments, i.e., the addition of fibrillar Zn(II)(1)(Aβ11-28)(2) to the apo-Aβ11-28 peptide, induced aggregation but not propagation of the Zn(II)(1)(Aβ11-28)(2)-type fibrils. This can be explained by the dynamic Zn(II) binding between soluble and aggregated Aβ11-28. As a consequence, dynamic Zn(II) binding has a strong impact on the aggregation behavior of the Aβ11-28 peptide and might be a relevant and so far little regarded parameter in other systems of metal ions and amyloidogenic peptides.     

Insights into the mechanisms of amyloid formation of Zn(II)-Ab11-28: pH-dependent zinc coordination and overall charge as key parameters for kinetics and the structure of Zn(II)-Ab11-28 aggregates

Self-assembly of amyloidogenic peptides and their metal complexes are of multiple interest including their association with several neurological diseases. Therefore, a better understanding of the role of metal ions in the aggregation process is of broad interest. We report pH-dependent structural and aggregation studies on Zn(II) binding to the amyloidogenic peptide Ab11-28. The results suggest that coordination of the N-terminal amine to Zn(II) is responsible for the inhibition of amyloid formation and the overall charge for amorphous aggregates.     

Histidine-rich branched peptides as Cu(II) and Zn(II) chelators with potential therapeutic application in Alzheimer's disease

Two histidine-rich branched peptides with one lysine as a branching unit have been designed and synthesized by solid-phase peptide synthesis. Their complex formation with Cu(II) and Zn(II) as well as their ability to attenuate the metal-ion induced amyloid aggregation has been characterized. Both peptides can keep Cu(II) and Zn(II) in complexed forms at pH 7.4 and can bind two equivalents of metal ions in solutions with excess metal. The stoichiometry, stability and structure of the complexes formed have been determined by pH potentiometry, UV-Vis spectrophotometry, circular dichroism, EPR and NMR spectroscopy and ESI-MS. Both mono- and bimetallic species have been detected over the whole pH range studied. The basic binding mode is either a tridentate {N(amino), N(amide), N(im)} or a histamine-type of coordination which is complemented by the binding of far imidazole or amino groups leading to macrochelate formation. The peptides were able to prevent Cu(II)-induced Aβ(1-40) aggregation but could not effectively compete for Zn(II) in vitro. Our results suggest that branched peptides containing potential metal-binding sites may be suitable metal chelators for reducing the risk of amyloid plaque formation in Alzheimer's disease.     

The Chaperone‐like Activity and Structure of Mutant H119G of Rat Lens αB‐crystallin: A Study of Divalent Metal Ion Binding Site

The molecular chaperone αB‐crystallin, the major player in maintaining the transparency of the eye lens, preventing the aggregation of stress‐damaged and aging lens proteins from aggregation. In nonlenticular cells, it is involved in various neurological diseases, diabetes, and cancer. The role of some metal ions in the αB‐crystallin biology has been reported. Theoretical calculations have proposed that the coordination sites involving His101, His119, Lys121, His18 and Glu99 of human αB‐crystallin were the binding sites for divalent metal ions. Our previous mutagenesis study suggested that His18 rat lens αB‐crystallin is a crucial binding site for Cu(II) and Zn(II) in terms of chaperone‐like activity and structure. In this study mutant H119G of rat lens αB‐crystalin was cloned and expressed to investigate whether His119 is the coordination binding site. Copper and zinc at 1 mM concentration significantly increase the chaperone‐like activity in wild type αB‐crystalin, whereas zinc, copper and magnesium at 1 mM reduced the activity of H119G significantly. The results from chaperone‐like activity, ANS fluorescence measurement and Far‐and Near‐UV CD studies suggest that the replacement of His119 with Glycine resulted in a conformational and minor environmental changes that decrease chaperone‐like activity in the presence of divalent ions suggested that His119 was a crucial binding site for Cu(II) and Zn(II), which was similar to our previous study results of His18. Both results together suggest that His18 and His119 coordinates each other for the binding site of Cu(II) and Zn(II) in terms of improving the chaperone‐like activity and stability of crystallin/metal ion complex.     

Zinc(II) complexes of ubiquitin: speciation, affinity and binding features

Intraneuronal inclusions consisting of hypermetallated, (poly-)ubiquitinated proteins are a hallmark of neurodegeneration. To highlight the possible role played by metal ions in the dysfunction of the ubiquitin-proteasome system, here we report on zinc(II)/ubiquitin binding in terms of affinity constants, speciation, preferential binding sites and effects on protein stability and self-assembly. Potentiometric titrations allowed us to establish that at neutral pH only two species, ZnUb and Zn(2)Ub, are present in solution, in line with ESI-MS data. A change in the diffusion coefficient of ubiquitin was observed by NMR DOSY experiments after addition of Zn(II) ions, and thus indicates metal-promoted formation of protein assemblies. Analysis of (1)H, (15)N, (13)Cα and (13)CO chemical-shift perturbation after equimolar addition of Zn(II) ions to ubiquitin outlined two different metal-binding modes. The first involves a dynamic equilibrium in which zinc(II) is shared between a region including Met1, Gln2, Ile3, Phe4, Thr12, Leu15, Glu16, Val17, Glu18, Ile61 and Gln62 residues, which represent a site already described for copper binding, and a domain comprising Ile23, Glu24, Lys27, Ala28, Gln49, Glu51, Asp52, Arg54 and Thr55 residues. A second looser binding mode is centred on His68. Differential scanning calorimetry evidenced that addition of increasing amounts of Zn(II) ions does not affect protein thermal stability; rather it influences the shape of thermograms because of the increased propensity of ubiquitin to self-associate. The results presented here indicate that Zn(II) ions may interact with specific regions of ubiquitin and promote protein-protein contacts.     

Dual nanomolar and picomolar Zn(II) binding properties of metallothionein

Each of the seven Zn(II) ions in the Zn(3)S(9) and Zn(4)S(11) clusters of human metallothionein is in a tetrathiolate coordination environment. Yet analysis of Zn(II) association with thionein, the apoprotein, and analysis of Zn(II) dissociation from metallothionein using the fluorescent chelating agents FluoZin-3 and RhodZin-3 reveal at least three classes of sites with affinities that differ by 4 orders of magnitude. Four Zn(II) ions are bound with an apparent average log K of 11.8, and with the methods employed, their binding is indistinguishable. This binding property makes thionein a strong chelating agent. One Zn(II) ion is relatively weakly bound, with a log K of 7.7, making metallothionein a zinc donor in the absence of thionein. The binding data demonstrate that Zn(II) binds with at least four species: Zn(4)T, Zn(5)T, Zn(6)T, and Zn(7)T. Zn(5)T and Zn(6)T bind Zn(II) with a log K of approximately 10 and are the predominant species at micromolar concentrations of metallothionein in cells. Central to the function of the protein is the reactivity of its cysteine side chains in the absence and presence of Zn(II). Chelating agents, such as physiological ligands with moderate affinities for Zn(II), cause dissociation of Zn(II) ions from metallothionein at pH 7.4 (Zn(7)T <==> Zn(7-n)T + nZn(2+)), thereby affecting the reactivity of its thiols. Thus, the rate of thiol oxidation increases in the presence of Zn(II) acceptors but decreases if more free Zn(II) becomes available. Thionein is such an acceptor. It regulates the reactivity and availability of free Zn(II) from metallothionein. At thionein/metallothionein ratios > 0.75, free Zn(II) ions are below a pZn (-log[Zn(2+)](free)) of 11.8, and at ratios < 0.75, relatively large fluctuations of free Zn(II) ions are possible (pZn between 7 and 11). These chemical characteristics match cellular requirements for Zn(II) and suggest how the molecular structures and redox chemistries of metallothionein and thionein determine Zn(II) availability for biological processes.     

Interaction of alpha-synuclein with divalent metal ions reveals key differences: a link between structure, binding specificity and fibrillation enhancement

The aggregation of alpha-synuclein (AS) is characteristic of Parkinson's disease and other neurodegenerative synucleinopathies. Interactions with metal ions affect dramatically the kinetics of fibrillation of AS in vitro and are proposed to play a potential role in vivo. We recently showed that Cu(II) binds at the N-terminus of AS with high affinity (K(d) approximately 0.1 microM) and accelerates its fibrillation. In this work we investigated the binding features of the divalent metal ions Fe(II), Mn(II), Co(II), and Ni(II), and their effects on AS aggregation. By exploiting the different paramagnetic properties of these metal ions, NMR spectroscopy provides detailed information about the protein-metal interactions at the atomic level. The divalent metal ions bind preferentially and with low affinity (millimolar) to the C-terminus of AS, the primary binding site being the (119)DPDNEA(124) motif, in which Asp121 acts as the main anchoring residue. Combined with backbone residual dipolar coupling measurements, these results suggest that metal binding is not driven exclusively by electrostatic interactions but is mostly determined by the residual structure of the C-terminus of AS. A comparative analysis with Cu(II) revealed a hierarchal effect of AS-metal(II) interactions on AS aggregation kinetics, dictated by structural factors corresponding to different protein domains. These findings reveal a strong link between the specificity of AS-metal(II) interactions and the enhancement of aggregation of AS in vitro. The elucidation of the structural basis of AS metal binding specificity is then required to elucidate the mechanism and clarify the role of metal-protein interactions in the etiology of Parkinson's disease.     

Metal-binding properties of an Hpn-like histidine-rich protein

The Hpn-like protein (Hpnl), a histidine- and glutamine-rich protein, is critical for Helicobacter pylori colonization in human gastric muscosa. In this study, the thermodynamic properties of Ni(II), Cu(II), Co(II), and Zn(II) toward Hpnl were studied by isothermal titration calorimetry (ITC). We found that Hpnl exhibits two independent binding sites for Ni(II) as opposed to one site for Cu(II), Co(II), and Zn(II). Protease digestion and chemical denaturation analysis further revealed that Ni(II) confers a higher stability upon Hpnl than other divalent metal ions. The potential Ni(II) binding sites are localized in the His-rich domain of Hpnl as confirmed by mutagenesis in combination with modification of histidine residues of the protein. We also demonstrated that the single mutants (H29A and H31A) and tetrameric mutant (H29-32A) cut nearly half of the binding capacity of Hpnl towards nickel ions, whereas other histidine residues (His30, 32, 38, 39, 40, and 41) are nonessential for nickel coordination. Escherichia coli cells that harbored H29A, H31A, and H29-32A mutant genes exhibited less tolerance toward high concentrations of extracellular nickel ions than those with the wild-type gene. Our combined data indicated that the conserved histidine residues, His29 and His31 in the His-rich domain of Hpnl, are critical for nickel binding, and such a binding is important for Hpnl protein to fulfill its biological functions.     

Study of the aggregation of human insulin Langmuir monolayer

The human insulin (HI) Langmuir monolayer at the air-water interface was systematically investigated in the presence and absence of Zn(II) ions in the subphase. HI samples were dissolved in acidic (pH 2) and basic (pH 9) aqueous solutions and then spread at the air-water interface. Spectroscopic data of aqueous solutions of HI show a difference in HI conformation at different pH values. Moreover, the dynamics of the insulin protein showed a dependence on the concentration of Zn(II) ions. In the absence of Zn(II) ions in the subphase, the acidic and basic solutions showed similar behavior at the air-water interface. In the presence of Zn(II) ions in the subphase, the surface pressure-area and surface potential-area isotherms suggest that HI may aggregate at the air-water interface. It was observed that increasing the concentration of Zn(II) ions in the acidic (pH 2) aqueous solution of HI led to an increase of the area at a specific surface pressure. It was also seen that the conformation of HI in the basic (pH 9) medium had a reverse effect (decrease in the surface area) with the increase of the concentration of Zn(II) ions in solution. From the compression-decompression cycles we can conclude that the aggregated HI film at air-water interface is not stable and tends to restore a monolayer of monomers. These results were confirmed from UV-vis and fluorescence spectroscopy analysis. Infrared reflection-absorption and circular dichroism spectroscopy techniques were used to determine the secondary structure and orientation changes of HI by zinc ions. Generally, the aggregation process leads to a conformation change from α-helix to β-strand and β-turn, and at the air-water interface, the aggregation process was likewise seen to induce specific orientations for HI in the acidic and basic media. A proposed surface orientation model is presented here as an explanation to the experimental data, shedding light for further research on the behavior of insulin as a Langmuir monolayer.     

Electrochemical Study of the Lipid‐Transfer Protein

Electrochemical study of barley grain lipid‐transfer protein (LTP) revealed that it may belong to the metal‐binding protein class. Using differential pulse polarography the presence of Cu(II) and Zn(II) ions in the native LTP structure was proved, as well as its affinity for binding Ni(II) ion. Application of a more sensitive electroanalytical technique, such as anodic stripping voltammetry with analyte preconcentration, revealed the presence of Pb(II) and Cd(II) ions and also enabled the following Hg(II) ion binding. Possible biological role of LTP in plant stress response and its contribution to barley phytoextraction potential are discussed.     

Insight into the binding of divalent cations to Sepia eumelanin from IR absorption spectroscopy

IR absorption spectroscopy is used to examine the binding of the divalent cations Mg(II), Ca(II), Zn(II) and Cu(II) to melanin granules isolated from the ink sacs of Sepia officinalis. The functional groups of the melanin granules interacting with the bound metal ions are deduced by examining the effect of metal concentration on transition frequencies associated with the COOH, NH and OH moieties of the pigment. The coordinating groups vary with metal ion and with concentration. For the experimental conditions used (initial solution pH of 4, ionic strength of 100 mM and a melanin concentration of 1 mg mL(-1)) Mg(II), Ca(II) and Zn(II) bind to carboxylate groups and Cu(II) binds predominantly to phenolic (catechol) groups However, at a concentration of 10 mM Cu(II) also shows evidence of binding to carboxylate and amine groups, reflecting a secondary binding site that becomes populated as the catechol sites are depleted.     

Probing metal binding in the 8-17 DNAzyme by TbIII luminescence spectroscopy

Metal-dependent cleavage activities of the 8-17 DNAzyme were found to be inhibited by Tb(III) ions, and the apparent inhibition constant in the presence of 100 microM of Zn(II) was measured to be 3.3+/-0.3 microM. The apparent inhibition constants increased linearly with increasing Zn(II) concentration, and the inhibition effect could be fully rescued with addition of active metal ions, indicating that Tb(III) is a competitive inhibitor and that the effect is completely reversible. The sensitized Tb(III) luminescence at 543 nm was dramatically enhanced when Tb(III) was added to the DNAzyme-substrate complex. With an inactive DNAzyme in which the GT wobble pair was replaced with a GC Watson-Crick base pair, the luminescence enhancement was slightly decreased. In addition, when the DNAzyme strand was replaced with a complete complementary strand to the substrate, no significant luminescence enhancement was observed. These observations suggest that Tb(III) may bind to an unpaired region of the DNAzyme, with the GT wobble pair playing a role. Luminescence lifetime measurements in D(2)O and H(2)O suggested that Tb(III) bound to DNAzyme is coordinated by 6.7+/-0.2 water molecules and two or three functional groups from the DNAzyme. Divalent metal ions competed for the Tb(III) binding site(s) in the order Co(II)>Zn(II)>Mn(II)>Pb(II)>Ca(II) approximately Mg(II). This order closely follows the order of DNAzyme activity, with the exception of Pb(II). These results indicate that Pb(II), the most active metal ion, competes for Tb(III) binding differently from other metal ions such as Zn(II), suggesting that Pb(II) may bind to a different site from that for the other metal ions including Zn(II) and Tb(III).     

Silica nanoparticles for fluorescence sensing of Zn(II): exploring the covalent strategy

Silica nanoparticles (about 15 nm diameters), which contain a derivative of 6-methoxy-8-(p-toluensulfonamido)-quinoline (TSQ) as a Zn(II) fluorescent probe covalently linked to the silica network, were prepared and studied as Zn(II) fluorescent chemosensors. The systems selectively detect Zn(II) ions in water rich solutions with a submicromolar sensitivity: 0.13 microM concentrations of Zn(II) can be measured with the only interference of Cu(II) and Cd(II) ions. Compared with free TSQ, the nanoparticles based systems have the advantage that they can be employed in aqueous solutions without aggregation problems while at the same time, they maintain a similar Zn(II) affinity and sensing ability. Addition of a second, substrate insensitive, fluorophore to the particles leads to the realization of a ratiometric sensor.     

Molecular modeling on Zn(II) binding modes of Alzheimer''''s amyloid β-peptide in insoluble aggregates and soluble complexes

Alzheimers disease (AD) is a progressive neu-rodegenerative illness relative to aging. One of the major pathological characters is that senile plaques (SP) occur in the brains of patients. Amyloid b-peptide (Ab) is the major constituent of senile plaques. The peptide is produced from a precursor membrane pro-tein (APP) by normal proteolytic processing and is released into extracellular fluids as a soluble peptide of 39—42 amino acids[1,2]. For AD patients, Ab ag-gregates and accumulates …     

Comparison of energy interaction parameters for the complexation of Pr(III) with glutathione reduced (GSH) in absence and presence of Zn(II) in aqueous and aquated organic solvents using 4f-4f transition spectra as PROBE

The coordination chemistry of glutathione reduced (GSH) is of great importance as it acts as excellent model system for the binding of metal ions. The GSH complexation with metal ions is involved in the toxicology of different metal ions. Its coordination behaviour for soft metal ions and hard metal ions is found different because of the structure of GSH and its different potential binding sites. In our work we have studied two chemically dissimilar metal ions viz. Pr(III), which prefer hard donor site like carboxylic groups and Zn(II) the soft metal ion which prefer peptide-NH and sulphydryl groups. The absorption difference and comparative absorption spectroscopy involving 4f-4f transitions of the heterobimetallic Complexation of GSH with Pr(III) and Zn(II) has been explored in aqueous and aquated organic solvents. The variation in the energy parameters like Slater-Condon (F(K)), Racah (E(K)) and Lande (xi(4f)), Nephelauxetic parameter (beta) and bonding parameter (b(1/2)) are computed to explain the nature of complexation.     

Mn(II) and Zn(II) interactions with peptide fragments from Parkinson's disease genes

Two peptide sequences from PARK9 Parkinson's disease gene, ProAspGluLysHisGluLeu, (P(1)D(2)E(3)K(4)H(5)E(6)L(7)) (1) and PheCysGlyAspGlyAlaAsnAspCysGly (F(1)C(2)G(3)D(4)G(5)A(6)N(7)D(8)C(9)G(10)) (2) were tested for Mn(II), Zn(II) and Ca(II) binding. The fragments are located from residues 1165 to 1171 and 1184 to 1193 in the PARK9 encoded protein. This protein can protect cells from poisoning of manganese, which is an environmental risk factor for a Parkinson's disease-like syndrome. Mono- and bi-dimensional NMR spectroscopy has been used to understand the details of metal binding sites at different pH values and at different ligand to metal molar ratios. Mn(II) and Zn(II) coordination with peptide (1) involves imidazole N(ε) or N(δ) of His(5) and carboxyl γ-O of Asp(2), Glu(3) and Glu(6) residues. Six donor atoms participate in Mn(II) binding resulting in a distorted octahedral geometry, possibly involving bidentate interaction of carboxyl groups; four donor atoms participate in Zn(II) binding resulting in a tetracoordinate geometry. Mn(II) and Zn(II) coordination involves the two cysteine residues with peptide (2); Mn(II) accepts additional ligand bonds from the carboxyl γ-O of Asp(4) and Asp(8) to complete the coordination sphere; the unoccupied sites may contain solvent molecules. The failure of Ca(II) ions to bind to either peptide (1) or (2) appears to result, under our conditions, from the absence of chelating properties in the chosen fragments.     

Mechanisms of ZnII-activated magnetic resonance imaging agents

We report on the mechanism of a series of Zn (II)-activated magnetic resonance contrast agents that modulate the access of water to a paramagnetic Gd (III) ion to create an increase in relaxivity upon binding of Zn (II). In the absence and presence of Zn (II), the coordination at the Gd (III) center is modulated by appended Zn (II) binding groups. These groups were systematically varied to optimize the change in coordination upon Zn (II) binding. We observe that at least one appended aminoacetate must be present as a coordinating group to bind Gd (III) and effectively inhibit access of water. At least two binding groups are required to efficiently bind Zn (II), creating an unsaturated complex and allowing access of water. (13)C isotopic labeling of the acetate binding groups for NMR spectroscopy provides evidence of a change in the metal coordination of these groups upon the addition of Zn (II) supporting our proposed mechanism of activation as presented.     

Crystallographic analysis of metal-ion binding to human ubiquitin

The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.     

Understanding ion sensing in Zn(II) porphyrins: spectroscopic and computational studies of nitrite/nitrate binding

The development of effective sensor elements relies on the ability of a chromophore to bind an analyte selectively and then study the binding through changes in spectroscopic signals. In this report the ability of Zn(II) Tetraphenyl Porphyrin (ZnTPP) to selectively bind nitrite over nitrate ions is examined. The results of Benesi-Hildebrand analysis reveals that ZnTPP binds NO(2)(-) and NO(3)(-) ions with association constants of 739 ± 70 M(-1) and 134 ± 15 M(-1), respectively. Interestingly, addition of a pyridine ligand to the fifth coordination site of the Zn(II) center enhances ion binding with the association constants increasing to 71,300 ± 8,000 M(-1) and 18,900 ± 3,000 M(-1) for nitrite and nitrate, respectively. Density functional theory calculations suggest a binding mechanism through which Zn(II)-porphyrin interactions are disrupted by ligand and base coordination to Zn(II), with Zn(II) having more favorable overlap with nitrite orbitals, which are less delocalized than nitrate orbitals. Overall, these provide new insights into the ability to tune the affinity and selectivity of porphyrin based sensors utilizing electronic factors associated with the central Zn(II) ion.