Alzheimer's Β-amyloid Peptide Research Articles

Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids.

Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.

Aquaporin-4 Mediated Aggregation of Alzheimer's Amyloid β-Peptide.

Clearance of Alzheimer's amyloid oligomers from the brain is crucial for preventing cell toxicity. Dementia complications arise as a result of apoptosis, which is caused by peptide plaques on the lipid surface of cells. Here, we employed all-atom and coarse-grained molecular dynamics simulations to investigate the aggregation of amyloid peptides at the lipid surface and the role of aquaporin-4 (AQP4) in facilitating peptide clearance from astrocytes. The network of protein-protein interactions through text mining revealed that the expression of AQP4 and amyloid aggregation were strongly correlated. It has also been revealed that the role of aquaporins in the etiology of Alzheimer's disease involves several interconnected proteins and pathways. The nature of aggregation at the surface of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was revealed by the interaction of amyloid oligomers. The membrane-bound pore region of AQP4 interacts with the peptide and slows its aggregation. This interaction maintains the helical content of the peptide while lowering its toxicity at the lipid surface. The hydrophobicity of the peptide also decreased because of these interactions, which may help in the removal of the peptide from astrocytes. Long-term coarse-grained MD simulations demonstrated different features of oligomer aggregation at the surface and strong oligomer attraction to AQP4, which inhibited aggregation. Additionally, the water dynamics of aquaporins demonstrate how the selectivity filter is broken to disrupt water flow. Our findings also provide insight into the physiological alterations in brain tissue associated with Alzheimer's disease, including water retention and increased water flow in the CSF. Furthermore, in vitro thioflavin fluorescence spectroscopy revealed a slower aggregation of the peptide in the presence of AQP4.

Brain p3-Alcβ peptide restores neuronal viability impaired by Alzheimer's amyloid β-peptide.

We propose a new therapeutic strategy for Alzheimer's disease (AD). Brain peptide p3-Alcβ37 is generated from the neuronal protein alcadein β through cleavage of γ-secretase, similar to the generation of amyloid β (Aβ) derived from Aβ-protein precursor/APP. Neurotoxicity by Aβ oligomers (Aβo) is the prime cause prior to the loss of brain function in AD. We found that p3-Alcβ37 and its shorter peptide p3-Alcβ9-19 enhanced the mitochondrial activity of neurons and protected neurons against Aβo-induced toxicity. This is due to the suppression of the Aβo-mediated excessive Ca2+ influx into neurons by p3-Alcβ. Successful transfer of p3-Alcβ9-19 into the brain following peripheral administration improved the mitochondrial viability in the brain of AD mice model, in which the mitochondrial activity is attenuated by increasing the neurotoxic human Aβ42 burden, as revealed through brain PET imaging to monitor mitochondrial function. Because mitochondrial dysfunction is common in the brain of AD patients alongside increased Aβ and reduced p3-Alcβ37 levels, the administration of p3-Alcβ9-19 may be a promising treatment for restoring, protecting, and promoting brain functions in patients with AD.

Inhibition studies on aggregation and cytotoxicity of Alzheimer's amyloid-β peptide.

Aberrant protein aggregation is associated with several, yet incurable neurodegenerative diseases including Alzheimer's and Parkinson's disease. Research of the last decade revealed that aggregation is the inherent property of the polypeptide chains and under non-physiological, appropriate conditions most of the proteins can aggregate and form polymers of various structures. However, our knowledge is scarce on the mechanisms that inhibit protein aggregation and there are only few molecules known that have an inhibitory effect on aggregation. We have been tested the effect of 13 in-house-designed inhibitor candidates in the size range of 500-1300 Da on the aggregation of amyloid-beta peptide (Aβ42) and on the structure and stability of the aggregates by various biophysical and spectroscopic methods (ThT fluorescence assay and TEM for aggregation, NMR measurements for interaction). These amphiphilic compounds have good solubility and potential interaction sites for Aβ42. Beyond their direct effect on Aβ42 aggregation, the inhibitor molecules have been characterized by cytotoxicity test (MTT assay) on cell cultures and in the case of promising candidates that were proved to be effective, in vivo in animal models. Many of the inhibitors or their by-products were found to be cytotoxic, however, we were able to sort out candidates that prevented Aβ42 cytotoxicity and have no harmful effect at the examined concentration ratio in vivo. These molecules can be promising candidates for further studies to work out effective therapies for neurodegenerative diseases in the future. Acknowledgements: This work has been carried out in collaboration of the Hungarian and Korean research groups supported bilaterally by the National Research, Development and Innovation Fund of Hungary (grant 2018-2.1.17-TÉT-KR-2018-00008 to J.K.) and the National Research Foundation of Korea (grant NRF-2018K1A3A1A39088040 to Y.-H.L.).

Bioinspired synthetic polymers-based inhibitors of Alzheimer's amyloid-β peptide aggregation

In this review, various types of synthetic polymer-based inhibitors of amyloid-β aggregations are discussed for their potential development as therapeutic agents for Alzheimer's disease treatment.

Binding Sites of a Positron Emission Tomography Imaging Agent in Alzheimer's β-Amyloid Fibrils Studied Using 19F Solid-State NMR.

Amyloid imaging by positron emission tomography (PET) is an important method for diagnosing neurodegenerative disorders such as Alzheimer's disease. Many 11C- and 18F-labeled PET tracers show varying binding capacities, specificities, and affinities for their target proteins. The structural basis of these variations is poorly understood. Here we employ 19F and 13C solid-state NMR to investigate the binding sites of a PET ligand, flutemetamol, to the 40-residue Alzheimer's β-amyloid peptide (Aβ40). Analytical high-performance liquid chromatography and 19F NMR spectra show that flutemetamol binds the current Aβ40 fibril polymorph with a stoichiometry of one ligand per four to five peptides. Half of the ligands are tightly bound while the other half are loosely bound. 13C and 15N chemical shifts indicate that this Aβ40 polymorph has an immobilized N-terminus, a non-β-sheet His14, and a non-β-sheet C-terminus. We measured the proximity of the ligand fluorine to peptide residues using 19F-13C and 19F-1H rotational-echo double-resonance (REDOR) experiments. The spectra show that three segments in the peptide, 12VHH14, 18VFF20, and 39VV40, lie the closest to the ligand. REDOR-constrained docking simulations indicate that these three segments form multiple binding sites, and the ligand orientations and positions at these sites are similar across different Aβ polymorphs. Comparison of the flutemetamol-interacting residues in Aβ40 with the small-molecule binding sites in other amyloid proteins suggest that conjugated aromatic compounds preferentially bind β-sheet surface grooves lined by aromatic, polar, and charged residues. These motifs may explain the specificity of different PET tracers to different amyloid proteins.

Ganglioside binding domains in proteins: Physiological and pathological mechanisms.

Gangliosides are anionic lipids that form condensed membrane clusters (lipid rafts) and exert major regulatory functions on a wide range of proteins. In this review, we propose a new view of the structural features of gangliosides with special emphasis on emerging properties associated with protein binding modes. We analyze the different possibilities of molecular associations of gangliosides in lipid rafts and the role of cholesterol in this organization. We are particularly interested in amide groups of N-acetylated sugars which make it possible to neutralize the negative charge of the carboxylate group of sialic acids. We refer to this effect as "NH trick" and we demonstrate that it is operative in GM1, GD1a, GD1b and GT1b gangliosides. The NH trick is key to understand the different topologies adopted by gangliosides (chalice-like at the edge of lipid rafts, condensed clusters in central areas) and their impact on protein binding. We define three major types of ganglioside-binding domains (GBDs): α-helical, loop shaped, and large flat surface. We describe the mode of interaction of each GBD with typical reference proteins: synaptotagmin, 5HT1A receptor, cholera and botulinum toxins, HIV-1 surface envelope glycoprotein gp120, SARS-CoV-2 spike protein, cellular prion protein, Alzheimer's β-amyloid peptide and Parkinson's disease associated α-synuclein. We discuss the common mechanisms and peculiarities of protein binding to gangliosides in the light of physiological and pathological conditions. We anticipate that innovative ganglioside-based therapies will soon show an exponential growth for the treatment of cancer, microbial infections, and neurodegenerative diseases.

Conformation-specific perturbation of membrane dynamics by structurally distinct oligomers of Alzheimer's amyloid-β peptide.

The accumulation of toxic soluble oligomers of the amyloid-β peptide (Aβ) is a key step in the pathogenesis of Alzheimer's disease. There are mainly two conformationally distinct oligomers, namely, prefibrillar and fibrillar oligomers, that are recognized by conformation-specific antibodies, anti-amyloid oligomer antibody (A11) and anti-amyloid fibrillar antibody (OC), respectively. Previous studies have shown that the interaction of Aβ oligomers with the lipid membrane is one of the key mechanisms of toxicity produced by Aβ oligomers. However, the mechanism by which structurally distinct Aβ oligomers interact with the lipid membrane remains elusive. In this work, we dissect the molecular mechanism underlying the interaction of structurally distinct Aβ42 oligomers with the lipid membrane derived from the brain total lipid extract. Using picosecond time-resolved fluorescence spectroscopy, we show that the A11-positive Aβ42 oligomers undergo a membrane-induced conformational change that promotes the deeper immersion of these oligomers into the lipid hydrocarbon region and results in an increase in the membrane micro-viscosity. In sharp contrast, OC-positive Aβ42 oligomers interact with the lipid membrane via electrostatic interactions between the negatively-charged lipid headgroup and positively-charged residues of Aβ42 without perturbing the membrane dynamics. We show that the two structurally distinct Aβ42 oligomers demonstrating different interaction mechanisms with the lipid membrane eventually lead to the formation of typical amyloid fibrils. Our findings provide the mechanistic underpinning of the perturbation of lipid membranes by two conformationally distinct Aβ42 oligomers and can be of prime importance in designing anti-Alzheimer's therapeutic agents targeting Aβ-membrane interactions.

Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data.

Molecular dynamic (MD) simulations are an important tool for studying protein aggregation processes, which play a central role in a number of diseases including Alzheimer's disease. However, MD simulations produce large amounts of data, requiring advanced methods to extract mechanistic insight into the process under study. Transition networks (TNs) provide an elegant method to identify (meta)stable states and the transitions between them from MD simulations. Here, we apply two different methods to generate TNs for protein aggregation: Markov state models (MSMs), which are based on kinetic clustering the state space, and TNs using conformational clustering. The similarities and differences of both methods are elucidated for the aggregation of the fragment Aβ16-22 of the Alzheimer's amyloid-β peptide. In general, both methods perform excellently in identifying the main aggregation pathways. The strength of MSMs is that they provide a rather coarse and thus simply to interpret picture of the aggregation process. Conformation-sorting TNs, on the other hand, outperform MSMs in uncovering mechanistic details. We thus recommend to apply both methods to MD data of protein aggregation in order to obtain a complete picture of this process. As part of this work, a Python script called ATRANET for automated TN generation based on a correlation analysis of the descriptors used for conformational sorting is made publicly available.

Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1–42)

We present solid-state NMR measurements of β-strand secondary structure and inter-strand organization within a 150-kDa oligomeric aggregate of the 42-residue variant of the Alzheimer's amyloid-β peptide (Aβ(1–42)). We build upon our previous report of a β-strand spanned by residues 30–42, which arranges into an antiparallel β-sheet. New results presented here indicate that there is a second β-strand formed by residues 11–24. Contrary to expectations, NMR data indicate that this second β-strand is organized into a parallel β-sheet despite the co-existence of an antiparallel β-sheet in the same structure. In addition, the in-register parallel β-sheet commonly observed for amyloid fibril structure does not apply to residues 11–24 in the 150-kDa oligomer. Rather, we present evidence for an inter-strand registry shift of three residues that likely alternate in direction between adjacent molecules along the β-sheet. We corroborated this unexpected scheme for β-strand organization using multiple two-dimensional NMR and 13C–13C dipolar recoupling experiments. Our findings indicate a previously unknown assembly pathway and inspire a suggestion as to why this aggregate does not grow to larger sizes.

Evaluating the Correlation between Alzheimer's Amyloid-β Peptides and Glaucoma in Human Aqueous Humor.

PurposeRecent studies suggest that glaucoma may share common pathogenic mechanisms with Alzheimer's disease. To test this hypothesis, we investigated the correlation between glaucoma and amyloid-β42 (Aβ42) concentration in human samples of aqueous humor (AH).MethodsEighty-one candidates for cataract or glaucoma surgery were consecutively enrolled, with a median age of 77 years; of these, 32 subjects were affected by glaucoma and 49 were controls. Before surgery, each patient received an ophthalmological examination including biometry, intraocular pressure (IOP) measurement, fundus photography, and determination of the mean thickness of the ganglion cell complex (GCC) and/or retinal nerve fiber layer. During the surgical procedure, an AH sample was collected and immediately processed for total protein (TP) and Aβ42 evaluation.ResultsAβ42 levels were not statistically different between the glaucomatous and control samples, but a significant increase in TP concentration was found in the AH of glaucoma patients compared with controls (P = 0.02). In addition, positive correlations were observed between TP and Aβ42 (r = 0.51; P < 0.0001), between TP and IOP (r = 0.44; P < 0.0001), and between Aβ42 and IOP (r = 0.22; P = 0.033).ConclusionsOur results indicate that an increased protein concentration in the AH could play a role in the pathogenesis of glaucomatous disease.Translational RelevanceThis study strongly supports the hypothesis that increased TP in the AH may have a pathogenic role in glaucoma. Further investigations are needed to clarify whether the protein enhancement represents a causative factor and whether it can be used as a marker of disease or as a novel therapeutic target.

Глюкагоноподобный пептид 1, головной мозг, нейродегенеративные заболевания: современный взгляд

Glucagon-like peptide 1, a hormone synthesized in the intestine, has attracted the attention of scientists with its connection with the brain. A number of studies have shown the effect of glucagon-like peptide 1 on the functions of the nervous system, such as thermogenesis, blood pressure control, energy homeostasis, neurogenesis. In addition, modulation of glucagon-like peptide 1 activity may affect the aggregation of amyloid β-peptide in Alzheimer’s disease and dopamine in Parkinson’s disease. Glucagon-like peptide 1 receptor agonists have shown a beneficial effect on animal brain ischemia by reducing the area of brain infarction, reducing neurological deficit due to inhibition of oxidative stress, apoptosis, and inflammatory response. Their positive effect on cognitive function in animals with type 2 diabetes mellitus or obesity has been proven, improving learning and memory. There is increasing evidence of the neuroprotective effect of glucagon-like peptide 1 receptor agonists in animals with neurodegenerative diseases, regardless of the presence of T2DM. However, further clinical studies are needed to study the feasibility of using these drugs to treat Parkinson’s disease, Alzheimer’s disease, and other forms of cognitive impairment in humans. The discussion of the above issues is the subject of this literature review.

Alignment of Alzheimer's disease amyloid β-peptide and klotho.

The cause of Alzheimer’s disease (AD) is poorly understood. In 1991, the amyloid hypothesis postulated that β-amyloid (Aβ) accumulation is a key element. It follows that clearing the brain of Aβ would be beneficial, which has not been the case. Therefore, Aβ is likely a result, not a cause, of AD and may be protective rather than harmful. The apolipoprotein E4 (apoE4) allele is the strongest genetic risk factor for AD. Klotho (KL), encoded by the KL gene, may be another AD-related protein. FGF21 is a circulating endocrine hormone, mainly secreted by the liver, mostly during fasting. FGF21 acts by binding to its receptor FGFR1 and co-receptor β-klotho. FGF21 is neuroprotective and could delay onset of AD. In the present study, the KL protein structure was examined to determine whether it may interact with Aβ. Protein data bank (pdb) entries for klotho and Aβ were searched on the RCSB Protein Data Bank for β-KL and AD amyloid β-peptide. The protein structures were superimposed and aligned on PYMOL v2.3.4 with the super command, which super aligns two protein selections. To evaluate the conservation and alignment of the Aβ and KL genomes across species, BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser, was used. The amino acid residues phe76-val96 of KL aligned closely with residues asp7-asn27 of Aβ. Cross-species comparison of KL revealed a high degree of alignment and conservation in the chimp and 27 other primates; however, less alignment and conservation were observed in the mouse, dog and elephant, even less in the chicken, western clawed frog (Xenopus tropicalis), zebrafish and lamprey. The current finding of amino acid residues phe76-val96 of klotho aligning closely with residues asp7-asn27 of Aβ suggests that Aβ can enhance the ability of klotho to draw FGF21 to regions of incipient neurodegeneration in AD. The problem arises with age. Older individuals do not heal or repair tissue damage as well as younger individuals. As neurodegeneration advances in an older individual, perhaps caused by neuroinflammation related to herpes simplex virus type 1, increasing amounts of amyloid are produced, forming an adhesive web, as the brain tries to hold the pathologic process in check. Meanwhile, the damage increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.

Merging memantine and ferulic acid to probe connections between NMDA receptors, oxidative stress and amyloid-β peptide in Alzheimer's disease

N-methyl-d-aspartate receptors (NMDAR) are critically involved in the pathogenesis of Alzheimer's disease (AD). Acting as an open-channel blocker, the anti-AD drug memantine preferentially targets NMDAR overactivation, which has been proposed to trigger neurotoxic events mediated by amyloid β peptide (Aβ) and oxidative stress. In this study, we applied a multifunctional approach by conjugating memantine to ferulic acid, which is known to protect the brain from Aβ neurotoxicity and neuronal death caused by ROS. The most interesting compound (7) behaved, like memantine, as a voltage-dependent antagonist of NMDAR (IC50 = 6.9 μM). In addition, at 10 μM concentration, 7 exerted antioxidant properties both directly and indirectly through the activation of the Nrf-2 pathway in SH-SY5Y cells. At the same concentration, differently from the parent compounds memantine and ferulic acid alone, it was able to modulate Aβ production, as revealed by the observed increase of the non-amyloidogenic sAPPα in H4-SW cells. These findings suggest that compound 7 may represent a promising tool for investigating NMDAR-mediated neurotoxic events involving Aβ burden and oxidative damage.

Nature-inspired design and evolution of anti-amyloid antibodies

Antibodies that recognize amyloidogenic aggregates with high conformational and sequence specificity are important for detecting and potentially treating a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. However, these types of antibodies are challenging to generate because of the large size, hydrophobicity, and heterogeneity of protein aggregates. To address this challenge, we developed a method for generating antibodies specific for amyloid aggregates. First, we grafted amyloidogenic peptide segments from the target polypeptide [Alzheimer's amyloid-β (Aβ) peptide] into the complementarity-determining regions (CDRs) of a stable antibody scaffold. Next, we diversified the grafted and neighboring CDR sites using focused mutagenesis to sample each WT or grafted residue, as well as one to five of the most commonly occurring amino acids at each site in human antibodies. Finally, we displayed these antibody libraries on the surface of yeast cells and selected antibodies that strongly recognize Aβ-amyloid fibrils and only weakly recognize soluble Aβ. We found that this approach enables the generation of monovalent and bivalent antibodies with nanomolar affinity for Aβ fibrils. These antibodies display high conformational and sequence specificity as well as low levels of nonspecific binding and recognize a conformational epitope at the extreme N terminus of human Aβ. We expect that this systematic approach will be useful for generating antibodies with conformational and sequence specificity against a wide range of peptide and protein aggregates associated with neurodegenerative disorders.

Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly.

Markov state models have become popular in the computational biochemistry and biophysics communities as a technique for identifying stationary and kinetic information of protein dynamics from molecular dynamics simulation data. In this paper, we extend the applicability of automated Markov state modeling to simulation data of molecular self-assembly and aggregation by constructing collective coordinates from molecular descriptors that are invariant to permutations of molecular indexing. Understanding molecular self-assembly is of critical importance if we want to deepen our understanding of neurodegenerative diseases where the aggregation of misfolded or disordered proteins is thought to be the main culprit. As a proof of principle, we demonstrate our Markov state model technique on simulations of the KFFE peptide, a subsequence of Alzheimer's amyloid-β peptide and one of the smallest peptides known to aggregate into amyloid fibrils in vitro. We investigate the different stages of aggregation up to tetramerization and show that the Markov state models clearly map out the different aggregation pathways. Of note is that disordered and β-sheet oligomers do not interconvert, leading to separate pathways for their formation. This suggests that amyloid aggregation of KFFE occurs via ordered aggregates from the very beginning. The code developed here is freely available as a Jupyter notebook called TICAgg, which can be used for the automated analysis of any self-assembling molecular system, protein, or otherwise.

The Norepinephrine Inhibits Alzheimer's Amyloid-β Peptide Aggregation by Binding to the C-Terminal Hydrophobic Region

The abnormal self-assembly of amyloid-β (Aβ) peptides into toxic prefibrillar aggregates is associated with the pathogenesis of Alzheimer's disease (AD). The inhibition of β-sheet-rich oligomers formation is considered as the primary therapeutic strategy for AD. Previous experimental studies reported that norepinephrine (NE), one of the neurotransmitters, is able to inhibit Aβ aggregation and disaggregate the preformed fibrils. However, the underlying inhibitory and disruptive mechanisms remain elusive. In this work, we performed extensive replica-exchange molecular dynamic (REMD) simulations on the conformational ensemble of Aβ1-42 dimer with and without NE molecules. Our results show that in the absence of NE molecules, Aβ1-42 dimer transiently adopts a β-hairpin involving two β-strands of residues 15QKLVFFA21 and residues 33GLMVGGVV40, whose β-strand regions strongly resemble those of the Aβ fibril structure (β1: residues Q15-A21, β2: residues I30-G37) reported in an electron paramagnetic resonance spectroscopy study. NE molecules greatly reduce the interpeptide β-sheet content and suppress the formation of the above-mentioned β-hairpin, leading to a more disordered coil-rich Aβ dimer. Four dominant binding sites are identified via contact probability and binding energy analyses, among which the C-terminal I31-V36 hydrophobic region is the most favorable one. Our data reveal that hydrophobic, aromatic stacking, cation-π and hydrogen-bonding interactions synergistically contribute to the NE-induced conformational shift. This work reveals the molecular mechanism of NE molecules against Aβ1-42 aggregation and provides valuable information for the development of new drug candidates against AD.

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer.

We investigated the effects of 17 widely used atomistic molecular mechanics force fields (MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we performed large-scale all-atom molecular dynamics simulations in explicit water on the dimer of the seven-residue fragment of the Alzheimer's amyloid-β peptide, Aβ16-22, for a total time of 0.34 ms. We compared the effects of these MMFFs by analyzing various global reaction coordinates, secondary structure contents, the fibril population, the in-register and out-of-register architectures, and the fibril formation time at 310 K. While the AMBER94, AMBER99, and AMBER12SB force fields do not predict any β-sheets, the seven force fields, AMBER96, GROMOS45a3, GROMOS53a5, GROMOS53a6, GROMOS43a1, GROMOS43a2, and GROMOS54a7, form β-sheets rapidly. In contrast, the following five force fields, AMBER99-ILDN, AMBER14SB, CHARMM22*, CHARMM36, and CHARMM36m, are the best candidates for studying amyloid peptide assembly, as they provide good balances in terms of structures and kinetics. We also investigated the assembly mechanisms of dimeric Aβ16-22 and found that the fibril formation rate is predominantly controlled by the total β-strand content.

How Fluorescent Tags Modify Oligomer Size Distributions of the Alzheimer Peptide

Within the complex aggregation process of amyloidogenic peptides into fibrils, early stages of aggregation play a central role and reveal fundamental properties of the underlying mechanism of aggregation. In particular, low-molecular-weight aggregates of the Alzheimer amyloid-β peptide (Aβ) have attracted increasing interest because of their role in cytotoxicity and neuronal apoptosis, typical of aggregation-related diseases. One of the main techniques used to characterize oligomeric stages is fluorescence spectroscopy. To this end, Aβ peptide chains are functionalized with fluorescent tags, often covalently bound to the disordered N-terminus region of the peptide, with the assumption that functionalization and presence of the fluorophore will not modify the process of self-assembly nor the final fibrillar structure. In this investigation, we systematically study the effects of four of the most commonly used fluorophores on the aggregation of Aβ (1–40). Time-resolved and single-molecule fluorescence spectroscopy have been chosen to monitor the oligomer populations at different fibrillation times, and transmission electron microscopy, atomic force microscopy and x-ray diffraction to investigate the structure of mature fibrils. Although the structures of the fibrils were only slightly affected by the fluorescent tags, the sizes of the detected oligomeric species varied significantly depending on the chosen fluorophore. In particular, we relate the presence of high-molecular-weight oligomers of Aβ (1–40) (as found for the fluorophores HiLyte 647 and Atto 655) to net-attractive, hydrophobic fluorophore-peptide interactions, which are weak in the case of HiLyte 488 and Atto 488. The latter leads for Aβ (1–40) to low-molecular-weight oligomers only, which is in contrast to Aβ (1–42). The disease-relevant peptide Aβ (1–42) displays high-molecular-weight oligomers even in the absence of significant attractive fluorophore-peptide interactions. Hence, our findings reveal the potentially high impact of the properties of fluorophores on transient aggregates, which needs to be included in the interpretation of experimental data of oligomers of fluorescently labeled peptides.

Regulation of Aggregation of Self-Associated Peptides, Including N-Terminal Fragments of the Alzheimer’s β-Amyloid Peptide, by Nitro Derivatives of Azoloazine

The potential of the nitro compounds of the azoloazine class as regulators of aggregation of natural self-associating peptides was demonstrated by the example of fragments of the Alzheimer β-amyloid peptide and the melittin cytolytic peptide from bee venom. Depending on the type of an azoloazine derivative, association of a peptide into insoluble aggregates either occurred or was suppressed up to the peptide aggregates dissolution. The sites and stoichiometry of the azoloazine binding to the examined peptides are determined in the associates. These effects were explained by a unique ability of the azoloazine nitro derivatives to dissociate in aqueous solutions with the formation of a stable aromatic anion with electrostatic affinity to basic amino acid residues of the peptide molecules. This property of nitroazoloazines was used for a test of their ability to regulate the aggregation processes. Therefore, the nitro derivatives of azoloazines are promising inducers or inhibitors of the aggregation of the Alzheimer β-amyloid peptide and, possibly, other peptides which can form amyloid deposits.