Hisashi Okumura

Proteins can aggregate to form amyloid fibrils, which are associated with a group of diseases collectively known as amyloidoses. Molecular dynamics simulations are widely used to study protein aggregation; however, it remains computationally challenging to investigate the entire aggregation process, from initial nucleation to the formation of mature amyloid fibrils, within a single simulation. In this study, we propose a Monte Carlo simulation based on a mathematical lattice model in which proteins are represented as spheres on a lattice. Motivated by the role of intramolecular β-sheet structures in accelerating aggregation, we classify protein states into three categories: monomer, intermediate possessing an intramolecular β-sheet structure, and fibril. By tuning the monomer-to-intermediate transition probability PMI and the intermediate-to-fibril transition probability PIF, both kinetics and morphology of amyloid fibril formation can be systematically controlled. When PMI is low, a lag time appears in the early stage of aggregation, whereas increasing PMI shortens the lag time. High values of both PMI and PIF lead to rapid aggregation and the formation of many short fibrils, while low values result in slower aggregation and fewer but longer fibrils. These results are consistent with experimental observations and indicate that amyloid fibril formation can be understood as a crystal growth process. This approach is expected to provide further insight into the universal mechanisms of amyloid fibril formation in homogeneous aqueous environments, as well as in heterogeneous and nonequilibrium systems.

Molecular dynamics simulations of Amyloid-β (Aβ) peptides in water were conducted to calculate the free energy profiles of their dissociation in bulk water and at a hydrophobic interface, as well as their transfer from the bulk to the interface, in order to discuss the thermodynamic cycle of oligomerization. The air/water interface was introduced as a typical hydrophobic interface, and the free energy associated with the process in which two Aβ monomers associate to form a dimer in bulk water, either directly or via the interface, was analyzed. The results show that the Aβ₄₂ monomer is stabilized at the interface by 6.9 kcal/mol, while the dimer and trimer become progressively less stable at the interface. This indicates that a hydrophobic interface can serve as a catalytic reaction field for Aβ oligomerization. Additionally, the model dependence of Aβ (Aβ₄₂, Aβ₄₀, Aβ_17-42, Aβ_15-23) on the free energy profile from the bulk to the interface, as well as the orientational structures of the Aβ₄₂ monomer, dimer, and trimer near the interface, were also discussed.

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

Oligomers of amyloid-β (Aβ) peptides are related to Alzheimer’s disease, and their formation is accelerated at hydrophilic–hydrophobic interfaces. We performed all-atom molecular dynamics simulations of Aβ(29–42) peptides in bulk water and at an air–water interface. In bulk water, the fragments formed stable aggregates, and the secondary structures were hardly changed. At the interface, the peptides were more easily separated from each other due to the low free-energy barrier and changed their secondary structures more frequently. This conformational flexibility is likely to promote amyloid fibril growth, suggesting a key role of interfacial environments in early aggregation processes.

There are various flows inside and outside cells in vivo. Nonequilibrium molecular dynamics (NEMD) simulation is a useful tool for understanding the effects of these flows on the dynamics of biomolecules. We propose an NEMD method to generate a Poiseuille-like flow between lipid bilayers. We extended the conventional equilibrium MD method to produce a flow by adding constant external force terms to the water molecules. Using the Lagrange multiplier method, the center of mass of the lipid bilayer is constrained so that the flow does not sweep away the lipid bilayer, but the individual lipid molecules fluctuate. The temperature of the system is controlled properly in the solution and membrane by using the Nose-Hoover thermostat. We found that the flow velocity increases linearly as the applied external force term increases. It is possible to estimate the appropriate value of acceleration to generate a flow with an arbitrary velocity using this proportional relation once a single short MD simulation is performed. We also found that the flow between two lipid bilayers is slower than the analytical solution of the Navier-Stokes equations between rigid parallel plates due to the interactions between water molecules and the membrane. This method can be applied not only to a flow on lipid membranes but also to a flow on soft surfaces generally.

Understanding the dynamic assembly process of amyloid β (Aβ) during fibril formation is essential for developing effective therapeutic strategies against Alzheimer's disease. Here, we employed high-speed atomic force microscopy to observe the growth of Aβ fibrils at the single-molecule level, focusing specifically on their interaction with anti-Aβ antibodies. Our findings show that fibril growth consists of intermittent periods of elongation and pausing, which are dictated by the alternating addition of Aβ monomers to protofilaments. We highlight the distinctive interaction of antibody 4396C, which specifically binds to the fibril ends in the paused state, suggesting a unique mechanism to hinder fibril elongation. Through real-time visualization of fibril growth and antibody interactions combined with molecular simulation, this study provides a refined understanding of Aβ assembly during fibril formation and suggests novel strategies for Alzheimer's therapy aimed at inhibiting the fibril elongation.

Polyglutamine (polyQ) diseases are devastating neurodegenerative disorders characterized by abnormal expansion of glutamine repeats within specific proteins. The aggregation of polyQ proteins is a critical pathological hallmark of these diseases. Arginine was identified as a promising inhibitory compound because it prevents polyQ-protein monomers from forming intra- and intermolecular β-sheet structures and hinders polyQ proteins from aggregating to form oligomers. Such an aggregation inhibitory effect was not observed in other amino acids. However, the underlying molecular mechanism of the aggregation inhibition and the factors that differentiate arginine from other amino acids, in terms of the inhibition of the polyQ-protein aggregation, remain poorly understood. Here, we performed replica-permutation molecular dynamics simulations to elucidate the molecular mechanism by which arginine inhibits the formation of the intramolecular β-sheet structure of a polyQ monomer. We found that the intramolecular β-sheet structure with more than four β-bridges of the polyQ monomer with arginine is more unstable than without any ligand and with lysine. We also found that arginine has 1.6-2.1 times more contact with polyQ than lysine. In addition, we revealed that arginine forms more hydrogen bonds with the main chain of the polyQ monomer than lysine. More hydrogen bonds formed between arginine and polyQ inhibit polyQ from forming the long intramolecular β-sheet structure. It is known that intramolecular β-sheet structure enhances intermolecular β-sheet structure between proteins. These effects are thought to be the reason for the inhibition of polyQ aggregation. This study provides insights into the molecular events underlying arginine's inhibition of polyQ-protein aggregation.

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.

Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not been explored, the dissociation of polyA aggregates likely reduces the cytotoxicity of polyA. Mid-infrared free electron laser (FEL) successfully dissociated multiple aggregates. However, whether the FEL dissociates polyA aggregates like other aggregates has not been tested. Here, we show that FEL at 6.1 μm experimentally weakened the extent of aggregation of a peptide with 13 alanine repeats (13A), and the irradiated 13A exerted lesser cytotoxicity to neuron-like cells than non-irradiated 13A. Then, we applied molecular dynamics (MD) simulation to follow the dissociation process by FEL. We successfully observed how the intermolecular β-sheet of polyA aggregates was dissociated and separated into monomers with helix structures upon FEL irradiation. After the dissociation by FEL, water molecules inhibited the reformation of polyA aggregates. We recently verified the same dissociation process using FEL-treated amyloid-β aggregates. Thus, a common mechanism underlies the dissociation of different protein aggregates that cause different diseases, polyA disease and Alzheimer’s disease. However, MD simulation indicated that polyA aggregates are less easily dissociated than amyloid-β aggregates and require longer laser irradiation due to hydrophobic alanine repeats.