Direct Correlation of Cell Toxicity to Conformational Ensembles of Genetic Aβ Variants

Impact of Au144 metal clusters on the structural and inhibitory mechanism of Aβ42 peptide: A theoretical approach

One of the main causes for Alzheimer disease is the abnormal self-assembly of the amyloid-beta (Aβ) peptide, which in turn forms a toxic β-rich aggregation. A recent study suggests that gold nanoparticles (AuNPs) can inhibit the Aβ aggregation. Nevertheless, the effects of AuNPs on Aβ peptide system are still ambiguous and needs exploration that is more detailed. Molecular dynamics simulations have been carried out to investigate the aggregation mechanism of Aβ₄₂ peptide for 500 ns. During simulation, C-terminus regions of Met 35-Ala42 residues exhibits β-sheet conformations. Meanwhile, the Au₁₄₄MC coordination induces substantial α-helical character, both α-helix and 3₁₀-helix structure at 0-500ns, in the region of Asp1-Arg5 and Val36-Ile41 residues. The Au₁₄₄MC strongly coordinates with Asp1, Ala2, Glu3, Phe4, Asp7, Tyr10 and Gln15 residues that plays the significant effects to loss the β-sheet geometry in the N-terminal region and it converted into random α-helix, turn and bend conformation. On comparing the RMSF of the Aβ₄₂ peptide and Aβ₄₂-Au₁₄₄MC complex shows that the coordination of Au₁₄₄MC results in greater rigidity of the Aβ₄₂ peptide backbone regions with exemptions for the Asp1, Ala2, Glu3, Leu34, Ile41 and Ala42 residues due to the strong binding between the metal cluster and the CHC (Leu17-Ala21) region. The structural stability of the Aβ₄₂ peptide and Aβ₄₂-Au₁₄₄MC complex is enhanced by the several intermolecular and intramolecular interactions and it was visibly revealed in the H-bond. From the above results, it is very evident that the Au₁₄₄MC can be used as inhibitor agent for the oligomerization of Aβ₄₂.

The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective

Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO₂, SO₂ and NO₂ that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ₄₂ peptide due to its interaction of toxic gas (CO, CO₂, SO₂ and NO₂). During the 400 ns simulation, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes have smaller Root Mean Square Deviation values when compared to the Aβ₄₂ peptide, which shows that the interaction of toxic gases (CO, CO₂, SO_2, and NO₂) would increase the Aβ₄₂ peptide structural stability. The radius of gyration analysis also supports that Aβ₄₂ interacted CO₂ and SO₂ complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ₄₂ interacted CO₂ and SO₂ complexes have a greater compact structure in comparison to Aβ₄₂ interacted CO and NO₂ complexes. Furthermore, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ₄₂.

Computing the Pathogenicity of Wilson's Disease ATP7B Mutations: Implications for Disease Prevalence

Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson's disease. Controversially, clinical prevalence seems much smaller than the prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed, although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations. Our results show that the quality of the methods varies widely. We show the importance of optimizing the threshold of the methods used to distinguish pathogenic from nonpathogenic mutations against data of clinically confirmed pathogenic and nonpathogenic mutations. We find that most methods use thresholds that predict too many ATP7B mutations to be pathogenic. Thus, our findings explain the current controversy on Wilson's disease prevalence because meta-analysis and text search methods include many computational estimates that lead to higher disease prevalence than clinically observed. As proteins and diseases differ widely, a one-size-fits-all threshold cannot distinguish pathogenic and nonpathogenic mutations efficiently, as shown here. We also show that amino acid changes with small evolutionary substitution probability, mainly due to amino acid volume, are more associated with the disease, implying a pathological effect on the conformational state of the protein, which could affect copper transport or adenosine triphosphate recognition and hydrolysis. These findings may be a first step toward a more quantitative genotype-phenotype relationship of Wilson's disease.

Metal Binding to Amyloid-β1-42: A Ligand Field Molecular Dynamics Study

Ligand field molecular mechanics simulation has been used to model the interactions of copper(II) and platinum(II) with the amyloid-β_1-42 peptide monomer. Molecular dynamics over several microseconds for both metalated systems are compared to analogous results for the free peptide. Significant differences in structural parameters are observed, both between Cu and Pt bound systems as well as between free and metal-bound peptide. Both metals stabilize the formation of helices in the peptide as well as reducing the content of β secondary structural elements compared to the unbound monomer. This is in agreement with experimental reports of metals reducing β-sheet structures, leading to formation of amorphous aggregates over amyloid fibrils. The shape and size of the peptide structures also undergo noteworthy change, with the free peptide exhibiting globular-like structure, platinum(II) system adopting extended structures, and copper(II) system resulting in a mixture of conformations similar to both of these. Salt bridge networks exhibit major differences: the Asp23-Lys28 salt bridge, known to be important in fibril formation, has a differing distance profile within all three systems studied. Salt bridges in the metal binding region of the peptide are strongly altered; in particular, the Arg5-Asp7 salt bridge, which has an occurrence of 71% in the free peptide, is reduced to zero in the presence of both metals.

Significantly different contact patterns between Aβ40 and Aβ42 monomers involving the N-terminal region

Aβ42 peptide, with two additional residues at C-terminus, aggregates much faster than Aβ40. We performed equilibrium replica-exchange molecular dynamics simulations of their monomers using our residue-specific force field. Simulated ³ J_{HNH α} -coupling constants agree excellently with experimental data. Aβ40 and Aβ42 have very similar local conformational features, with considerable β-strand structures in the segments: A2-H6 (A), L17-A21 (B), A30-V36 (C) of both peptides and V39-I41 (D) of Aβ42. Both peptides have abundant A-B and B-C contacts, but Aβ40 has much more contacts between A and C than Aβ42, which may retard its aggregation. Only Aβ42 has considerable A-B-C-D topology. Decreased probability of A-C contact in Aβ42 relates to the competition from C-D contact. Increased A-C contact probability may also explain the slower aggregation of A2T and A2V mutants of Aβ42.

1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid β-protein Oligomer and Fibril Formation

The early oligomerization of amyloid β-protein (Aβ) is a crucial step in the etiology of Alzheimer's disease (AD), in which soluble and highly neurotoxic oligomers are produced and accumulated inside neurons. In search of therapeutic solutions for AD treatment and prevention, potent inhibitors that remodel Aβ assembly and prevent neurotoxic oligomer formation offer a promising approach. In particular, several polyphenolic compounds have shown anti-aggregation properties and good efficacy on inhibiting oligomeric amyloid formation. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose is a large polyphenol that has been shown to be effective at inhibiting aggregation of full-length Aβ_1-40 and Aβ_1-42, but has the opposite effect on the C-terminal fragment Aβ_25-35. Here, we use a combination of ion mobility coupled to mass spectrometry (IMS-MS), transmission electron microscopy (TEM) and molecular dynamics (MD) simulations to elucidate the inhibitory effect of PGG on aggregation of full-length Aβ_1-40 and Aβ_1-42. We show that PGG interacts strongly with these two peptides, especially in their N-terminal metal binding regions, and suppresses the formation of Aβ_1-40 tetramer and Aβ_1-42 dodecamer. By exploring multiple facets of polyphenol-amyloid interactions, we provide a molecular basis for the opposing effects of PGG on full-length Aβ and its C-terminal fragments.

Alzheimer's disease due to loss of function: A new synthesis of the available data

Alzheimer's Disease (AD) is a highly complex disease involving a broad range of clinical, cellular, and biochemical manifestations that are currently not understood in combination. This has led to many views of AD, e.g. the amyloid, tau, presenilin, oxidative stress, and metal hypotheses. The amyloid hypothesis has dominated the field with its assumption that buildup of pathogenic β-amyloid (Aβ) peptide causes disease. This paradigm has been criticized, yet most data suggest that Aβ plays a key role in the disease. Here, a new loss-of-function hypothesis is synthesized that accounts for the anomalies of the amyloid hypothesis, e.g. the curious pathogenicity of the Aβ42/Aβ40 ratio, the loss of Aβ caused by presenilin mutation, the mixed phenotypes of APP mutations, the poor clinical-biochemical correlations for genetic variant carriers, and the failure of Aβ reducing drugs. The amyloid-loss view accounts for recent findings on the structure and chemical features of Aβ variants and their coupling to human patient data. The lost normal function of APP/Aβ is argued to be metal transport across neuronal membranes, a view with no apparent anomalies and substantially more explanatory power than the gain-of-function amyloid hypothesis. In the loss-of-function scenario, the central event of Aβ aggregation is interpreted as a loss of soluble, functional monomer Aβ rather than toxic overload of oligomers. Accordingly, new research models and treatment strategies should focus on remediation of the functional amyloid balance, rather than strict containment of Aβ, which, for reasons rationalized in this review, has failed clinically.

Molecular Dynamics Study on the Inhibition Mechanisms of Drugs CQ1-3 for Alzheimer Amyloid-β40 Aggregation Induced by Cu(2.)

The aggregation of amyloid-β (Aβ) peptide induced by Cu(2+) is a key factor in development of Alzheimer's disease (AD), and metal ion chelation therapy enables treatment of AD. Three CQi (i = 1, 2, and 3 with R = H, Cl, and NO2, respectively) drugs had been verified experimentally to be much stronger inhibitors than the pioneer clioquinol (CQ) in both disaggregation of Aβ40 aggregate and reduction of toxicity induced by Cu(2+) binding at low pH. Due to the multiple morphologies of Cu(2+)-Aβ40 complexes produced at different pH states, we performed a series of molecular dynamics simulations to explain the structural changes and morphology characteristics as well as intrinsic disaggregation mechanisms of three Cu(2+)-Aβ40 models in the presence of any of the three CQi drugs at both low and high pH states. Three inhibition mechanisms for CQi were proposed as "insertion", "semi-insertion", and "surface" mechanisms, based on the morphologies of CQi-model x (CQi-x, x = 1, 2, and 3) and the strengths of binding between CQi and the corresponding model x. The insertion mechanism was characterized by the morphology with binding strength of more than 100 kJ/mol and by CQi being inserted or embedded into the hydrophobic cavity of model x. In those CQi-x morphologies with lower binding strength, CQi only attaches on the surface or inserts partly into Aβ peptide. Given the evidence that the binding strength is correlated positively with the effectiveness of drug to inhibit Aβ aggregation and thus to reduce toxicity, the data of binding strength presented here can provide a reference for one to screen drugs. From the point of view of binding strength, CQ2 is the best drug. Because of the special role of Asp23 in both Aβ aggregation and stabilizing the Aβ fibril, the generation of a H-bond between CQ3 and Asp23 of the Aβ40 peptide is believed to be responsible for CQ3 having the strongest disaggregation capacity. Therefore, besides strong binding, stronger propensity to H-bond with Asp23 would be another key factor to be taken seriously into account in drug screens. Meanwhile, the structural characteristics of drug CQi itself are also worthy of attention. First, the increasing polarity from CQ1 and CQ2 to CQ3 in turn results in increasing probability and strength of the interaction between the drug and the N-terminal (NT) region of Aβ40, which obviously inhibits Aβ peptide aggregation induced by Cu(2+) binding. Second, both the benzothiazole ring and phenol ring of CQi can overcome the activation energy barrier (∼16 kJ/mol) to rotate flexibly around the intramolecular C7-N14 bond to achieve the maximum match and interaction with the ambient Aβ40 residues. Such a structural feature of CQi paves the new way for ones in selection and modification of a drug.