A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils

Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.     

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 …     

Manipulation and capture of Aβ amyloid fibrils and monomers by DC insulator gradient dielectrophoresis (DC-iGDEP)

Here we report a novel method for the manipulation and concentration of Aβ amyloid fibrils, implicated in Alzheimer's disease, using DC insulating gradient dielectrophoresis (DC-iGDEP). Fibril enrichment was found to be ～400%. Simulations suggest that capture of the full range of amyloid protein aggregates is possible with optimized device design.     

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.     

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 Aβ_1-42 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 Aβ_13-23 and studied progress of amyloid formation using 500 ns 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.     

Iron(II) binding to amyloid-β, the Alzheimer's peptide

Iron has been implicated in Alzheimer's disease, but until now no direct proof of Fe(II) binding to the amyloid-β peptide (Aβ) has been reported. We used NMR to evidence Fe(II) coordination to full-length Aβ40 and truncated Aβ16 peptides at physiological pH and to show that the Fe(II) binding site is located in the first 16 amino-acid residues. Fe(II) caused selective broadening of some NMR peaks that was dependent on the Fe:Aβ stoichiometry and temperature. Analysis of Fe(II) broadening effect in the (1)H, (13)C, and 2D NMR data established that Asp1, Glu3, the three His, but not Tyr10 nor Met35 are the residues mainly involved in Fe(II) coordination.     

A total synthesis of (±)-α-cyclopiazonic acid using a cationic cascade as a key step

The indole alkaloid α-cyclopiazonic acid 1 has been synthesised by a route, which features at its core an acid-catalysed cationic cascade cyclisation terminated by a sulfonamide group.     

Disposition of copper(II) inβ-cyclodextrin

Distances of glucose protons in-cyclodextrin (BCD) from copper(II) in copper(II)--cyclodextrin have been determined from¹H NMR spin-lattice relaxation time (T ₁) measurements for the first time. Very lowT _1p /T _2p values indicated the dipolar mechanism to be the most dominant one in determining the paramagnetic contribution to relaxation. The distances of copper(II) from BCD glucose protons indicated copper(II) to be present almost in the centre, inside the cavity in the same plane as H-1 and H-4. An average distance of about 5.0–5.9 Å was obtained for copper(II) from the H-2, H-3, H-1, H-4 and H-6 a and b protons in BCD.     

Charge-compensated Zn metallocenes with σ-/π-chelating carboranyl ligands for the formation of constrained geometry Ru(II) and Ni(II) complexes

Charge-compensated zinc metallocenes of types [(η(3)-C(2)B(9)H(10))(2)Zn][(η(1)-NMe(2))ZnEt](2) (5) and [{η(3)-(Me)C(2)B(9)H(9)}(2)Zn][(η(1)-NMe(2))ZnEt](2) (6) were produced by reacting σ-/π-chelating aminoalkyl dicarbollides, 7-Me(2)N(H)CH(2)-7,8-C(2)B(9)H(11) (1) and 7-Me(2)N(H)CH(2)-8-Me-7,8-C(2)B(9)H(10) (2), with diethylzinc. Zincocene 5 proved to be an excellent synthon for the formation of dicarbollide-based σ-/π-type constrained Ru and Ni complexes.     

A new Zn(II) complex of unusual unidentate coordination of 4,4′-bipyridine, a new precursor for the preparation of zinc(II) oxide nanoparticles

A 4,4′-bipyridine Zn(II) complex [Zn(4,4′-bipy)₂(H₂O)₄](ClO₄)₂·4(4,4′-bipy) is synthesized, characterized by elemental analysis, IR, ¹H NMR, ¹³C NMR spectroscopy, and studied by X-ray crystallography. The compound forms monomeric units as a result of unusual unidentate coordination of 4,4′-bipy ligands. The thermal stability of the compound is studied by thermal analyses. Furthermore, the complex is luminescent with emission maxima at 329 nm in the methanol solvent. Different sizes of zinc(II) oxide nanoparticles are prepared by calcination of the [Zn(4,4′-bipy)₂(H₂O)₄](ClO₄)₂·4(4,4′-bipy) compound at two different temperatures. These nanostructures are characterized by X-ray powder diffraction and scanning electron microscopy.     

One-pot synthesis of 1,2,3-triazoles from boronic acids in water using Cu(II)-β-cyclodextrin complex as a nanocatalyst

We report here the one-pot synthesis of 1,2,3-triazoles of arylboronic acids in water. An efficient method has been developed for the synthesis of 1,2,3-triazoles via a one-pot reaction of an arylboronic acid with sodium azide in the presence of Cu(2)-β-CD (CD = Cyclodextrin) as a nanocatalyst in water followed by a click cyclization reaction with an alkyne at room temperature in air without any additives. This method is simple, rapid, and high yielding.     

Thermochemical study of coordination equilibria in the zinc(II)-β-alanine-water system in aqueous solution

The heats of formation of β-alanine (HAla) complexes with Zn²⁺ ion at temperatures of 288.15, 298.15, and 308.15 K and ionic strengths of 0.25, 0.50, and 0.75 mol/l (KNO₃) were determined by calorimetry; the heats of dilution of a zinc nitrate solution in supporting electrolyte solutions were found for introduction of appropriate corrections. The standard heats of complexation in the zinc(II)-β-alanine-water system were determined. The standard thermodynamic characteristics of zinc(II) complexation with β-alanine and standard enthalpies of formation of ZnAla⁺ and ZnAla₂ complex species were calculated.     

β-Cyclodextrin as a photostabilizer of the plant growth regulator 2-(1-naphthyl) acetamide in aqueous solution

The plant growth regulator 2-(1-naphthyl) acetamide (NAAm) is susceptible to degradation by sunlight and UV light in aqueous solution. Its inclusion complex with β-cyclodextrin (β-CD) was characterized by absorption and fluorescence spectroscopy and its photodegradation was compared with that of aqueous solutions of NAAm. The complex was formed with a stoichiometric ratio of 1:1 with a binding constant of 651 M^?1. The photodegradation behavior of NAAm in the inclusion complex NAAm:β-CD was investigated using both UV (λ = 254 nm) and simulated solar light (Suntest) irradiation. It was found that the NAAm:β-CD complex increases NAAm photostability towards photochemical degradation markedly. In addition, an influence of β-CD concentration was also observed on NAAm degradation rate: higher β-CD concentrations lead to a slower photoinduced transformation. Moreover, some differences were found in the photoproducts in the presence and absence of the cyclodextrin, indicating inhibition of some of the mechanistic pathways. β-CD stabilizes NAAm photodegradation towards sunlight and UV irradiation, enhancing its efficient application on formulations for the treatment of fruits and vegetables.     

Carbonyl ylide formation from the rhodium (II) acetate catalyzed reaction of a α-diazoketone

Reaction of the α-diazoketone derived from 7-carboxyphthalide with rhodium acetate results in an internal cyclization to give a six-ring carbonyl ylide which is subsequently converted to 7-carbomethoxyphthalide.     

Molecular modeling of the inhibitory mechanism of copper(II) on aggregation of amyloid B-peptide

Alzheimer’s disease (AD) is a devastating form of progressive dementia for which no curative therapies exist. Aggregation of amyloid β-peptide (A?) into fi-brils is a key pathological event and the hallmark of AD. Considerable experimental data imply th…     

Electroreduction of Dy(III) assisted by Zn and its co-deposition with Zn(II) in LiCl–KCl molten salt

To recover dysprosium (Dy) from LiCl–KCl molten salt, the electrochemical mechanism of Dy(III) on liquid Zn electrode and co-deposition of Dy(III) and Zn(II) on W electrode were studied using electrochemical methods. Cyclic voltammetry results demonstrated that the redox process of Dy on liquid Zn electrode is reversible and controlled by diffusion. Reverse chronopotentiograms showed that the transition time ratio of reduction and oxidation is ~3:1, revealing the redox of Dy on liquid Zn electrode is a kind of soluble–soluble system: Dy(III) + 3e⁻ = (Dy–Zn)_solution. The half-wave potential of Dy(III) was almost constant with the increase in scanning rate. The electrochemical separation of metallic Dy from the molten salt was performed using constant potential electrolysis, and the product characterized using X-ray diffraction and scanning electron microscopy–energy-dispersive X-ray spectroscopy was the thermodynamic unstable compound DyZn₅. Also, the co-deposition mechanism of Dy(III) and Zn(II) was explored, indicating that Dy(III) could deposit on pre-deposited Zn and form Dy–Zn compounds: Zn(II) + 2e⁻ = Zn and xDy(III) + yZn + 3xe⁻ = Dy_xZn_y. Moreover, the effect of Dy(III) concentration on the formation of Dy–Zn compounds was investigated. The redox peak currents corresponding to different Dy–Zn compounds changed with the increase in Dy(III) concentration. The co-deposition of Dy(III) and Zn(II) was performed using constant current electrolysis at diverse Dy(III) concentrations. The different Dy–Zn compounds were produced by controlling Dy(III) concentration.     

Dynamics of carbide formation in iron-supported catalysts of the Fischer–Tropsch process promoted by copper and potassium

The kinetics of the formation of iron carbides during the activation of iron-coated catalyst for Fischer–Tropsch synthesis promoted by copper and potassium, and by carbon monoxide and syngas, is studied. It is established that the presence of copper lowers the initial temperature of hematite reduction to magnetite and leads to the formation of carbide in both CO and СО/Н₂. Potassium slows the rate of magnetite formation, but it accelerates the formation of iron oxide. It is shown that the rate of carbide formation during magnetite reduction for catalysts is half that in the reaction of hematite reduction to magnetite in both CO and СО/Н₂.     

Ring-opening polymerization of ε-caprolactone catalysed by (pyridyl)benzoazole Zn(II) and Cu(II) complexes

This paper describes the synthesis of (pyridyl)benzoazole Zn(II) and Cu(II) complexes and their applications as catalysts in ring-opening polymerization (ROP) of ε-caprolactone (ε-CL). Reactions of 2-(3-pyridyl)-1H-benzimidazole (L1), 2-(2-pyridyl)-1H-benzothiazole (L2) and 2-(2-pyridyl)-1H-benzimidazole (L3) with Zn(II) and Cu(II) acetates produced the corresponding complexes; [Zn₂(L1)₂(OAc)₄)] (1), [Cu₂(L1)₂(OAc)₄] (2), [Zn(L2)(OAc)₂)] (3), [Zn(L3)(OAc)₂)] (4) and [Cu(L3), (OAc)₂)] (5). Molecular structures of complexes 2 and 5a revealed that while L1 adopts a monodentate binding mode, through the pyridyl nitrogen atom, L3 exhibits a bidentate coordination mode. All the complexes formed active catalysts in the ROP of ε-CL to afford moderate molecular weight polymers. The kinetics of the ROP reactions of ε-CL were pseudo-first-order with respect to monomer and catalysts.     

Steric effect on the formation of columnar phases in β-diketonate copper(II) complexes

A systematic study of the mesomorphic properties of three series of copper(II) complexes based on β-diketonate ligands containing branched side chains is reported. These disc-like compounds have four, six and eight flexible alkoxy side chains appended to the central core, in which two or four side chains were substituted by bulkier secondary alkoxy groups: 1-methylbutyloxy R ' = C₅(2°) or 1-methylheptyloxy R ' = C₈(2°). The mesomorphic results indicated that at least eight side chains are required to form stable columnar mesophases; other compounds with four or six side chains are not mesogenic regardless of the combination of the carbon length on the alkoxy or secondary alkoxy groups of the side chains. The compounds 3 with shorter R ' = C₅(2°) side chains were all non-mesogenic regardless of the carbon length of three alkoxy side chains (R = C₈, C₁₀, C₁₂) used. However, when the longer 1-methylheptyloxy side chain R ' = C₈(2°) was substituted, the compounds 3b-3e with various alkoxy groups (R = C₆, C₇, C₈, C₁₀, C₁₂) exhibited columnar phases. The mesophases were characterized and identified as columnar hexagonal phases (Col_h), as expected, by thermal analysis and optical polarized microscopy. The presence of the introduced secondary alkoxy groups apparently appeared to influence the formation of columnar phases. The clearing points were relatively lower than other similar copper(II) compounds not substituted by secondary alkoxy side chains.