Amyloid β-protein (Aβ) assembly is hypothesized to be a seminal neuropathologic event in Alzheimer's disease (AD). We used an unbiased D-amino acid substitution strategy to determine structure-assembly relationships of 76 different Aβ40 and Aβ42 peptides. We determined the effects of the substitutions on peptide oligomerization, secondary structure dynamics, fibril assembly dynamics, and fibril morphology. Our experiments revealed that the assembly of Aβ42 was more sensitive to chiral substitutions than was Aβ40 assembly. Substitutions at identical positions in the two peptides often, but not always, produced the same effects on assembly. Sites causing substantial effects in both Aβ40 and Aβ42 include His14, Gln15, Ala30, Ile31, Met35, and Val36. Sites whose effects were unique to Aβ40 include Lys16, Leu17, and Asn 27, whereas sites unique to Aβ42 include Phe20 and Ala21. These sites may be appropriate targets for therapeutic agents that inhibit or potentiate, respectively, these effects.

Amyloid β-protein (Aβ) assembly is a seminal process in Alzheimer's disease. Elucidating the mechanistic features of this process is thought to be vital for the design and targeting of therapeutic agents. Computational studies of the most pathologic form of Aβ, the 42-residue Aβ42 peptide, have suggested that hydrogen bonding involving Ser26 may be particularly important in organizing a monomer folding nucleus and in subsequent peptide assembly. To study this question, we experimentally determined structure-activity relationships among Aβ42 peptides in which Ser26 was replaced with Gly, Ala, α-aminobutryic acid (Abu), or Cys. We observed that aliphatic substitutions (Ala and Abu) produced substantially increased rates of formation of β-sheet, hydrophobic surface, and fibrils, and higher levels of cellular toxicity. Replacement of the Ser hydroxyl group with a sulfhydryl moiety (Cys) did not have these effects. Instead, this peptide behaved like native Aβ42, even though the hydropathy of Cys was similar to that of Abu and very different from that of Ser. We conclude that H bonding of Ser26 is the factor most important in its contribution to Aβ42 conformation, assembly, and subsequent toxicity.

A variety of species express the amyloid β-protein (Aβ (the term "Aβ" refers both to Aβ40 and Aβ42, whereas "Aβ40" and "Aβ42" refer to each isoform specifically). Those species expressing Aβ with primary structure identical to that expressed in humans have been found to develop amyloid deposits and Alzheimer's disease-like neuropathology. In contrast, the Aβ sequence in mice and rats contains three amino acid substitutions, Arg5Gly, His13Arg, and Tyr10Phe, which apparently prevent the development of AD-like neuropathology. Interestingly, the brush-tailed rat, Octodon degus, expresses Aβ containing only one of these substitutions, His13Arg, and does develop AD-like pathology. We investigate here the biophysical and biological properties of Aβ peptides from humans, mice (Mus musculus), and rats (Octodon degus). We find that each peptide displays statistical coil → β-sheet secondary structure transitions, transitory formation of hydrophobic surfaces, oligomerization, formation of annuli, protofibrils, and fibrils, and an inverse correlation between rate of aggregation and aggregate size (faster aggregation produced smaller aggregates). The rank order of assembly rate was mouse > rat > Aβ42. The rank order of neurotoxicity of assemblies formed by each peptide immediately after preparation was Aβ42 > mouse ≈ rat. These data do not support long-standing hypotheses that the primary factor controlling development of AD-like neuropathology in rodents is Aβ sequence. Instead, the data support a hypothesis that assembly quaternary structure and organismal responses to toxic peptide assemblies mediate neuropathogenetic effects. The implication of this hypothesis is that a valid understanding of disease causation within a given system (organism, tissue, etc.) requires the coevaluation of both biophysical and cell biological properties of that system.

One of the earliest events in amyloid beta-protein (A beta) self-association is nucleation of A beta monomer folding through formation of a turn at G1y25-Lys28. We report here the effects of structural changes at the center of the turn, G1y25-Ser26, on A beta 42 conformational dynamics and assembly. We used "click peptide" chemistry to quasi-synchronously create A beta 42 from 26-O-acyliso-A beta 42 (iA beta 42) through a pH jump from 3 to 7.4. We also synthesized N-alpha-acetyl-Ser26-iA beta 42 (Ac-iA beta 42), which cannot undergo 0 N acyl chemistry, to study the behavior of this ester form of A beta 42 itself at neutral pH. Data from experiments monitoring increases in beta-sheet formation (thioflavin T, CD), hydrodynamic radius (RH), scattering intensity (quasielastic light scattering spectroscopy), and extent of oligomerization (ion mobility spectroscopy mass spectrometry) were quite consistent. A rank order of Ac-iA beta 42 > iA beta 42 > A beta 42 was observed. Photochemically cross-linked iA beta 42 displayed an oligomer distribution with a prominent dimer band that was not present with A beta 42. These dimers also were observed selectively in iA beta 42 in ion mobility spectrometry experiments. The distinct biophysical behaviors of iA beta 42 and A beta 42 appear to be due to the conversion of iA beta 42 into "pure" A beta 42 monomer, a nascent form of A beta 42 that does not comprise the variety of oligomeric and aggregated states present in pre-existent A beta 42. These results emphasize the importance of the Gly25-Ser26 dipeptide in organizing A beta 42 monomer structure and thus suggest that drugs altering the interactions of this dipeptide with neighboring side-chain atoms or with the peptide backbone could be useful in therapeutic strategies targeting formation of Ap oligomers and higher-order assemblies. (C) 2014 Elsevier Ltd. All rights reserved.

One of the earliest events in amyloid β-protein (Aβ) self-association is nucleation of Aβ monomer folding through formation of a turn at Gly25-Lys28. We report here the effects of structural changes at the center of the turn, Gly25-Ser26, on Aβ42 conformational dynamics and assembly. We used "click peptide" chemistry to quasi-synchronously create Aβ42 from 26-O-acyliso-Aβ42 (iAβ42) through a pH jump from 3 to 7.4. We also synthesized Nα-acetyl-Ser26-iAβ42 (Ac-iAβ42), which cannot undergo O→N acyl chemistry, to study the behavior of this ester form of Aβ42 itself at neutral pH. Data from experiments monitoring increases in β-sheet formation (thioflavin T, CD), hydrodynamic radius (RH), scattering intensity (quasielastic light scattering spectroscopy), and extent of oligomerization (ion mobility spectroscopy-mass spectrometry) were quite consistent. A rank order of Ac-iAβ42>iAβ42>Aβ42 was observed. Photochemically cross-linked iAβ42 displayed an oligomer distribution with a prominent dimer band that was not present with Aβ42. These dimers also were observed selectively in iAβ42 in ion mobility spectrometry experiments. The distinct biophysical behaviors of iAβ42 and Aβ42 appear to be due to the conversion of iAβ42 into "pure" Aβ42 monomer, a nascent form of Aβ42 that does not comprise the variety of oligomeric and aggregated states present in pre-existent Aβ42. These results emphasize the importance of the Gly25-Ser26 dipeptide in organizing Aβ42 monomer structure and thus suggest that drugs altering the interactions of this dipeptide with neighboring side-chain atoms or with the peptide backbone could be useful in therapeutic strategies targeting formation of Aβ oligomers and higher-order assemblies.

Aβ42 and Aβ40 are the two primary alloforms of the amyloid β-protein (Aβ) found in humans. The two additional residues at the C-terminus of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single-molecule force microscopy (SMFS) to probe Aβ42 and Aβ40, and corresponding C-termini mutants to characterize their interpeptide interactions within dimers. The dynamic force spectroscopy (DFS) analysis revealed an elevated stability of Aβ42 dimers (0.18 s) compared with Aβ40 dimers (0.11 s). Probing the transient structures of both dimers demonstrated a dramatic difference in the folding patterns of monomers in dimers, with the primary contributions arising from the C-terminal interactions for Aβ42 and the N-terminal interactions for Aβ40. Mutations in the C-termini change the contributing interactions for both peptides. Gly33Val-Val36Pro-Gly38Val (VPV) substitutions increase the stability of transient dimers more than three-fold for both Aβ42 and Aβ40. This stabilization is explained by changes in the peptide folding patterns, observed by a decrease in the N-terminal interactions for Aβ40 and an increase in the central and C-terminal interactions for [VPV]Aβ42. The double substitution pP, Val36 to D-enantiomer Pro and Gly37 to L-Pro, decreases the stability of dimers, as evidenced by similar lifetimes of [pP]Aβ42 (0.11 s) and Aβ40 (0.11 s). Probing the dimer's structures revealed a surprising similarity of the interpeptide interaction patterns for [pP]Aβ42 and Aβ40, which was predominately through the N-termini. Overall, our findings demonstrate directly the effect of local sequence on the global structural reorganization of Aβ monomers within dimers and on their aggregation propensity.

Alzheimer’s disease (AD) is strongly infl uenced by genetic factors as evidenced by numerous family and twin studies. Over the past two decades, others and we have co-discovered three early-onset familial AD genes, APP, PSEN1, and PSEN2, which can carry any of >200 fully penetrant mutations characterized by mendelian inheritance. For late-onset AD, the most prevalent and highest impact risk factor is the epsilon 4 variant of APOE, which increases risk by 3.7-fold in the heterozygous state and >10-fold when two copies are inherited. As part of our Alzheimer’s Genome Project funded by the Cure Alzheimer’s Fund and the NIMH, we have been identifying novel AD candidate genes. In Bertram et al. (2008), we reported genome-wide association of AD with several loci including the spinocerebellar ataxia 1 gene, ATXN1, and the SIGLEC3 gene, CD33. Functional studies of the ATXN1 gene carried out both in vitro and in vivo in ATXN1 knockout mice show that ATXN1 can regulate Aβ levels via modulation of β-secretase. CD33 is just one of several genes (TREM2, CR1, etc) involved in the innate immune system of the brain that have been associated with AD risk. In addition, we discovered association of AD with ADAM10, which encodes the major α-secretase in the brain. Re-sequencing of this gene in the best associated AD families led to two rare mutations that tightly co-segregated with AD in seven (of 1000) AD families screened, all with average age of onset ~70 years. We have shown both mutations to impair ADAM10 non-amyloidogenic cleavage of APP in vitro and in transgenic mice, including double trangenics with AD (tg2576) mice. Thus, these are the fi rst rare, highly penetrant mutations reported for late-onset AD. We have also carried out genome-wide association studies on >800 well-characterized late-onset AD families (NIMH and NIA-LOAD samples) using Aff ymetrix genotyping arrays containing either one million (6.0) or 20,000 coding SNPs. More recently, we have performed whole genome sequencing (Illumina, Hiseq) on over 1500 samples from AD families/sibships. The elucidation of the genes and functional variants infl uencing risk for AD should continue to enhance our understanding of AD etiology and pathogenesis. Ultimately, these genes will be used to predict risk for AD and guide novel the development of therapies for the eff ective treatment and prevention of this terrible disease. O3 Functional genetics – an approach to mechanisms in Alzheimer’s disease Mikko Hiltunen Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland Molecular Neurodegeneration 2013, 8(Suppl 1):O3

Background The current model for the development of Alzheimer’s (AD), Parkinson’s, Huntington’s, prion, and other neurodegenerative diseases involves protein misfolding as the early step followed by spontaneous aggregation, with specific proteins identified as the primary initiators for disease development. Therefore, elucidating the properties of the disease-prone misfolded states, understanding the mechanism of their formation, and identification of their most toxic forms will open prospects for the development of early diagnostics and specific therapeutics for these diseases.

Aβ42 and Aβ40 are the two primary alloforms of human amyloid β−protein (Aβ). The two additional C−terminal residues of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single−molecule force microscopy to characterize interpeptide interactions for Aβ42 and Aβ40 and corresponding mutants. We discovered a dramatic difference in the interaction patterns of Aβ42 and Aβ40 monomers within dimers. Although the sequence difference between the two peptides is at the C−termini, the N−terminal segment plays a key role in the peptide interaction in the dimers. This is an unexpected finding as N−terminal was considered as disordered segment with no effect on the Aβ peptide aggregation. These novel properties of Aβ proteins suggests that the stabilization of N−terminal interactions is a switch in redirecting of amyloids form the neurotoxic aggregation pathway, opening a novel avenue for the disease preventions and treatments.

Misfolding and aggregation of the amyloid β-protein (Aβ) are hallmarks of Alzheimer's disease. Both processes are dependent on the environmental conditions, including the presence of divalent cations, such as Cu2+. Cu2+ cations regulate early stages of Aβ aggregation, but the molecular mechanism of Cu2+ regulation is unknown. In this study we applied single molecule AFM force spectroscopy to elucidate the role of Cu2+ cations on interpeptide interactions. By immobilizing one of two interacting Aβ42 molecules on a mica surface and tethering the counterpart molecule onto the tip, we were able to probe the interpeptide interactions in the presence and absence of Cu2+ cations at pH 7.4, 6.8, 6.0, 5.0, and 4.0. The results show that the presence of Cu2+ cations change the pattern of Aβ interactions for pH values between pH 7.4 and pH 5.0. Under these conditions, Cu2+ cations induce Aβ42 peptide structural changes resulting in N-termini interactions within the dimers. Cu2+ cations also stabilize the dimers. No effects of Cu2+ cations on Aβ-Aβ interactions were observed at pH4.0, suggesting that peptide protonation changes the peptide-cation interaction. The effect of Cu2+ cations on later stages of Aβ aggregation was studied by AFM topographic images. The results demonstrate that substoichiometric Cu2+ cations accelerate the formation of fibrils at pH 7.4 and 5.0, whereas no effect of Cu2+ cations was observed at pH 4.0. Taken together, the combined AFM force spectroscopy and imaging analyses demonstrate that Cu2+ cations promote both the initial and the elongation stages of Aβ aggregation, but protein protonation diminishes the effect of Cu2+.

Alzheimer's disease (AD) is linked to the aberrant assembly of the amyloid β-protein (Aβ). The (21)AEDVGSNKGA(30) segment, Aβ(21-30), forms a turn that acts as a monomer folding nucleus. Amino acid substitutions within this nucleus cause familial forms of AD. To determine the biophysical characteristics of the folding nucleus, we studied the biologically relevant acetyl-Aβ(21-30)-amide peptide using experimental techniques (limited proteolysis, thermal denaturation, urea denaturation followed by pulse proteolysis, and electron microscopy) and computational methods (molecular dynamics). Our results reveal a highly stable foldon and suggest new strategies for therapeutic drug development.

Mutations in the amyloid β-protein (Aβ) precursor gene cause autosomal dominant Alzheimer disease in a number of kindreds. In two such kindreds, the English and the Tottori, the mutations produce amyloid β-proteins containing amino acid substitutions, H6R and D7N, respectively, at the peptide N terminus. To elucidate the structural and biological effects of the mutations, we began by examining monomer conformational dynamics and oligomerization. Relative to their wild type homologues, and in both the Aβ40 and Aβ42 systems, the English and Tottori substitutions accelerated the kinetics of secondary structure change from statistical coil → α/β → β and produced oligomer size distributions skewed to higher order. This skewing was reflected in increases in average oligomer size, as measured using electron microscopy and atomic force microscopy. Stabilization of peptide oligomers using in situ chemical cross-linking allowed detailed study of their properties. Each substitution produced an oligomer that displayed substantial β-strand (H6R) or α/β (D7N) structure, in contrast to the predominately statistical coil structure of wild type Aβ oligomers. Mutant oligomers functioned as fibril seeds, and with efficiencies significantly higher than those of their wild type homologues. Importantly, the mutant forms of both native and chemically stabilized oligomers were significantly more toxic in assays of cell physiology and death. The results show that the English and Tottori mutations alter Aβ assembly at its earliest stages, monomer folding and oligomerization, and produce oligomers that are more toxic to cultured neuronal cells than are wild type oligomers.

Amyloid β-protein (Aβ) oligomers may be the proximate neurotoxins in Alzheimer's disease (AD). “Oligomer” is an ill-defined term because many kinds have been reported and they often exist in rapid equilibrium with monomers and higher-order assemblies. We report here results of studies in which specific oligomers have been stabilized structurally, fractionated in pure form, and then studied by using a combination of CD spectroscopy, Thioflavin T fluorescence, EM, atomic force microscopy (AFM), and neurotoxicity assays. Aβ monomers were largely unstructured, but oligomers exhibited order-dependent increases in β-sheet content. EM and AFM data suggest that dimerization and subsequent monomer addition are processes in which significant and asymmetric monomer conformational changes occur. Oligomer secondary structure and order correlated directly with fibril nucleation activity. Neurotoxic activity increased disproportionately (order dependence >1) with oligomer order. The structure–activity correlations reported here significantly extend our understanding of the conformational dynamics, structure, and relative toxicity of pure Aβ oligomers of specific order.

Oligomers of the amyloid beta-protein (Abeta) play an important role in Alzheimer's disease (AD). We hypothesized that AD patients have a central nervous system environment that promotes Abeta oligomerization. We investigated the effect of cerebrospinal fluid (CSF) from 33 patients with AD and 33 age-matched, non-demented controls on oligomerization of Abeta1-40 and Abeta1-42 using the technique of photo-induced cross-linking of unmodified proteins. CSF inhibited oligomerization of both Abeta1-40 and Abeta1-42. This inhibitory effect was significantly weaker in AD patients than in non-demented controls. Our results indicate that AD patients have a CSF environment favorable for Abeta oligomerization.

Understanding the structural and assembly dynamics of the amyloid β-protein (Aβ) has direct relevance to the development of therapeutic agents for Alzheimer disease. To elucidate these dynamics, we combined scanning amino acid substitution with a method for quantitative determination of the Aβ oligomer frequency distribution, photo-induced cross-linking of unmodified proteins (PICUP), to perform “scanning PICUP.” Tyr, a reactive group in PICUP, was substituted at position 1, 10, 20, 30, or 40 (for Aβ40) or 42 (for Aβ42). The effects of these substitutions were probed using circular dichroism spectroscopy, thioflavin T binding, electron microscopy, PICUP, and mass spectrometry. All peptides displayed a random coil → α/β → β transition, but substitution-dependent alterations in assembly kinetics and conformer complexity were observed. Tyr1-substituted homologues of Aβ40 and Aβ42 assembled the slowest and yielded unusual patterns of oligomer bands in gel electrophoresis experiments, suggesting oligomer compaction had occurred. Consistent with this suggestion was the observation of relatively narrow [Tyr1]Aβ40 fibrils. Substitution of Aβ40 at the C terminus decreased the population conformational complexity and substantially extended the highest order of oligomers observed. This latter effect was observed in both Aβ40 and Aβ42 as the Tyr substitution position number increased. The ability of a single substitution (Tyr1) to alter Aβ assembly kinetics and the oligomer frequency distribution suggests that the N terminus is not a benign peptide segment, but rather that Aβ conformational dynamics and assembly are affected significantly by the competition between the N and C termini to form a stable complex with the central hydrophobic cluster.

In recent years, small protein oligomers have been implicated in the aetiology of a number of important amyloid diseases, such as type 2 diabetes, Parkinson's disease and Alzheimer's disease. As a consequence, research efforts are being directed away from traditional targets, such as amyloid plaques, and towards characterization of early oligomer states. Here we present a new analysis method, ion mobility coupled with mass spectrometry, for this challenging problem, which allows determination of in vitro oligomer distributions and the qualitative structure of each of the aggregates. We applied these methods to a number of the amyloid-β protein isoforms of Aβ40 and Aβ42 and showed that their oligomer-size distributions are very different. Our results are consistent with previous observations that Aβ40 and Aβ42 self-assemble via different pathways and provide a candidate in the Aβ42 dodecamer for the primary toxic species in Alzheimer's disease.

The structure of the 21-30 fragment of the amyloid beta-protein (Abeta) was investigated by ion mobility mass spectrometry and replica exchange dynamics simulations. Mutations associated with familial Alzheimer's disease (E22G, E22Q, E22K, and D23N) of Abeta(21-30) were also studied, in order to understand any structural changes that might occur with these substitutions. The structure of the WT peptide shows a bend and a perpendicular turn in the backbone which is maintained by a network of D23 hydrogen bonding. Results for the mutants show that substitutions at E22 do little to alter the overall structure of the fragment. A substitution at D23 resulted in a change of structure for Abeta(21-30). A comparison of these gas-phase studies to previous solution-phase studies reveals that the peptide can fold in the absence of solvent to a structure also seen in solution, highlighting the important role of the D23 hydrogen bonding network in stabilizing the fragment's folded structure.

*Corresponding authors. J.-E. Shea i Department of Chemistry and Bioch California, Santa Barbara, CA 93106 addresses: shea@chem.ucsb.edu; bo † C.W., M.M.M., and S.L.B. contri work. Abbreviations used: Aβ, amyloid C-terminal fragment; AD, Alzheime replica exchange molecular dynami mobility mass spectrometry; ATD, a distribution; MD, molecular dynam nano-electrospray ionization; MALD laser desorption/ionization.

A beta 40 and A beta 42 are peptides that adopt similar random-coil structures in solution. A beta 42, however, is significantly more neurotoxic than A beta 40 and forms amyloid fibrils much more rapidly than A beta 40. Here, mass spectrometry and ion mobility spectrometry are used to investigate a mixture of A beta 40 and A beta 42. The mass spectrum for the mixed solution shows the presence of a heterooligomer composed of equal parts of A beta 40 and A beta 42. Ion mobility results indicate that this mixed species comprises an oligomer distribution extending to tetramers. A beta 40 atone produces such a distribution, whereas A beta 42 alone produces oligomers as large as dodecamers. This indicates that A beta 40 inhibits A beta 42 oligomerization.

The C-terminus of amyloid beta-protein (Abeta) 42 plays an important role in this protein's oligomerization and may therefore be a good therapeutic target for the treatment of Alzheimer's disease. Certain C-terminal fragments (CTFs) of Abeta42 have been shown to disrupt oligomerization and to strongly inhibit Abeta42-induced neurotoxicity. Here we study the structures of selected CTFs [Abeta(x-42); x=29-31, 39] using replica exchange molecular dynamics simulations and ion mobility mass spectrometry. Our simulations in explicit solvent reveal that the CTFs adopt a metastable beta-structure: beta-hairpin for Abeta(x-42) (x=29-31) and extended beta-strand for Abeta(39-42). The beta-hairpin of Abeta(30-42) is converted into a turn-coil conformation when the last two hydrophobic residues are removed, suggesting that I41 and A42 are critical in stabilizing the beta-hairpin in Abeta42-derived CTFs. The importance of solvent in determining the structure of the CTFs is further highlighted in ion mobility mass spectrometry experiments and solvent-free replica exchange molecular dynamics simulations. A comparison between structures with solvent and structures without solvent reveals that hydrophobic interactions are critical for the formation of beta-hairpin. The possible role played by the CTFs in disrupting oligomerization is discussed.