Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study

Perspective for Molecular Dynamics Simulation Studies of Amyloid-β Aggregates

The cause of Alzheimer's disease is related to aggregates such as oligomers and amyloid fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies have been conducted to understand the molecular mechanism of the formation and disruption of Aβ aggregates. In this Perspective, the MD simulation studies are classified into four categories, focusing on the target systems: aggregation of Aβ peptides in bulk solution, Aβ aggregation at the interface, aggregation inhibitor against Aβ peptides, and nonequilibrium MD simulation of Aβ aggregates. MD simulation studies in these categories are first reviewed. Future perspectives in each category are then presented. Finally, the overall perspective is presented on how MD simulations of Aβ aggregates can be utilized for developing Alzheimer's disease treatment.

Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease

The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.

Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease

The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.

Evolution of large Aβ16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aβ16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences.

Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers

Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.

Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics

The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ_13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ_13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.

Self-Assembly of Amyloid-Beta (Aβ) Peptides from Solution to Near In Vivo Conditions

Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is important to develop compounds or conditions to alter the aggregation pathways and suppress the toxicity and potentially aid in the development of drugs. However, the complexity of protein aggregation and the transient order/disorder of oligomers along the pathways to fibril are very challenging. In this Perspective, we discuss computational studies of amyloid polypeptides carried out under various conditions, including conditions closely mimicking in vivo and point out the challenges in obtaining physiologically relevant results, focusing mainly on the amyloid-beta Aβ peptides.

Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity

Amyloid β-peptide (Aβ) misfolding into β-sheet structures triggers neurotoxicity inducing Alzheimer’s disease (AD). Molecules able to reduce or to impair Aβ aggregation are highly relevant as possible AD treatments since they should protect against Aβ neurotoxicity. We have studied the effects of the interaction of dynorphins, a family of opioid neuropeptides, with Aβ₄₀ the most abundant species of Aβ. Biophysical measurements indicate that Aβ₄₀ interacts with Big Dynorphin (BigDyn), lowering the amount of hydrophobic aggregates, and slowing down the aggregation kinetics. As expected, we found that BigDyn protects against Aβ₄₀ aggregates when studied in human neuroblastoma cells by cell survival assays. The cross-interaction between BigDyn and Aβ₄₀ provides insight into the mechanism of amyloid pathophysiology and may open up new therapy possibilities.

Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity

The amyloid cascade hypothesis states that senile plaques, composed of amyloid β (Aβ) fibrils, play a key role in Alzheimer’s disease (AD). However, recent experiments have shown that Aβ oligomers are more toxic to neurons than highly ordered fibrils. The molecular mechanism underlying this observation remains largely unknown. One of the possible scenarios for neurotoxicity is that Aβ peptides create pores in the lipid membrane that allow Ca²⁺ ions to enter cells, resulting in a signal of cell apoptosis. Hence, one might think that oligomers are more toxic due to their higher ability to create ion channels than fibrils. In this work, we study the effect of Aβ42 dodecamer and fibrils on a neuronal membrane, which is similar to that observed in AD patients, using all-atom molecular dynamics simulations. Due to short simulation times, we cannot observe the formation of pores, but useful insight on the early events of this process has been obtained. Namely, we showed that dodecamer distorts the lipid membrane to a greater extent than fibrils, which may indicate that ion channels can be more easily formed in the presence of oligomers. Based on this result, we anticipate that oligomers are more toxic than mature fibrils, as observed experimentally. Moreover, the Aβ–membrane interaction was found to be governed by the repulsive electrostatic interaction between Aβ and the ganglioside GM1 lipid. We calculated the bending and compressibility modulus of the membrane in the absence of Aβ and obtained good agreement with the experiment. We predict that the dodecamer will increase the compressibility modulus but has little effect on the bending modulus. Due to the weak interaction with the membrane, fibrils insignificantly change the membrane elastic properties.

The role of the half-turn in determining structures of Alzheimer's Aβ wild-type and mutants

Half-turns are shown to be the main determinants of many experimental Alzheimer's Aβ fibril structures. Fibril structures contain three half-turn types, βα_Rβ, βα_Lβ and βεβ which each result in a ∼90° bend in a β-strand. It is shown that only these half-turns enable cross-β stacking and thus the right-angle fold seen in fibrils is an intrinsic feature of cross-β. Encoding a strand as a conformational sequence in β, α_R, α_L and ε(β_L), pairwise combination rules for consecutive half-turns are used to decode this sequence to give the backbone path. This reveals how structures would be dramatically affected by a deletion. Using a wild-type Aβ(42) fibril structure and the pairwise combination rules, the Osaka deletion is predicted to result in exposure of surfaces that are mutually shielding from the solvent. Molecular dynamics simulations on an 11-mer β-sheet of Alzheimer's Aβ(40) of the Dutch (E22Q), Iowa (D23N), Arctic (E22G), and Osaka (E22Δ) mutants, show the crucial role glycine plays in the positioning of βα_Rβ half-turns. Their "in-phase" positions along the sequence in the wild-type, Dutch mutant and Iowa mutant means that the half-folds all fold to the same side creating the same closed structure. Their out-of-phase positions in Arctic and Osaka mutants creates a flatter structure in the former and an S-shape structure in the latter which, as predicted, exposes surfaces on the inside in the closed wild-type to the outside. This is consistent with the gain of interaction model and indicates how domain swapping might explain the Osaka mutant's unique properties.

Kinetic and thermodynamic stability comparison for the fibrillar form of small amyloid-β(1-42) oligomers using scaled molecular dynamics

Amyloid-β (Aβ) oligomers act as intermediates for several neurodegenerative disease-relevant fibril formations. However, gaining insight into the oligomer to fibril conversion process remains a challenge due to the transient nature of small Aβ. In this study, we probe the kinetic and thermodynamic stabilities of small Aβ(1-42) oligomers in fibrillar conformations to understand from what size these aggregates start forming stable fibrils. With no definite structures available for small Aβ42 aggregates, we have started with oligomers extracted from mature fibrils having four, five, six and nine chains stacked together, and have performed order-to-disorder transition on these systems. Using scaled molecular dynamics (sMD) simulation, the timescale for breaking the native contacts of fibrils has been compared. The results indicate that the kinetic stability of oligomers increases with size, especially at the C-terminus end beyond five-chain oligomers. The free energy of breaking the contacts at the β-sheet regions in the structures has been obtained on an unscaled potential from a free energy extrapolation (FEE) approach. The values show that although stable minima are obtained for larger oligomers due to the enhanced stability of the C-terminus ends, fully stable fibril formation may require aggregates larger than the ones considered in our study. Additionally, dissimilar kinetics for the unbinding of terminal chains across all the oligomers has been observed. The interaction energy values calculated from unscaled MD simulations reveal the crucial role of water in our observations. Our work provides the application of an easy-to-deploy method that sheds light on interactions which could be significant in the early stages of Aβ42 fibril formation.

Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations

Alzheimer's disease (AD) is a neurodegenerative disorder and one of the main causes of dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming initial clusters and then fibril structure and plaques. Other neurodegenerative diseases such as type 2 diabetes, amyotrophic lateral sclerosis, and Parkinson's disease follow a similar mechanism. Therefore, inhibition of Aβ aggregation is considered an effective way to prevent AD. Recent experiments have provided evidence that oligomers are more toxic agents than mature fibrils, prompting researchers to investigate various factors that may influence their properties. One of these factors is nanomechanical stability, which plays an important role in the self-assembly of Aβ and possibly other proteins. This stability is also likely to be related to cell toxicity. In this work, we compare the mechanical stability of Aβ-tetramers and fibrillar structures using a structure-based coarse-grained (CG) approach and all-atom molecular dynamics simulation. Our results support the evidence for an increase in mechanical stability during the Aβ fibrillization process, which is consistent with in vitro AFM characterization of Aβ42 oligomers. Namely, using a CG model, we showed that the Young modulus of tetramers is lower than that of fibrils and, as follows from the experiment, is about 1 GPa. Hydrogen bonds are the dominant contribution to the detachment of one chain from the Aβ fibril fragment. They tend to be more organized along the pulling direction, whereas in the Aβ tetramers no preference is observed.