O-Glycosylation Induces Amyloid-ß To Form New Fibril Polymorphs Vulnerable for Degradation.

Brain accumulation of amyloid-ß (Aß) peptides (resulting from a disrupted balance between biosynthesis and clearance) occurs during the progression of Alzheimer's disease (AD). Aß peptides have diverse posttranslational modifications (PTMs) that variously modulate Aß aggregation into fibrils, but understanding the mechanistic roles of PTMs in these processes remains a challenge. Here, we chemically synthesized three homogeneously modified isoforms of Aß (1-42) peptides bearing Tyr10 O-glycosylation, an unusual PTM initially identified from the cerebrospinal fluid samples of AD patients. We discovered that O-glycans significantly affect both the aggregation and degradation of Aß42. By combining cryo-EM and various biochemical assays, we demonstrate that a Galß1-3GalNAc modification redirects Aß42 to form a new fibril polymorphic structure that is less stable and more vulnerable to Aß-degrading enzymes (e.g., insulin-degrading enzyme). Thus, beyond showing how particular O-glycosylation modifications affect Aß42 aggregation at the molecular level, our study provides powerful experimental tools to support further investigations about how PTMs affect Aß42 fibril aggregation and AD-related neurotoxicity.

Application of DNP-enhanced solid-state NMR to studies of amyloid-ß peptide interaction with lipid membranes.

The cellular membrane disruption induced by the aggregation of Aß peptide has been proposed as a plausible cause of neuronal cell death during Alzheimer's disease. The molecular-level details of the Aß interaction with cellular membranes were previously probed using solid state NMR (ssNMR), however, due to the limited sensitivity of the latter, studies were limited to samples with high Aß-to-lipid ratio. The dynamic nuclear polarization (DNP) is a technique for increasing the sensitivity of NMR. In this work we demonstrate the feasibility of DNP-enhanced ssNMR studies of Aß40 peptide interacting with various model liposomes: (1) a mixture of zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG); (2) a mixture of POPC, POPG, cholesterol, sphingomyelin and ganglioside GM1; (3) the synaptic plasma membrane vesicles (SPMVs) extracted from rat brain tissues. In addition, DNP-ssNMR was applied to capturing changes in Aß40 conformation taking place upon the peptide insertion into POPG liposomes. The signal enhancements under conditions of DNP allow carrying out informative 2D ssNMR experiments with about 0.25 mg of Aß40 peptides (i.e. reaching Aß40-to-lipid ratio of 1:200). In the studied liposome models, the 13C NMR chemical shifts at many 13C-labelled sites of Aß40 are characteristic of ß-sheets. In addition, in POPG liposomes the peptide forms hydrophobic contacts F19-L34 and F19-I32. Both the chemical shifts and hydrophobic contacts of Aß40 in POPG remain the same before and after 8 h of incubation. This suggests that conformation at the 13C-labelled sites of the peptide is similar before and after the insertion process. Overall, our results demonstrate that DNP helps to overcome the sensitivity limitation of ssNMR, and thereby expand the applicability of ssNMR for charactering the Aß peptide interacting with lipids.

Mutual structural effects of unmodified and pyroglutamylated amyloid ß peptides during aggregation.

Amyloid ß (Aß) peptide aggregates are linked to Alzheimer's disease (AD). Posttranslationally pyroglutamylated Aß (pEAß) occurs in AD brains in significant quantities and is hypertoxic, but the underlying structural and aggregation properties remain poorly understood. Here, the structure and aggregation of Aß1-40 and pEAß3-40 are analyzed separately and in equimolar combination. Circular dichroism data show that Aß1-40 , pEAß3-40 , and their combination assume α-helical structure in dry state and transition to unordered structure in aqueous buffer. Aß1-40 and the 1:1 combination gradually acquire ß-sheet structure while pEAß3-40 adopts an α-helix/ß-sheet conformation. Thioflavin-T fluorescence studies suggest that the two peptides mutually inhibit fibrillogenesis. Fourier transform infrared (FTIR) spectroscopy identifies the presence of ß-turn and α-helical structures in addition to ß-sheet structure in peptides in aqueous buffer. The kinetics of transitions from the initial α-helical structure to ß-sheet structure were resolved by slow hydration of dry peptides by D2 O vapor, coupled with isotope-edited FTIR. These data confirmed the mutual suppression of ß-sheet formation by the two peptides. Remarkably, pEAß3-40 maintained a significant fraction of α-helical structure in the combined sample, implying a reduced ß-sheet propensity of pEAß3-40 . Altogether, the data imply that the combination of unmodified and pyroglutamylated Aß peptides resists fibrillogenesis and favors the prefibrillar state, which may underlie hypertoxicity of pEAß.

A Cu-bis(imidazole) Substrate Intermediate Is the Catalytically Competent Center for Catechol Oxidase Activity of Copper Amyloid-ß.

Interaction of copper ions with Aß peptides alters the redox activity of the metal ion and can be associated with neurodegeneration. Many studies deal with the characterization of the copper binding mode responsible for the reactivity. Oxidation experiments of dopamine and related catechols by copper(II) complexes with the N-terminal amyloid-ß peptides Aß16 and Aß9, and the Aß16[H6A] and Aß16[H13A] mutant forms, both in their free amine and N-acetylated forms show that efficient reactivity requires the oxygenation of a CuI-bis(imidazole) complex with a bound substrate. Therefore, the active intermediate for catechol oxidation differs from the proposed "in-between state" for the catalytic oxidation of ascorbate. During the catechol oxidation process, hydrogen peroxide and superoxide anion are formed but give only a minor contribution to the reaction.

Deuterium solid-state NMR quadrupolar order rotating frame relaxation with applications to amyloid-ß fibrils.

We describe a new method for measuring molecular dynamics based on the deuterium solid-state nuclear magnetic resonance (NMR) quadrupolar order rotating frame relaxation rate R1ρ,Q under static conditions. The observed quadrupolar order coherence is created using the broad-band Jeener-Broekaert excitation and is locked with a weak radio frequency (RF) field. We describe the experimental and theoretical approaches and show applications to a selectively deuterated valine side chain of the phosphorylated amyloid-ß (1-40) fibrils phosphorylated at the serine-8 position. The R1ρ,Q rate is sensitive to the rotameric exchange mode. For biological samples, the low spin-lock field in the 5- to 10-kHz range has the advantage of avoiding sample heating and dehydration. Thus, it provides an alternative to approaches based on single-quantum coherence, which require larger spin-lock fields.

Aluminium Binding to Modified Amyloid-ß Peptides: Implications for Alzheimer's Disease.

Aluminium (Al) is clearly neurotoxic and considerable evidence exists that Al may play a role in the aetiology or pathogenesis of Alzheimer's disease (AD). Nevertheless, the link between AD pathology and Al is still open to debate. Therefore, we investigated here the interaction of aluminium ions with two Aß peptide fragments and their analogues. First, we synthesised by the Fmoc/tBu solid-phase peptide synthesis (SPPS) strategy using an automated peptide synthesiser two new peptides starting from the Aß(1-16) native peptide fragment. For this purpose, the three histidine residues (H6, H13, and H14) of the Aß(1-16) peptide were replaced by three alanine and three serine residues to form the modified peptides Aß(1-16)A36,13,14 and Aß(1-16)S36,13,14 (primary structures: H-1DAEFRADSGYEVAAQK16-NH2 and H-1DAEFRSDSGYEVSSQK16-NH2). In addition, the Aß(9-16) peptide fragment (H-9GYEVHHQK16-NH2) and its glycine analogues, namely Aß(9-16)G110, (H-9GGEVHHQK16-NH2), Aß(9-16)G213,14 (H-9GYEVGGQK16-NH2), and Aß(9-16)G310,13,14 (H-9GGEVGGQK16-NH2), were manually synthesised in order to study Al binding to more specific amino acid residues. Both the peptides and the corresponding complexes with aluminium were comparatively investigated by mass spectrometry (MS), circular dichroism spectroscopy (CD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR). Al-peptide molecular ions and Al-fragment ions were unambiguously identified in the MS and MS/MS spectra. AFM images showed dramatic changes in the film morphology of peptides upon Al binding. Our findings from the investigation of N-terminal 1-16 and even 9-16 normal and modified sequences of Aß peptides suggest that they have the capability to be involved in aluminium ion binding associated with AD.

Fibrillization of 40-Residue ß-Amyloid Peptides in Membrane-Like Environments Leads to Different Fibril Structures and Reduced Molecular Polymorphisms.

The molecular-level polymorphism in ß-Amyloid (Aß) fibrils have recently been considered as a pathologically relevant factor in Alzheimer's disease (AD). Studies showed that the structural deviations in human-brain-seeded Aß fibrils potentially correlated with the clinical histories of AD patients. For the 40-residue Aß (Aß40) fibrils derived from human brain tissues, a predominant molecular structure was proposed based on solid-state nuclear magnetic resonance (ssNMR) spectroscopy. However, previous studies have shown that the molecular structures of Aß 40 fibrils were sensitive to their growth conditions in aqueous environments. We show in this work that biological membranes and their phospholipid bilayer mimics serve as environmental factors to reduce the structural heterogeneity in Aß40 fibrils. Fibrillization in the presence of membranes leads to fibril structures that are significantly different to the Aß40 fibrils grown in aqueous solutions. Fibrils grown from multiple types of membranes, including the biological membranes extracted from the rats' synaptosomes, shared similar ssNMR spectral features. Our studies emphasize the biological relevance of membranes in Aß40 fibril structures and fibrillization processes.

Inhibition of REV-ERBs stimulates microglial amyloid-beta clearance and reduces amyloid plaque deposition in the 5XFAD mouse model of Alzheimer's disease.

A promising new therapeutic target for the treatment of Alzheimer's disease (AD) is the circadian system. Although patients with AD are known to have abnormal circadian rhythms and suffer sleep disturbances, the role of the molecular clock in regulating amyloid-beta (Aß) pathology is still poorly understood. Here, we explored how the circadian repressors REV-ERBα and ß affected Aß clearance in mouse microglia. We discovered that, at Circadian time 4 (CT4), microglia expressed higher levels of the master clock protein BMAL1 and more rapidly phagocytosed fibrillary Aß1-42 (fAß1-42 ) than at CT12. BMAL1 directly drives transcription of REV-ERB proteins, which are implicated in microglial activation. Interestingly, pharmacological inhibition of REV-ERBs with the small molecule antagonist SR8278 or genetic knockdown of REV-ERBs-accelerated microglial uptake of fAß1-42 and increased transcription of BMAL1. SR8278 also promoted microglia polarization toward a phagocytic M2-like phenotype with increased P2Y12 receptor expression. Finally, constitutive deletion of Rev-erbα in the 5XFAD model of AD decreased amyloid plaque number and size and prevented plaque-associated increases in disease-associated microglia markers including TREM2, CD45, and Clec7a. Altogether, our work suggests a novel strategy for controlling Aß clearance and neuroinflammation by targeting REV-ERBs and provides new insights into the role of REV-ERBs in AD.

ß-amyloid model core peptides: Effects of hydrophobes and disulfides.

The mechanism by which a disordered peptide nucleates and forms amyloid is incompletely understood. A central domain of ß-amyloid (Aß21-30) has been proposed to have intrinsic structural propensities that guide the limited formation of structure in the process of fibrillization. In order to test this hypothesis, we examine several internal fragments of Aß, and variants of these either cyclized or with an N-terminal Cys. While Aß21-30 and variants were always monomeric and unstructured (circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMRS)), we found that the addition of flanking hydrophobic residues in Aß16-34 led to formation of typical amyloid fibrils. NMR showed no long-range nuclear overhauser effect (nOes) in Aß21-30, Aß16-34, or their variants, however. Serial 1 H-15 N-heteronuclear single quantum coherence spectroscopy, 1 H-1 H nuclear overhauser effect spectroscopy, and 1 H-1 H total correlational spectroscopy spectra were used to follow aggregation of Aß16-34 and Cys-Aß16-34 at a site-specific level. The addition of an N-terminal Cys residue (in Cys-Aß16-34) increased the rate of fibrillization which was attributable to disulfide bond formation. We propose a scheme comparing the aggregation pathways for Aß16-34 and Cys-Aß16-34, according to which Cys-Aß16-34 dimerizes, which accelerates fibril formation. In this context, cysteine residues form a focal point that guides fibrillization, a role which, in native peptides, can be assumed by heterogeneous nucleators of aggregation.

Observation of ß-Amyloid Peptide Oligomerization by Pressure-Jump NMR Spectroscopy.

Brain tissue of Alzheimer's disease patients invariably contains deposits of insoluble, fibrillar aggregates of peptide fragments of the amyloid precursor protein (APP), typically 40 or 42 residues in length and referred to as Aß40 and Aß42. However, it remains unclear whether these fibrils or oligomers constitute the toxic species. Depending on sample conditions, oligomers can form in a few seconds or less. These oligomers are invisible to solution NMR spectroscopy, but they can be rapidly (<1 s) resolubilized and converted to their NMR-visible monomeric constituents by raising the hydrostatic pressure to a few kbar. Hence, utilizing pressure-jump NMR, the oligomeric state can be studied at residue-specific resolution by monitoring its signals in the monomeric state. Oligomeric states of Aß40 exhibit a high degree of order, reflected by slow longitudinal 15N relaxation (T1 > 5 s) for residues 18-21 and 31-34, whereas the N-terminal 10 residues relax much faster (T1 ≤ 1.5 s), indicative of extensive internal motions. Transverse relaxation rates rapidly increase to ca. 1000 s-1 after the oligomerization is initiated.

Native Ion Mobility-Mass Spectrometry Reveals the Formation of ß-Barrel Shaped Amyloid-ß Hexamers in a Membrane-Mimicking Environment.

The mechanisms behind the Amyloid-ß (Aß) peptide neurotoxicity in Alzheimer's disease are intensely studied and under debate. One suggested mechanism is that the peptides assemble in biological membranes to form ß-barrel shaped oligomeric pores that induce cell leakage. Direct detection of such putative assemblies and their exact oligomeric states is however complicated by a high level of heterogeneity. The theory consequently remains controversial, and the actual formation of pore structures is disputed. We herein overcome the heterogeneity problem by employing a native mass spectrometry approach and demonstrate that Aß(1-42) peptides form coclusters with membrane mimetic detergent micelles. The coclusters are gently ionized using nanoelectrospray and transferred into the mass spectrometer where the detergent molecules are stripped away using collisional activation. We show that Aß(1-42) indeed oligomerizes over time in the micellar environment, forming hexamers with collision cross sections in agreement with a general ß-barrel structure. We also show that such oligomers are maintained and even stabilized by addition of lipids. Aß(1-40) on the other hand form significantly lower amounts of oligomers, which are also of lower oligomeric state compared to Aß(1-42) oligomers. Our results thus support the oligomeric pore hypothesis as one important cell toxicity mechanism in Alzheimer's disease. The presented native mass spectrometry approach is a promising way to study such potentially very neurotoxic species and how they could be stabilized or destabilized by molecules of cellular or therapeutic relevance.

Engineered peptidic constructs metabolize amyloid ß by self-assembly-driven reactions.

Inspired by the unique mechanism of proteolytic maturation of host cell factor-1, we designed small peptide-based constructs that selectively recognized amyloid ß (Aß) and cleaved it in a non-catalytic manner initially around the α-secretase cleavage-site, thus termed as "artificial α-secretases". "Artificial α-secretases" also cleaved Aß on the cleavage-sites of other Aß processing enzymes by prolonged treatment, as evidenced by time-resolved MALDI-TOF-mass analyses.

Site-specific glycation of Aß1-42 affects fibril formation and is neurotoxic.

Aß1-42 is involved in Alzheimer's disease (AD) pathogenesis and is prone to glycation, an irreversible process where proteins accumulate advanced glycated end products (AGEs). Nϵ-(Carboxyethyl)lysine (CEL) is a common AGE associated with AD patients and occurs at either Lys-16 or Lys-28 of Aß1-42. Methyglyoxal is commonly used for the unspecific glycation of Aß1-42, which results in a complex mixture of AGE-modified peptides and makes interpretation of a causative AGE at a specific amino acid residue difficult. We address this issue by chemically synthesizing defined CEL modifications on Aß1-42 at Lys-16 (Aß-CEL16), Lys-28 (Aß-CEL28), and Lys-16 and -28 (Aß-CEL16&28). We demonstrated that double-CEL glycations at Lys-16 and Lys-28 of Aß1-42 had the most profound impact on the ability to form amyloid fibrils. In silico predictions indicated that Aß-CEL16&28 had a substantial decrease in free energy change, which contributes to fibril destabilization, and a increased aggregation rate. Single-CEL glycations at Lys-28 of Aß1-42 had the least impact on fibril formation, whereas CEL glycations at Lys-16 of Aß1-42 delayed fibril formation. We also tested these peptides for neuronal toxicity and mitochondrial function on a retinoic acid-differentiated SH-SY5Y human neuroblastoma cell line (RA-differentiated SH-SY5Y). Only Aß-CEL16 and Aß-CEL28 were neurotoxic, possibly through a nonmitochondrial pathway, whereas Aß-CEL16&28 showed no neurotoxicity. Interestingly, Aß-CEL16&28 had depolarized the mitochondrial membrane potential, whereas Aß-CEL16 had increased mitochondrial respiration at complex II. These results may indicate mitophagy or an alternate route of metabolism, respectively. Therefore, our results provides insight into potential therapeutic approaches against neurotoxic CEL-glycated Aß1-42.

Platinum(II) O,S Complexes Inhibit the Aggregation of Amyloid Model Systems.

Platinum(II) complexes with different cinnamic acid derivatives as ligands were investigated for their ability to inhibit the aggregation process of amyloid systems derived from Aß, Yeast Prion Protein Sup35p and the C-terminal domain of nucleophosmin 1. Thioflavin T binding assays and circular dichroism data indicate that these compounds strongly inhibit the aggregation of investigated peptides exhibiting IC50 values in the micromolar range. MS analysis confirms the formation of adducts between peptides and Pt(II) complexes that are also able to reduce amyloid cytotoxicity in human SH-SY5Y neuroblastoma cells. Overall data suggests that bidentate ligands based on ß-hydroxy dithiocinnamic esters can be used to develop platinum or platinoid compounds with anti-amyloid aggregation properties.

Efficient synthesis and characterisation of the amyloid beta peptide, Aß1-42, using a double linker system.

The amyloidogenic Aß42 peptide was efficiently prepared using a double linker system, markedly improving solubility and chromatographic peak resolution, thus enabling full characterisation using standard techniques. The tag was readily cleaved with sodium hydroxide and removed by aqueous extraction, affording Aß42 in high purity and yield for biophysical characterisation studies.

Surveying the Energy Landscapes of Aß Fibril Polymorphism.

Many unrelated proteins and peptides have been found spontaneously to form amyloid fibers above a critical concentration. Even for a single sequence, however, the amyloid fold is not a single well-defined structure. Although the cross-ß hydrogen bonding pattern is common to all amyloids, all other aspects of amyloid fiber structures are sensitive to both the sequence of the aggregating peptides and the solvent conditions under which the aggregation occurs. Amyloid fibers are easy to identify and grossly characterize using microscopy, but their insolubility and aperiodicity along the dimensions transverse to the fiber axis have complicated detailed experimental structural characterization. In this paper, we explore the landscape of possibilities for amyloid protofilament structures that are made up of a single stack of peptides associated in a parallel in-register manner. We view this landscape as a two-dimensional version of the usual three-dimensional protein folding problem: the survey of the two-dimensional folds of protein ribbons. Adopting this view leads to a practical method of predicting stable protofilament structures of arbitrary sequences. We apply this scheme to variants of Aß, the amyloid forming peptide that is characteristically associated with Alzheimer's disease. Consistent with what is known from experiment, we find that Aß protofibrils are polymorphic. To our surprise, however, the ribbon-folding landscape of Aß turned out to be strikingly simple. We confirm that, at the level of the monomeric protofilament, the landscape for the Aß sequence is reasonably well funneled toward structures that are similar to those that have been determined by experiment. The landscape has more distinct minima than does a typical globular protein landscape but fewer and deeper minima than the landscape of a randomly shuffled sequence having the same overall composition. It is tempting to consider the possibility that the significant degree of funneling of Aß's ribbon-folding landscape has arisen as a result of natural selection. More likely, however, the intermediate complexity of Aß's ribbon-folding landscape has come from the post facto selection of the Aß sequence as an object of study by researchers because only by having a landscape with some degree of funneling can ordered aggregation of such a peptide occur at in vivo concentrations. In addition to predicting polymorph structures, we show that predicted solubilities of polymorphs correlate with experiment and with their elongation free energies computed by coarse-grained molecular dynamics.

Carbonic anhydrase inhibition selectively prevents amyloid ß neurovascular mitochondrial toxicity.

Mounting evidence suggests that mitochondrial dysfunction plays a causal role in the etiology and progression of Alzheimer's disease (AD). We recently showed that the carbonic anhydrase inhibitor (CAI) methazolamide (MTZ) prevents amyloid ß (Aß)-mediated onset of apoptosis in the mouse brain. In this study, we used MTZ and, for the first time, the analog CAI acetazolamide (ATZ) in neuronal and cerebral vascular cells challenged with Aß, to clarify their protective effects and mitochondrial molecular mechanism of action. The CAIs selectively inhibited mitochondrial dysfunction pathways induced by Aß, without affecting metabolic function. ATZ was effective at concentrations 10 times lower than MTZ. Both MTZ and ATZ prevented mitochondrial membrane depolarization and H2 O2 generation, with no effects on intracellular pH or ATP production. Importantly, the drugs did not primarily affect calcium homeostasis. This work suggests a new role for carbonic anhydrases (CAs) in the Aß-induced mitochondrial toxicity associated with AD and cerebral amyloid angiopathy (CAA), and paves the way to AD clinical trials for CAIs, FDA-approved drugs with a well-known profile of brain delivery.

Fluorescence quenching by lipid encased nanoparticles shows that amyloid-ß has a preferred orientation in the membrane.

Short range plasmonic fields around a nanoparticle can modulate fluorescence or Raman processes. In lipid encased nanoparticles, this can potentially measure the relative depths of different parts of a membrane protein from the surface. We employ this technique to discover that membrane inserted amyloid-ß oligomers have a preferred molecular orientation.

Preparation and Screening of Catalytic Amyloid Assemblies.

Aggregation of proteins into amyloids has long been recognized as one of the major contributors to disease and aging. Amyloids are known to catalyze their own formation but they have been considered the rock-bottom thermodynamic minimum of the protein fold without much functionality. We have recently demonstrated that aggregation of short peptides in the presence of metal ions gives rise to efficient catalytic activity. Here we present a detailed protocol for the synthesis and purification of these peptides and the preparation of amyloid-like fibrils. Then we describe an easy-to-perform, high-throughput assay to measure their hydrolytic activity.

Incorporation of an Azobenzene ß-Turn Peptidomimetic into Amyloid-ß to Probe Potential Structural Motifs Leading to ß-Sheet Self-Assembly.

Alzheimer's disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-ß (Aß) peptide. An important goal in AD research is to characterize the structural basis for how Aß aggregates exert their noxious effects on neurons. We describe herein synthetic steps to incorporate a light-controlled ß-turn mimetic, 3-(3-aminomethylphenylazo)-phenylacetic acid (AMPP), into the backbone of a putative turn region within Aß. AMPP adopts a rigid ß-hairpin turn when azobenzene is in the cis conformation, and can adopt an extended "ß-arc" turn in the trans-azobenzene conformation. The long lifetimes of these conformationally stable isomers permit detailed biochemical analyses that help to clarify the controversial role played by these two types of turns during the toxic misfolding pathway of Aß. Methods to photo-nucleate the cis- or trans-AMPP isomeric turns in aqueous buffer are also described. Finally, we detail selected techniques to characterize the Aß aggregates derived from these photoisomerized variants.