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The aggregation of proteins into amyloid fibrils is associated with several neurodegenerative diseases. In Parkinson's disease it is believed that the aggregation of [alpha]-synuclein ([alpha]-syn) from monomers by intermediates into amyloid fibrils is the toxic disease-causative mechanism. Here, we studied the structure of [alpha]-syn in its amyloid state by using various biophysical approaches. Quenched hydrogen/deuterium exchange NMR spectroscopy identified five [beta]-strands within the fibril core comprising residues 35-96 and solid-state NMR data from amyloid fibrils comprising the fibril core residues 30-110 confirmed the presence of [beta]-sheet secondary structure. The data suggest that [beta]-strand interacts with [beta]2, [beta]2 with [beta]3, [beta]3 with [beta]4, and [beta]4 with [beta]5. High-resolution cryoelectron microscopy revealed the protofilament boundaries of [approximately equal to]2 x 3.5 nm. Based on the-combination of these data and published structural studies, a fold of [alpha]-syn in the fibrils is proposed and discussed. amyloid | NMR | Parkinson's disease | structure | aggregation

The synthesis, characterization and metal coordinating ability of the multifunctional carbohydrate-containing compounds that are used for the treatment of Alzheimer's disease are described. The results show that the various phenolic moieties of the apo-chelators can act as antioxidants, hence contributing to the multifunctional nature of the potential Alzheimer's disease therapeutics.

A study is conducted to show that the primary ozonolysis product of cholesterol, 3[beta]-hydroxy-5-oxo-5,6-secocholestan-6-al(KA) rapidly promotes human apolipoprotein (apo)C-II amyloid fibril formation in vitro. During the study KA randomly modified six different lysine residues with primarily one KA attached per apoC-II molecule.

The amyloid [beta] 1-42 (A[beta]1-42) monomer structure is assessed with a 790 ns molecular dynamics (MD) simulation. The results of the Cu(II)/A[beta]1-42 systems are compared with that of Cu(II)-free A[beta]1-42 simulation.

Various methodologies including spectrophotometry, spectrofluorometry and surface plasmon resonance (SPR) are used to study the formation of Alzheimer's [beta]-amyloid fibrils (fA[beta]) by various anti-amyloidogenic compounds. The in vitro experiments reveal that flavonoids inhibit a preferential and reversible binding to the amyloid fibril structure of fA[beta], which leads to the amyloidogenic effect against the fibrils.

Various lipid monolayers and vesicles are used as model membranes to study and observe a new class of cell membrane glycolipids called the gangliosides, [G.sub.M1] that highly meditate amyloid-[beta] fibrilllogenesis of Alzheimer's disease. The results of the study show that the interactions between the amyloid-[beta] peptide and [G.sub.M1] in the cell membrane helps in the phenomenon of fibrillogenesis and on the other hand, the membrane disruption causes toxicity in the peptide.

Neurogenesis is a subject of intense interest and extensive research, but it stands at the center of a bitter debate over ethical and practical problems. Neurodegenerative diseases, such as Alzheimer's disease (AD), accompanied by a shifting balance between neurogenesis and neurodegeneration, are suitable for stimulation of neurogenesis for the benefit of diseased patients. We have previously shown that Abs against the EFRH sequence of [beta]-amyloid peptide (A[beta]P) prevent aggregation and disaggregate A[beta]P both in vitro and in vivo. EFRH, located in the soluble tail of the N-terminal region, acts as a regulatory site controlling both solubilization and disaggregation processes in the A[beta]P molecule, Here we show that anti-EFRH immunotherapy of a platelet-derived amyloid precursor protein transgenic mouse model of AD stimulates endogenous neurogenesis, suggested by elevated numbers of BrdU-incorporated cells, most of which are colocalized with a marker of mature neurons, NeuN. These newly born neurons expressed the activity-dependent gene Zif268, indicating their functional integration and participation in response to synaptic input in the brain. These findings suggest that anti-amyloid immunotherapy may promote recovery from AD or other diseases related to A[beta]P overproduction and neurotoxicity by restoring neuronal population, as well as cognitive functions in treated patients. amyloid [beta] | immunotherapy | neurodegenerative diseases | platelet-derived amyloid precursor protein transgenic mice

An inhibitor that abolishes Abeta fibrillation is discovered using virtual screening in conjunction with thioflavin T fluorescence assay and atomic force microscopy determination. Circular dichroism spectroscopic study reveals that the binding of the inhibitor increases the beta-sheet content of ABeta peptide either by stabilizing the C-terminal beta-sheet conformation or by inducing the intermolecular beta-sheet formation and prevents fibrillation by blocking understand hydrogen bond formation of the pleated beta-sheet structure commonly found in amyloid fibrils.

A systematic study of the effect of 11 physiologically relevant factors on beta2-microglubulin (beta2m) fibrillogenesis at pH 7.0 without denaturants is described. The factors that could facilitate formation of beta2m fibrils in and around the sites of amyloid deposition are identified by comparing the behavior of wild-type beta2m with the variants in the presence or absence of different additives and standardizing the assay for fibril formation.

Experimental evidence suggests that the folding and aggregation of the amyloid [beta]-protein (A[beta]) into oligomers is a key pathogenetic event in Alzheimer's disease. Inhibiting the pathologic folding and oligomerization of A[beta] could be effective in the prevention and treatment of Alzheimer's disease. Here, using all-atom molecular dynamics simulations in explicit solvent, we probe the initial stages of folding of a decapeptide segment of A[beta], A[[beta].sub.21-30], shown experimentally to nucleate the folding process. In addition, we examine the folding of a homologous decapeptide containing an amino acid substitution linked to hereditary cerebral hemorrhage with amyloidosis-Dutch type, [Gln-22]A[[beta].sub.21-30]. We find that: (i) when the decapeptide is in water, hydrophobic interactions and transient salt bridges between Lys-28 and either Glu-22 or Asp-23 are important in the formation of a loop in the Val-24-Lys-28 region of the wild-type decapeptide; (ii) in the presence of salt ions, salt bridges play a more prominent role in the stabilization of the loop; (iii) in water with a reduced density, the decapeptide forms a helix, indicating the sensitivity of folding to different aqueous environments; and (iv) the 'Dutch' peptide in water, in contrast to the wild-type peptide, fails to form a long-lived Val-24-Lys-28 loop, suggesting that loop stability is a critical factor in determining whether A[beta] folds into pathologic structures. molecular dynamics | Alzheimer's disease | hydrophobic interactions | salt bridges

An independently folded extracellular domain of human amyloid-beta precursor protein (APP) localized proximal to the amyloid-beta peptides (A betas) sequence is identified, and its three dimensional structure is characterized by NMR spectroscopy. The domain consist of four alpha-helices, three of which form a tight antiparallel bundle and constitutes the C-terminal half of the central extracellular region of APP, concern in the regulation of APP cleavage.

Several studies are conducted for the identification of different compounds that can be used for the recognition of primarily A[beta] trimers, as well as tetramers. The results demonstrate that these compounds can be easily employed as the probes for the early A[beta] oligomers.

The interaction of [beta]-amyloid ([beta]A) with wild-type (wt) transthyretin (TTR) as well as two mutants, F87M/L110M, engineered to be a stable monomer, and T119M, a naturally occurring mutant with a tetrameric stability higher than that of the wild type is examined. Light scattering and electron microscopy studies have shown that the outcome of the TTR-A[beta] interaction has depended on TTR quaternary structure.

The effect of the pH on the affinities of a set of inhibitors, with a variety of chemical motifs, for the ectodomain region of BACE-1 is studied by a surface plasmon resonance (SPR) biosensor based assay. The cell-based assays have shown a correlation between high inhibitor affinity at both acidic and neutral pH values, with optimal cell response, thus providing new venues for the search of potent BACE-1 inhibitors that are active at the cellular level.

The mechanism by which amyloid fibrils form is understood by preparing covalently linked dimeric amyloid-[beta] (A[beta]) peptides and analyzing the kinetics of the fibril-forming process. The results have highlighted the importance of conformational flexibility of the A[beta] molecule and a balance in the association and dissociation rate for the formation of rigid amyloid fibrils.

The direct carbon-detected NMR method is used to characterize the structure and dynamics of partially unfolded intermediates of the 99-residue protein [beta]-2-microglobulin, which is the major component of insoluble aggregates occurring in dialysis-related amyloidosis. Comparison of the conformational properties of the molten globule-like intermediates with levels of deuterium incorporation into amyloid fibrils of [beta]-2-microglobulin revealed a close relationship between the conformational properties of the metastable intermediates and the [beta]-sheet-rich insoluble aggregates of [beta]-2-microglobulin.

A study is conducted to demonstrate the potential application of engineered proteolytic nanobody to cleave [beta]-amyloid (A[beta]) at its [alpha]-secretase site for therapeutic value. Targeted proteolysis of human amyloid precursor protein (APP) and A[beta] with catalytic nanobodies is found to represent a novel therapeutic approach for treating AlzheimerEs disease (AD) where potentially harmful side effects could be minimized.

Unrestrained, all-atom MD simulations were used to explore interactions of the two full-length Alzheimer amyloid [beta] peptides (A[beta]40 and A[beta]42) with the fully active form of insulin degrading enzyme (IDE). The atomistic level details provided by the MD simulations could be used to demonstrate binding and degrading mechanisms of the A[beta] peptides by IDE.

A prochelator SWH is described that is enzymatically activated by [beta]-secretase to produce a high affinity copper chelator CP. The studies have shown that once activated, CP has sequestered copper from amyloid-[beta], has prevented and disassembled copper-induced amyloid-[beta] aggregation and has diminished copper-promoted reactive oxygen species formation.

The dependence of C-terminal fragments (CTFs) of amyloid [beta]-protein (A[beta]42) aqueous solubility, aggregation kinetics, and morphology on peptide length and sequence and the correlation between these characteristics and inhibition of A[beta]42-induced toxicity were examined to understand the parameters that regulated aggrgation of CTFs. The data obtained provide better insight into the physical characteristics that affect CTF activity and improve the design, synthesize, and test future generations of inhibitors.

Series of evidence which provide insight into significant application of soluble amyloid-[beta] (A[beta]) oligomers as well as fibrils in the etiology of Alzheimer's disease (AD) are discussed. The need to develop optimal mass spectrometry (MS) analysis procedures to explore and explain the hypothesis related to the stabilization of endogenous A[beta] oligomers by covalent cross-linking induced via unknown cellular agents are also discussed.

PP-Leu, a tridecapeptide analogue of broad-spectrum antiviral peptides termed [thetas]-defensins which potently inhibited amyloid [beta]-protein (A[beta]) oligomer and fibril formation mediated through sequestration of the amyloidogenic A? peptide in colloid-like assemblies is reported. The combination of assembly inhibitory activity and protease resistance revealed the potential application of PP-Leu as therapeutic value.

The design, synthesis and testing of a curcumin-derivatized near-infrared (NIR) probe (CRANAD-2) are described. CRANAD-2 has all the requirements of a NIR contrast agent for detecting amyloid-[beta] (A[beta]) plaques both in vivo and in vitro.

The K3 U-turn atomic coordinates and molecular dynamic (MD) simulations are utilized to model K3 channels in the [[beta].sub.2]-microglobulin ([[beta].sub.2]m) amyloid membrane deposits that are linked to dialysis-related amyloidosis (DRA) in hemodialysis patients. The results provide insight into the [[beta].sub.2]m-induced DRA which could be mediated by ion channels formed by its K3 fragment and its ability to form ion channels that might play a generic role in toxicity.

Studies are carried out to clarify which amyloid-[beta] protein (A[beta]) morphology or aggregation species have induced the strongest proinflammatory response by using human THP-1 monocytes as a model system. The results have shown that an intermediate stage of A[beta](1-42) fibrillar precursor is optimal for inducing a proinflammatory response in THP-1 monocytes.

Site-specific [super 13]C and [super 15]N labeling is used in conjunction with hyperfine sublevel correlation (HYSCORE) spectroscopy to identify the carbonyl of Alanine-2 as an oxygen ligand in one of the pH-dependent [Cu.sup.2+] coordination modes of [beta]-amyloid peptide (A[beta]). Polarization of the carbonyl moiety by [Cu.sup.2+] has promoted amide hydrolysis and cleavage of the peptide bond between Ala2 and Glu3, which has provided a chemical mechanism for the generation of truncated A[beta] 3-40/42 species found in Alzheimer's disease (AD) plaques.

Two independent methods, fluorescence quenching and circular dichroism were employed to measure the affinity of [Cu.sup.2+] for both monomeric and fibrillar amyloid [beta] (A[beta])(1-42). The second binding site observed in A[beta](1-42) upon addition of methanol provide insight into the hydrophobic interactions that block the formation of weaker carboxylate-rich A[beta] complex.

A study was condcted to determine the ability of engineered nanocarriers composed of diverse core-shell architectures to modulate Cu levels under physiological conditions through bypassing the cellular Cu uptake systems. The results revealed that nanocarriers depending on the nature of the surrounding shell which functioned by mediating import of Cu across cellular membranes, increased levels of bioavailable Cu, and affected amyloid[beta] turnover could find potential use for treatment of metal ion deficiency disorders.

Combination of mass spectrometry and ion mobility spectrometry are used to explore a mixture of A[beta]40 and A[beta]42 peptides that adopt similar random-coil structures in solution. The mass spectrum for the mixed solution showed the presence of a heterooligomer composed of equal parts of A[beta]40 and A[beta]42 and ion mobility results indicated that the mixed species to be comprised of an oligomer distribution extending to tetramers.

Several studies are conducted to explain the interactions taking place between the C-terminal domain of proSP-C (CTC) with the amyloid [beta] (A[beta])-peptide and medin. CTC is shown to exhibit a great anti-amyloid effect, hence acting against the transmembrane segments and structural motifs.

Several NMR studies are conducted to present the structural characterization of the soluble amyloid [beta]-peptide oligomers. These oligomers are shown to be highly stable and even have the capability of altering the synaptic activity.

The traditional dye Thioflavin-T is used for designing new multifunctional molecules that contain both amyloid binding and metal chelating properties. The results have shown that the new multifunctional thioflavin-based chelating agents can be used as Alzheimer's disease therapeutics.

The amyloid-[beta][Cu.sup.I] (A[beta][Cu.sup.I]) is characterized by pursuing the X-ray absorption (XAS) and electron paramagnetic resonance (EPR) spectroscopy of A[beta][Cu.sup.II] and A[beta][Cu.sup.I]. The results have helped in hypnotizing that the [Cu.sup.I] is ligated by His13 and His14 in a linear coordination environment in A[beta], that A[beta] might be playing a neuroprotective role and that metal-mediated oxidative damage of A[beta] has occurred over multiple redox cycles.