Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations

Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation

β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer's (AD), Parkinson's (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif accessible to amyloidogenic proteins in their monomeric and oligomeric states. Here, to investigate implications of β-hairpins in amyloid formation, potential β-hairpin-forming amyloidogenic segments in the human proteome were predicted based on sequence similarity with β-hairpins previously observed in Aβ, α-synuclein, and islet amyloid polypeptide, amyloidogenic proteins associated with AD, PD, and T2D, respectively. These three β-hairpins, established upon binding to the engineered binding protein β-wrapin AS10, are characterized by proximity of two sequence segments rich in hydrophobic and aromatic amino acids, with high β-aggregation scores according to the TANGO algorithm. Using these criteria, 2505 potential β-hairpin-forming amyloidogenic segments in 2098 human proteins were identified. Characterization of a test set of eight protein segments showed that seven assembled into Thioflavin T-positive aggregates and four formed β-hairpins in complex with AS10 according to NMR. One of those is a segment of prostatic acid phosphatase (PAP) comprising amino acids 185-208. PAP is naturally cleaved into fragments, including PAP(248-286) which forms functional amyloid in semen. We find that PAP(185-208) strongly decreases the protein concentrations required for fibril formation of PAP(248-286) and of another semen amyloid peptide, SEM1(86-107), indicating that it promotes nucleation of semen amyloids. In conclusion, β-hairpin-forming amyloidogenic protein segments could be identified in the human proteome with potential roles in functional or disease-related amyloid formation.

A turn for the worse: Aβ β-hairpins in Alzheimer's disease

Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.

Protein Corona Formation and Aggregation of Amyloid β 1-40-Coated Gold Nanocolloids

Amyloid fibrillogenesis is a pathogenic protein aggregation process that occurs through a highly ordered process of protein-protein interactions. To better understand the protein-protein interactions involved in amyloid fibril formation, we formed nanogold colloid aggregates by stepwise additions of ∼2 nmol of amyloid β 1-40 peptide (Aβ1-40) at pH ∼3.7 and ∼25 °C. The processes of protein corona formation and building of gold colloid [diameters (d) of 20 and 80 nm] aggregates were confirmed by a red-shift of the surface plasmon resonance (SPR) band, λpeak, as the number of Aβ1-40 peptides [N(Aβ1-40)] increased. The normalized red-shift of λpeak, Δλ, was correlated with the degree of protein aggregation, and this process was approximated as the adsorption isotherm explained by the Langmuir-Freundlich model. As the coverage fraction (θ) was analyzed as a function of ϕ, which is the N(Aβ1-40) per total surface area of nanogold colloids available for adsorption, the parameters for explaining the Langmuir-Freundlich model were in good agreement for both 20 and 80 nm gold, indicating that ϕ could define the stage of the aggregation process. Surface-enhanced Raman scattering (SERS) imaging was conducted at designated values of ϕ and suggested that a protein-gold surface interaction during the initial adsorption stage may be dependent on the nanosize. The 20 nm gold case seems to prefer a relatively smaller contacting section, such as a -C-N or C═C bond, but a plane of the benzene ring may play a significant role for 80 nm gold. Regardless of the size of the particles, the β-sheet and random coil conformations were considered to be used to form gold colloid aggregates. The methodology developed in this study allows for new insights into protein-protein interactions at distinct stages of aggregation.

Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains

Heterologous interactions between different amyloid-forming proteins, also called cross-interactions, may have a critical impact on disease-related amyloid formation. β-hairpin conformers of amyloid-forming proteins have been shown to affect homologous interactions in the amyloid self-assembly process. Here, we applied two β-hairpin-forming peptides derived from immunoglobulin light chains as models to test how heterologous β-hairpins modulate the fibril formation of Parkinson's disease-associated protein α-synuclein (αSyn). The peptides SMAhp and LENhp comprise β-strands C and C' of the κ4 antibodies SMA and LEN, which are associated with light chain amyloidosis and multiple myeloma, respectively. SMAhp and LENhp bind with high affinity to the β-hairpin-binding protein β-wrapin AS10 according to isothermal titration calorimetry and NMR spectroscopy. The addition of SMAhp and LENhp affects the kinetics of αSyn aggregation monitored by Thioflavin T (ThT) fluorescence, with the effect depending on assay conditions, salt concentration, and the applied β-hairpin peptide. In the absence of agitation, substoichiometric concentrations of the hairpin peptides strongly reduce the lag time of αSyn aggregation, suggesting that they support the nucleation of αSyn amyloid fibrils. The effect is also observed for the aggregation of αSyn fragments lacking the N-terminus or the C-terminus, indicating that the promotion of nucleation involves the interaction of hairpin peptides with the hydrophobic non-amyloid-β component (NAC) region.

Insights into the Mixture of Aβ24 and Aβ42 Peptides from Atomistic Simulations

Amyloid-β (Aβ) oligomers play a central role in Alzheimer's disease (AD). Plaques of AD patients consist of Aβ40 and Aβ42 peptides and truncated Aβ peptides. The Aβ24 peptide, identified in human AD brains, was found to impair Aβ42 clearance through the brain-blood barrier. The Aβ24 peptide was also shown to reduce Aβ42 aggregation kinetics in pure buffer, but the underlying mechanism is unknown at atomistic level. In this study, we explored the conformational ensemble of the equimolar mixture of Aβ24 and Aβ42 by replica exchange molecular dynamics simulations and compared it to our previous results on the pure Aβ42 dimer. Our simulations demonstrate that the truncation at residue 24 changes the secondary, tertiary, and quaternary structures of the dimer, offering an explanation of the slower aggregation kinetics of the mixture.

Suppression of amyloid-β fibril growth by drug-engineered polymorph transformation

Fibrillization of the protein amyloid β is assumed to trigger Alzheimer's pathology. Approaches that target amyloid plaques, however, have garnered limited clinical success, and their failures may relate to the scarce understanding of the impact of potential drugs on the intertwined stages of fibrillization. Here, we demonstrate that bexarotene, a T-cell lymphoma medication with known antiamyloid activity both in vitro and in vivo, suppresses amyloid fibrillization by promoting an alternative fibril structure. We employ time-resolved in situ atomic force microscopy to quantify the kinetics of growth of individual fibrils and supplement it with structure characterization by cryo-EM. We show that fibrils with structure engineered by the drug nucleate and grow substantially slower than "normal" fibrils; remarkably, growth remains stunted even in drug-free solutions. We find that the suppression of fibril growth by bexarotene is not because of the drug binding to the fibril tips or to the peptides in the solution. Kinetic analyses attribute the slow growth of drug-enforced fibril polymorph to the distinctive dynamics of peptide chain association to their tips. As an additional benefit, the bexarotene fibrils kill primary rat hippocampal neurons less efficiently than normal fibrils. In conclusion, the suggested drug-driven polymorph transformation presents a mode of action to irreversibly suppress toxic aggregates not only in Alzheimer's but also potentially in myriad diverse pathologies that originate with protein condensation.

Key Residue for Aggregation of Amyloid-β Peptides

It is known that oligomers of amyloid-β (Aβ) peptide are associated with Alzheimer's disease. Aβ has two isoforms: Aβ40 and Aβ42. Although the difference between Aβ40 and Aβ42 is only two additional C-terminal residues, Aβ42 aggregates much faster than Aβ40. It is unknown what role the C-terminal two residues play in accelerating aggregation. Since Aβ42 is more toxic than Aβ40, its oligomerization process needs to be clarified. Moreover, clarifying the differences between the oligomerization processes of Aβ40 and Aβ42 is essential to elucidate the key factors of oligomerization. Therefore, to investigate the dimerization process, which is the early oligomerization process, Hamiltonian replica-permutation molecular dynamics simulations were performed for Aβ40 and Aβ42. We identified a key residue, Arg5, for the Aβ42 dimerization. The two additional residues in Aβ42 allow the C-terminus to form contact with Arg5 because of the electrostatic attraction between them, and this contact stabilizes the β-hairpin. This β-hairpin promotes dimer formation through the intermolecular β-bridges. Thus, we examined the effects of amino acid substitutions of Arg5, thereby confirming that the mutations remarkably suppressed the aggregation of Aβ42. Moreover, the mutations of Arg5 suppressed the Aβ40 aggregation. It was found by analyzing the simulations that Arg5 is important for Aβ40 to form intermolecular contacts. Thus, it was clarified that the role of Arg5 in the oligomerization process varies due to the two additional C-terminal residues.

Monitoring early-stage β-amyloid dimer aggregation by histidine site-specific two-dimensional infrared spectroscopy in a simulation study

Monitoring early-stage β-amyloid (Aβ) dimerization is a formidable challenge for understanding neurological diseases. We compared β-sheet formation and histidine site-specific two-dimensional infrared (2D IR) spectroscopic signatures of Aβ dimers with different histidine states (δ; N^δ1-H, ε; N^ε2-H, or π; both protonated). Molecular dynamics (MD) simulations revealed that β-sheet formation is favored for the δδδ:δδδ and πππ:πππ tautomeric isomers showing strong couplings and frequent contacts between the central hydrophobic core and C-terminus compared with the εεε:εεε isomer. Characteristic blue-shifts in the 2D IR central bands were observed upon monomer-dimer transformation. The εεε:εεε dimer exhibited larger frequency shifts than δδδ:δδδ and πππ:πππ implying that the red-shift may have a correlation with N^δ1-H(δ) protonation. Our results support the tautomerization/protonation hypothesis that attributes Aβ misfolding to histidine tautomers as a possible primary initiator for Aβ aggregation and facilitates the application of histidine site-specific 2D IR spectroscopy for studying early-stage Aβ self-assembly.

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.

Effect of Surface-Chelated Cu2+ on Amyloid-β Peptide Fibrillation

Abnormal interactions of copper (Cu) ions with amyloid-β (Aβ) peptides are believed to play an important role in the pathogenesis of Alzheimer's disease (AD). However, there is still debate as to the exact role of Cu ions in Aβ amyloidosis despite extensive studies on Aβ-Cu interactions. Unlike previously reported works, we herein study the effect of surface-chelated Cu²⁺, rather than the more usual solution-phase dissolved Cu²⁺, on Aβ aggregation. Through the combination of single molecule fluorescent tracking, atomic force microscopy imaging experiments, and all-atom molecular dynamic simulations, we show that the surface-chelated Cu²⁺ dynamically interacts with Aβ chains, restricts their 2D-diffusivity on the surface, and retards their fibrillation, while the designated surfaces without Cu²⁺ facilitate the 2D-diffusivity of Aβ chains for better interpeptide interaction and promote Aβ fibrillation. We offer a microscopic molecular insight into the retardation mechanism of surface-chelated Cu²⁺ on Aβ fibrillation, suggesting that the surface-bound pools of metal ions are critical in AD progression and drug design.

Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.

Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations

Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.

Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils

Amyloid fibrillization is an exceedingly complex process in which incoming peptide chains bind to the fibril while concertedly folding. The coupling between folding and binding is not fully understood. We explore the molecular pathways of association of Aβ40 monomers to fibril tips by combining time-resolved in situ scanning probe microscopy with molecular modeling. The comparison between experimental and simulation results shows that a complex supported by nonnative contacts is present in the equilibrium structure of the fibril tip and impedes fibril growth in a supersaturated solution. The unraveling of this frustrated state determines the rate of fibril growth. The kinetics of growth of freshly cut fibrils, in which the bulk fibril structure persists at the tip, complemented by molecular simulations, indicate that this frustrated complex comprises three or four monomers in nonnative conformations and likely is contained on the top of a single stack of peptide chains in the fibril structure. This pathway of fibril growth strongly deviates from the common view that the conformational transformation of each captured peptide chain is templated by the previously arrived peptide. The insights into the ensemble structure of the frustrated complex may guide the search for suppressors of Aβ fibrillization. The uncovered dynamics of coupled structuring and assembly during fibril growth are more complex than during the folding of most globular proteins, as they involve the collective motions of several peptide chains that are not guided by a funneled energy landscape.

Energy landscapes of protein aggregation and conformation switching in intrinsically disordered proteins

The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of 'simple' protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.

The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β

Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.

Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations

Water plays a crucial role in the formation and destruction of biomolecular structures. The mechanism for destroying biomolecular structures was thought to be an active breaking of hydrogen bonds by water molecules. However, using nonequilibrium molecular dynamics simulations, in which an amyloid-β amyloid fibril was destroyed via infrared free-electron laser (IR-FEL) irradiation, we discovered a new mechanism, in which water molecules disrupt protein aggregates. The intermolecular hydrogen bonds formed by C═O and N-H in the fibril are broken at each pulse of laser irradiation. These bonds spontaneously re-form after the irradiation in many cases. However, when a water molecule happens to enter the gap between C═O and N-H, it inhibits the re-formation of the hydrogen bonds. Such sites become defects in the regularly aligned hydrogen bonds, from which all hydrogen bonds in the intermolecular β-sheet are broken as the fraying spreads. This role of water molecules is entirely different from other known mechanisms. This new mechanism can explain the recent experiments showing that the amyloid fibrils are not destroyed by laser irradiation under dry conditions. Additionally, we found that helix structures form more after the amyloid disruption; this is because the resonance frequency is different in a helix structure. Our findings provide a theoretical basis for the application of IR-FEL to the future treatment of amyloidosis.

Impact of the Rat R5G, Y10F, and H13R Mutations on Tetrameric Aβ42 β-Barrel in a Lipid Bilayer Membrane Model

Three amino acid substitutions distinguish rat and human Aβ42 peptides and contribute to the difference in toxicity properties. Indeed, aged rodents rarely develop the characteristic lesions of Alzheimer's disease in contrast to humans. Both peptides form, however, amyloid fibrils in buffer solution, but their affinities to the membrane vary. In particular, there is experimental evidence that the rat Aβ42 peptide does not induce Ca²⁺ fluxes in cells. We recently designed a tetrameric β-barrel structure and showed that this model is severely destabilized for Aβ40 human compared to its Aβ42 human counterpart, explaining the absence of ionic currents of Aβ40 in planar lipid bilayers. In this study, we asked whether our model is destabilized for the rat Aβ42 peptide by using extensive replica exchange molecular dynamics simulation in a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer membrane. Our results show that the much lower propensity of aged rodents to develop Alzheimer's disease symptoms might be correlated to its tetrameric β-barrel stability in the cell membrane.

Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations

Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST₁₄) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ₄₂ aggregates. Furthermore, SST₁₄’s presence was also found to promote the formation of toxic Aβ₄₂ oligomers in vitro. In order to elucidate how SST₁₄ influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ₄₂ or Aβ₄₀ peptides with SST₁₄ molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ₄₂ in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ₄₂–SST₁₄, Aβ₄₂–AVP, and Aβ₄₀–SST₁₄. The Aβ₄₂–SST₁₄ mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST₁₄ or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST₁₄ was found to impede aggregation in the Aβ₄₂–SST₁₄ system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ₄₂–SST₁₄ oligomerization.

Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST₁₄), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST₁₄ might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.

Cholesterol Molecules Alter the Energy Landscape of Small Aβ1-42 Oligomers

Small amyloid-β (Aβ) oligomers are believed to be key pathogenic species in Alzheimer's disease (AD). One suggested toxicity mechanism is the detergent model where oligomers remove lipid molecules from the bilayer. Senile plaques of AD patients also accumulate a 1:1 ratio of cholesterol/Aβ. What are the dominant structures of small Aβ42 oligomers with cholesterol molecules in aqueous solution? Here, we answer this question by performing atomistic replica exchange molecular dynamics simulations of Aβ42 dimers and trimers. Our simulations demonstrate that the interactions with cholesterol molecules change completely the energy landscape of small Aβ42 oligomers. This result shows that simulations in the bulk solution cannot recapitulate aggregation in the brain extracellular space.

Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation

Aggregates and fibrils of intrinsically disordered α-synuclein are associated with Parkinson's disease. Within a non-amyloid β component (NAC) spanning from the 61st to the 95th residue of α-synuclein, an 11-residue segment called NACore (₆₈GAVVTGVTAVA₇₈) is an essential region for both fibril formation and cytotoxicity. Although NACore peptides alone are known to form aggregates and amyloid fibrils, the mechanisms of aggregation and fibrillation remain unknown. This study investigated the dimerization process of NACore peptides as the initial stage of the aggregation and fibrillation processes. We performed an isothermal-isobaric replica-permutation molecular dynamics simulation, which is one of the efficient sampling methods, for the two NACore peptides in explicit water over 96 μs. The simulation succeeded in sampling a variety of dimer structures. An analysis of secondary structure revealed that most of the NACore dimers form intermolecular β-bridges. In particular, more antiparallel β-bridges were observed than parallel β-bridges. We also found that intramolecular secondary structures such as α-helix and antiparallel β-bridge are stabilized in the pre-dimer state. However, we identified that the intermolecular β-bridges tend to form directly between residues with no specific structure rather than via the intramolecular β-bridges. This is because the NACore peptides still have a low propensity to form the intramolecular secondary structures even though they are stabilized in the pre-dimer state.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer’s disease. Their aggregation is enhanced at hydrophilic–hydrophobic interfaces, such as a cell membrane surface and air-water interface, and is inhibited by polyphenols, such as myricetin and rosmarinic acid. We review molecular dynamics (MD) simulation approaches of a full-length Aβ peptide, Aβ40, and Aβ(16–22) fragments in these environments. Since these peptides have both hydrophilic and hydrophobic amino acid residues, they tend to exist at the interfaces. The high concentration of the peptides accelerates the aggregation there. In addition, Aβ40 forms a β-hairpin structure, and this structure accelerates the aggregation. We also describe the inhibition mechanism of the Aβ(16–22) aggregation by polyphenols. The aggregation of Aβ(16–22) fragments is caused mainly by the electrostatic attraction between charged amino acid residues known as Lys16 and Glu22. Since polyphenols form hydrogen bonds between their hydroxy and carboxyl groups and these charged amino acid residues, they inhibit the aggregation.

β-Turn exchanges in the α-synuclein segment 44-TKEG-47 reveal high sequence fidelity requirements of amyloid fibril elongation

The folding of turns and β-hairpins has been implicated in amyloid formation, with diverse potential consequences such as promotion or inhibition of fibril nucleation, fibril elongation, or off-pathway oligomer formation. In the Parkinson's disease-associated protein α-synuclein (αS), a β-hairpin comprised of residues 36-56 was detected in complex with an engineered binding protein, with a turn formed by the αS sequence segment 44-TKEG-47. Molecular dynamics simulations revealed extensive populations of transient β-hairpin conformations in this region in free, monomeric αS. Here, we investigated potential effects of turn formation on αS fibril formation by studying the aggregation kinetics of an extensive set of αS variants with between two and four amino acid exchanges in the 44-TKEG-47 segment. The exchanges were chosen to specifically promote formation of β1-, β1'-, or β2'-turns. All variants assembled into amyloid fibrils, with increased β1'- or β2'-turn propensity associated with faster aggregation and increased β1-turn propensity with slower aggregation compared to wild-type (WT) αS. Atomic force microscopy demonstrated that β-turn exchanges altered fibril morphology. In cross-elongation experiments, the turn variants showed a low ability to elongate WT fibril seeds, and, vice versa, WT monomer did not efficiently elongate turn variant fibril seeds. This demonstrates that sequence identity in the turn region is crucial for efficient αS fibril elongation. Elongation experiments of WT fibril seeds in the presence of both WT and turn variant monomers suggest that the turn variants can bind and block WT fibril ends to different degrees, but cannot efficiently convert into the WT fibril structure. Our results indicate that modifications in the 44-TKEG-47 segment strongly affect amyloid assembly by driving αS into alternative fibril morphologies, whose elongation requires high sequence fidelity.

The F19W mutation reduces the binding affinity of the transmembrane Aβ11-40 trimer to the membrane bilayer

Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.

αB-Crystallin Chaperone Inhibits Aβ Aggregation by Capping the β-Sheet-Rich Oligomers and Fibrils

Inhibiting the cytotoxicity of amyloid aggregation by endogenous proteins is a promising strategy against degenerative amyloid diseases due to their intrinsically high biocompatibility and low immunogenicity. In this study, we investigated the inhibition mechanism of the structured core region of αB-crystallin (αBC) against Aβ fibrillization using discrete molecular dynamics simulations. Our computational results recapitulated the experimentally observed Aβ binding sites in αBC and suggested that αBC could bind to various Aβ aggregate species during the aggregation process-including monomers, dimers, and likely other high molecular weight oligomers, protofibrils, and fibrils-by capping the exposed β-sheet elongation surfaces. Thus, the nucleation of Aβ oligomers into fibrils and the fibril growth could be inhibited. Mechanistic insights obtained from our systematic computational studies may aid in the development of novel therapeutic strategies to modulate the aggregation of pathological, amyloidogenic protein in degenerative diseases.

Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations

Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ and tau proteins, and the α-synuclein protein, key players in Alzheimer's and Parkinson's diseases, respectively are fully disordered at the monomer level. The structural heterogeneity of the monomeric and oligomeric states and the high self-assembly propensity of these three IDPs have precluded experimental structural determination. Simulations have been used to determine the atomic structures of these IDPs. In this article, we review recent computer models to capture the equilibrium ensemble of Aβ, tau and α-synuclein proteins at different association steps in aqueous solution and present new results of the PEP-FOLD framework on α-synuclein monomer.

Tau R3-R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations

In Alzheimer's disease, neurofibrillary lesions correlate with cognitive deficits and consist of inclusions of tau protein with cross-β structure. A stable dimeric form of soluble tau has been evidenced in the cells, but its high-resolution structure is missing in solution. We know, however, that cryo-electron microscopy (c-EM) of full-length tau in the brain of an individual with AD displays a core of eight β-sheets with a C-shaped architecture spanning the R3-R4 repeat domain, while the rest of the protein is very flexible. To address the conformational ensemble of the dimer, we performed atomistic replica exchange molecular dynamics simulations on the tau R3-R4 domain starting from the c-EM configuration. We find that the wild type tau R3-R4 dimer explores elongated, U-shaped, V-shaped, and globular forms rather than the C-shape. Phosphorylation of Ser356, pSer356, is known to block the interaction between the tau protein and the amyloid-β42 peptide. Standard molecular dynamics simulations of this phosphorylated sequence for a total of 5 μs compared to its wild type counterpart show a modulation of the population of β-helices and accessible topologies and a decrease of intermediates near the fibril-like conformers.

Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide

There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ_11-40 trimer from the U-shape conformation and MD simulations starting from Aβ_1-40 dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ₄₀ oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ₄₀ peptide.

Symmetry-breaking transitions in the early steps of protein self-assembly

Protein misfolding and subsequent self-association are complex, intertwined processes, resulting in development of a heterogeneous population of aggregates closely related to many chronic pathological conditions including Type 2 Diabetes Mellitus and Alzheimer's disease. To address this issue, here, we develop a theoretical model in the general framework of linear stability analysis. According to this model, self-assemblies of peptides with pronounced conformational flexibility may become, under particular conditions, unstable and spontaneously evolve toward an alternating array of partially ordered and disordered monomers. The predictions of the theory were verified by atomistic molecular dynamics (MD) simulations of islet amyloid polypeptide (IAPP) used as a paradigm of aggregation-prone polypeptides (proteins). Simulations of dimeric, tetrameric, and hexameric human-IAPP self-assemblies at physiological electrolyte concentration reveal an alternating distribution of the smallest domains (of the order of the peptide mean length) formed by partially ordered (mainly β-strands) and disordered (turns and coil) arrays. Periodicity disappears upon weakening of the inter-peptide binding, a result in line with the predictions of the theory. To further probe the general validity of our hypothesis, we extended the simulations to other peptides, the Aβ(1-40) amyloid peptide, and the ovine prion peptide as well as to other proteins (SOD1 dimer) that do not belong to the broad class of intrinsically disordered proteins. In all cases, the oligomeric aggregates show an alternate distribution of partially ordered and disordered monomers. We also carried out Surface Enhanced Raman Scattering (SERS) measurements of hIAPP as an experimental validation of both the theory and in silico simulations.

Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation

The aggregation of the amyloid (Aβ) peptide of 39-43 amino acids into plaques is observed in the brain of Alzheimer's disease (AD) patients, but the mechanisms underlying the neurotoxicity of Aβ oligomers are still elusive. One suggested initial mechanism is related to the implications of amyloid membrane interactions, but characterization of these assemblies is challenging by experimental means. In this study, we have explored the stability of a trimer of Aβ11-40 in parallel and antiparallel β-sheet structures for the wild-type sequence and its F20W mutant in a dipalmitoylphosphatidylcholine membrane using atomistic replica exchange molecular dynamic simulations. We show that both the U-shape organization and the assembly of β-hairpins are maintained in the membrane and are resistant to the mutation F20W. In contrast the models are destabilized by the F19P mutation. Overall, our results indicate that these two assemblies represent minimal seeds or nuclei for the formation of either amyloid fibrils, a variety of β-barrel pores, or various aggregates for many Aβ sequences in a membrane-mimicking environment.

Combining molecular dynamics simulations and experimental analyses in protein misfolding

The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.

Aggregation of disease-related peptides

Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.

Distinct Primary Nucleation of Polymorphic Aβ Dimers Yields to Distinguished Fibrillation Pathways

Polymorphic Aβ dimers are the smallest toxic species that play a role in the pathology of Alzheimer's disease. There is great interest in understanding the malfunctions that yield to these toxic species and in providing insights into the molecular mechanisms of the primary nucleation. Herein, we present a first work that demonstrates two distant edges states of Aβ dimers. The first is the so-called "random coil" state dimer that mimics the primary seeding/nucleation that is far from a fibrillation state. The second is the "fibril-like" state dimer that is structurally in close proximity to the fibril, a well-organized state into a fibril-like structure. We show for the first time that a conformational change of one monomer within the dimer impedes primary nucleation, while less fluctuations and relatively large number of interactions in nucleation domains induce the primary nucleation to produce toxic stable species. Overall, the current study exhibits a diversity of primary nucleation in each dimer state, suggesting distinct molecular mechanisms of fibril formation. The conformations of the early stage Aβ dimers that were achieved may provide crucial data for designing inhibitors to impede the primary nucleation.

Spontaneous self-assembly of amyloid β (1-40) into dimers

The self-assembly and fibrillation of amyloid β (Aβ) proteins is the neuropathological hallmark of Alzheimer's disease. However, the molecular mechanism of how disordered monomers assemble into aggregates remains largely unknown. In this work, we characterize the assembly of Aβ (1-40) monomers into dimers using long-time molecular dynamics simulations. Upon interaction, the monomers undergo conformational transitions, accompanied by change of the structure, leading to the formation of a stable dimer. The dimers are stabilized by interactions in the N-terminal region (residues 5-12), in the central hydrophobic region (residues 16-23), and in the C-terminal region (residues 30-40); with inter-peptide interactions focused around the N- and C-termini. The dimers do not contain long β-strands that are usually found in fibrils.

Binary Structure of Amyloid Beta Oligomers Revealed by Dual Recognition Mapping

Amyloid beta (Aβ) oligomers are widely considered to be the causative agent of Alzheimer's disease (AD), a progressive neurodegenerative disorder. Determining the structure of oligomers is, therefore, important for understanding the disease and developing therapeutic agents; however, elucidating the structure has been proven difficult due to heterogeneity, noncrystallinity, and variability. Herein, we investigated homo- and hetero-oligomers of Aβ40 and Aβ42 using atomic force microscopy (AFM) and revealed characteristics of the molecular structure. By examining the surface of individual oligomers with sequential N- and C-terminus specific antibody-tethered tips, we simultaneously mapped the N- and C-terminus distributions and the elastic modulus. Interestingly, both the N- and C-termini of Aβ peptides were recognized on the oligomer surface, and the termini detected pixel regions exhibited a lower elastic modulus than silent pixel regions. These two types of regions were randomly distributed on the oligomer surface.

Role of hydrophobic residues for the gaseous formation of helical motifs

The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid-β (1-40) dimer (2Aβ). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving 19FFAED23, consistent with infrared spectroscopy data on an Aβ segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains "shield" helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.

Ordered and Disordered Segments of Amyloid-β Drive Sequential Steps of the Toxic Pathway

While the roles of intrinsically disordered protein domains in driving interprotein interactions are increasingly well-appreciated, the mechanism of toxicity of disease-causing disordered proteins remains poorly understood. A prime example is Alzheimer's disease (AD) associated amyloid beta (Aβ). Aβ oligomers are highly toxic partially structured peptide assemblies with a distinct ordered region (residues ∼10-40) and a shorter disordered region (residues ∼1-9). Here, we investigate the role of this disordered domain and its relation to the ordered domain in the manifestation of toxicity through a set of Aβ fragments and stereoisomers designed for this purpose. We measure their effects on lipid membranes and cultured neurons, probing their toxicity, intracellular distributions, and specific molecular interactions using the techniques of confocal imaging, lattice light sheet imaging, fluorescence lifetime imaging, and fluorescence correlation spectroscopy. Remarkably, we find that neither part-Aβ_10-40 or Aβ_1-9, is toxic by itself. The ordered part (Aβ_10-40) is the major determinant of how Aβ attaches to lipid bilayers, enters neuronal cells, and localizes primarily in the late endosomal compartments. However, once Aβ enters the cell, it is the disordered part (only when it is connected to the rest of the peptide) that has a strong and stereospecific interaction with an unknown cellular component, as demonstrated by distinct changes in the fluorescence lifetime of a fluorophore attached to the N-terminal. This interaction appears to commit Aβ to the toxic pathway. Our findings correlate well with Aβ sites of familial AD mutations, a significant fraction of which cluster in the disordered region. We conclude that, while the ordered region dictates attachment and cellular entry, the key to toxicity lies in the ordered part presenting the disordered part for a specific cellular interaction.

Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids

The omega-3 and omega-6 polyunsaturated fatty acids are two important components of cell membranes in human brains. When incorporated into phospholipids, omega-3 slows the progression of Alzheimer's disease (AD), whereas omega-6 is linked to increased risk of AD. Little is known on the amyloid-β (Aβ) conformations in membranes rich in omega-3 and omega-6 phospholipids. Herein, the structural properties of the Aβ_29-42 dimer embedded in both fatty acid membranes were comparatively studied to a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) bilayer using all-atom molecular dynamics (MD) simulations. Starting from α-helix, both omega-6 and omega-3 membranes promote new orientations and conformations of the dimer, in agreement with the observed dependence of Aβ production upon addition of these two fatty acids. This conformational result is corroborated by atomistic MD simulations of the dimer of the 99 amino acid C-terminal fragment of amyloid precursor protein spanning the residues 15-55. Starting from β-sheet, omega-6 membrane promotes helical and disordered structures of Aβ_29-42 dimer, whereas omega-3 membrane preserves the β-sheet structures differing however from those observed in POPC. Remarkably, the mixture of the two fatty acids and POPC depicts another conformational ensemble of the Aβ_29-42 dimer. This finding demonstrates that variation in the abundance of the molecular phospholipids, which changes with age, modulates membrane-embedded Aβ oligomerization.

Looking at the Disordered Proteins through the Computational Microscope

Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.

Molecular simulation aspects of amyloid peptides at membrane interface

The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.

Pathways of Amyloid-β Aggregation Depend on Oligomer Shape

One of the main research topics related to Alzheimer's disease is the aggregation of the amyloid-β peptide, which was shown to follow different pathways for the two major alloforms of the peptide, Aβ40 and the more toxic Aβ42. Experimental studies emphasized that oligomers of specific sizes appear in the early aggregation process in different quantities and might be the key toxic agents for each of the two alloforms. We use transition networks derived from all-atom molecular dynamics simulations to show that the oligomers leading to the type of oligomer distributions observed in experiments originate from compact conformations. Extended oligomers, on the other hand, contribute more to the production of larger aggregates thus driving the aggregation process. We further demonstrate that differences in the aggregation pathways of the two Aβ alloforms occur as early as during the dimer stage. The higher solvent-exposure of hydrophobic residues in Aβ42 oligomers contributes to the different aggregation pathways of both alloforms and also to the increased cytotoxicity of Aβ42.