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

Alpha-synuclein phosphorylation induces amyloid conversion via enhanced electrostatic bridging: Insights from molecular modeling of the full-length protein

Fibril formation from alpha-synuclein is a key point in Parkinson's disease, multiple system atrophy, and other synucleinopathies. The mechanism of the amyloid-like conversion followed by the formation of pre-fibrillar soluble oligomers and fibrils is not completely clear; furthermore, it is unclear how the Parkinson's disease-related point mutations located in the pre-NAC region enhance fibrillation. In the present paper, atomistic replica exchange molecular dynamics simulations of the full-length alpha-synuclein and its two mutants, A53T and E46K, elucidated amyloid conversion intermediates. Both mutants demonstrated an enhanced tendency for the conversion but in different manners; the main intermediate conformations populated in the WT alpha-synuclein conformational ensemble disappeared due to mutations, indicating a different conversion pathway. Analysis of the preferable beta-hairpin positions and intermediate conformations seems to reflect a tendency to form a particular amyloid fibril polymorph. A strong elevation of amyloid transformation level was shown also for Ser129-phosphorylated alpha-synuclein. Altered intermediate conformations, the most preferable beta-hairpin positions in the NAC region, and prevalent salt bridges propose the formation of so-called polymorph 2 or even a novel type of fibrils. A better understanding of the detailed mechanism of the amyloid conversion sheds light on the effect of Lewy body-related phosphorylation and might help in the development of new therapeutics for synucleinopathies.

Structure specific neuro-toxicity of α-synuclein oligomer

Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.

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.

Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time

The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins.

Transmembrane β-Barrel Models of α-Synuclein Oligomers

The aggregation of α-synuclein is implicated in a number of neurodegenerative diseases, such as Parkinson's and Multiple System Atrophy, but the role of these aggregates in disease development is not clear. One possible mechanism of cytotoxicity is the disturbance or permeabilization of cell membranes by certain types of oligomers. However, no high-resolution structure of such membrane-embedded complexes has ever been determined. Here we construct and evaluate putative transmembrane β-barrels formed by this protein. Examination of the α-synuclein sequence reveals two regions that could form membrane-embedded β-hairpins: 64-92 (the NAC), and 35-56, which harbors many familial Parkinson's mutations. The stability of β-barrels formed by these hairpins is examined first in implicit membrane pores and then by multimicrosecond all-atom simulations. We find that a NAC region barrel remains stably inserted and hydrated for at least 10 μs. A 35-56 barrel remains stably inserted in the membrane but dehydrates and collapses if all His50 are neutral or if His50 is replaced by Q. If half of the His50 are doubly protonated, the barrel takes an oval shape but remains hydrated for at least 10 μs. Possible implications of these findings for α-synuclein pathology are discussed.

Exploring the Curvature-Dependence of Boron Nitride Nanoparticles on the Inhibition of hIAPP Aggregation

Nanoparticles, particularly carbon nanoparticles, have gathered significant interest in the field of anti-aggregation research. However, due to their cytotoxicity, the exploration of biocompatible nanoparticles has become a new frontier in the quest for drugs against human amyloid diseases. The application of non-cytotoxic and biocompatible boron nitride (BN) nanoparticles against amyloid aggregation has been probed to tackle this issue. BN nanoparticles displayed inhibitory activity against the aggregation of Aβ and α-syn peptides. In this work, the effect of BN nanoparticles on the dimerization of hIAPP, which is associated with the pathogenesis of type 2 diabetes, is studied. BN nanoparticles prevent the misfolding of hIAPP into β-sheet-rich aggregates. On varying the curvature, the nanoparticles display variation in the interaction preference with hIAPP. Interestingly, as the hydrophobicity of the nanoparticles increases from (5,5) BN nanotube to BN nanosheet, the interaction propensity shifts from N-terminal to the amyloid prone C-terminal of hIAPP. The hydrophobic and aromatic stacking interactions are a contributing factor toward the binding between hIAPP and BN. Due to this, the flat surface of the nanosheet shows better interaction potential toward hIAPP, compared to the nanotubes. Further, the nanoparticles can also disassemble preformed hIAPP fibrils, and the effect is more pronounced for (5,5) nanotube and the nanosheet. This study provides insight into the inhibitory mechanism of hIAPP aggregation by boron nitride nanoparticles and also an understanding of the significance of the curvature of nanoparticles in their interaction with amyloid peptides, which is valuable for the design of antiamyloid drugs.

The Role of Protein-L-isoaspartyl Methyltransferase (PIMT) in the Suppression of Toxicity of the Oligomeric Form of Aβ42, in Addition to the Inhibition of Its Fibrillization

The oligomeric form of amyloid-β peptide (Aβ42) plays a crucial role in the pathogenesis of Alzheimer's disease (AD) and is responsible for cognitive deficits. The soluble oligomers are believed to be more toxic compared to the fibril form. Protein-L-isoaspartyl methyltransferase (PIMT) is a repair enzyme that converts aberrant isoAsp residues, formed spontaneously on isomerization of normal Asp and Asn residues, back to typical Asp. It was shown to inhibit the fibrillization of Aβ42 (containing three Asp residues), and here, we investigate its effect on the size, conformation, and toxicity of Aβ42 oligomers (AβO). Far-UV CD indicated a shift in the conformational feature of AβOs from the random coil to β-sheet in the presence of PIMT. Binding of bis-ANS to different AβOs (obtained using different concentrations of Aβ42 monomer) indicated the correlation of size of oligomers to hydrophobicity: the smallest AβO having the highest hydrophobicity is the most toxic. Dynamic light scattering showed an increase in size of AβO with the addition of PIMT, a contrasting role to that on Aβ fibril. Assays using PC12-derived neurons showed the neuroprotective role of PIMT against AβO-induced toxicity. Furthermore, we have elaborated on the molecular mechanism of the antifibrillar action of PIMT and how this function is correlated with its enzymatic activity. PIMT has a more pronounced effect on AβO as compared to a small heat shock protein, pointing to its importance for the amelioration of the adverse effect of both Aβ42 oligomers and fibrils.

Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations

As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.

Unveiling the impact of oxidation-driven endogenous protein interactions on the dynamics of amyloid-β aggregation and toxicity

Cytochrome c (Cyt c), a multifunctional protein with a crucial role in controlling cell fate, has been implicated in the amyloid pathology associated with Alzheimer's disease (AD); however, the interaction between Cyt c and amyloid-β (Aβ) with the consequent impact on the aggregation and toxicity of Aβ is not known. Here we report that Cyt c can directly bind to Aβ and alter the aggregation and toxicity profiles of Aβ in a manner that is dependent on the presence of a peroxide. When combined with hydrogen peroxide (H₂O₂), Cyt c redirects Aβ peptides into less toxic, off-pathway amorphous aggregates, whereas without H₂O₂, it promotes Aβ fibrillization. The mechanisms behind these effects may involve a combination of the complexation between Cyt c and Aβ, the oxidation of Aβ by Cyt c and H₂O₂, and the modification of Cyt c by H₂O₂. Our findings demonstrate a new function of Cyt c as a modulator against Aβ amyloidogenesis.

Effect of Cosolutes on the Aggregation of a Tau Fragment: A Combined Experimental and Simulation Approach

The intrinsically disordered protein Tau represents the main component of neurofibrillary tangles that are a hallmark of Alzheimer's disease. A small fragment of Tau, known as paired helical filament 6 (PHF6), is considered to be important for the formation of the β-structure core of the fibrils. Here we study the aggregation of this fragment in the presence of different cosolutes, including urea, TMAO, sucrose and 2-hydroxypropyl-β-cyclodextrin (2-HPβCD), using both experiments and molecular dynamics simulations. A novel implicit solvation approach (MIST - Model with Implicit Solvation Thermodynamics) is used, where an energetic contribution based on the concept of transfer free energies describes the effect of the cosolutes. The simulation predictions are compared to thioflavin-T and atomic force microscopy results, and the good agreement observed confirms the predictive ability of the computational approach herein proposed. Both simulations and experiments indicate that PHF6 aggregation is inhibited in the presence of urea and 2-HPβCD, while TMAO and sucrose stabilize associated conformations. The remarkable ability of HPβCD to inhibit aggregation represents an extremely promising result for future applications, especially considering the widespread use of this molecule as a drug carrier to the brain and as a solubilizer/excipient in pharmaceutical formulations.

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.

Differential Binding and Conformational Dynamics of Tau Microtubule-Binding Repeats with a Preformed Amyloid-β Fibril Seed

Both senile plaques formed by amyloid-β (Aβ) and neurofibrillary tangles (NFTs) comprised of tau are pathological hallmarks of Alzheimer's disease (AD). The accumulation of NFTs better correlates with the loss of cognitive function than senile plaques, but NFTs are rarely observed without the presence of senile plaques. Hence, cross-seeding of tau by preformed Aβ amyloid fibril seeds has been proposed to drive the aggregation of tau and exacerbate AD progression, but the molecular mechanism remains unknown. Here, we first identified cross-interaction hotspots between Aβ and tau using atomistic discrete molecular dynamics simulations (DMD) and confirmed the critical role of the four microtubule-binding repeats of tau (R1-R4) in the cross-interaction with Aβ. We further investigated the binding structure and dynamics of each tau repeat with a preformed Aβ fibril seed. Specifically, R1 and R3 preferred to bind the Aβ fibril lateral surface instead of the elongation end. In contrast, R2 and R4 had higher binding propensities to the fibril elongation end than the lateral surface, enhancing β-sheet content by forming hydrogen bonds with the exposed hydrogen bond donors and acceptors. Together, our results suggest that the four repeats play distinct roles in driving the binding of tau to different surfaces of an Aβ fibril seed. Binding of tau to the lateral surface of Aβ fibril can increase the local concentration, while the binding to the elongation surface promotes β-sheet formation, both of which reduce the free energy barrier for tau aggregation nucleation and subsequent fibrillization.

Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling

Treatment for Alzheimer's disease (AD) can be more effective in the early stages. Although we do not completely understand the aetiology of the early stages of AD, potential pathological factors (amyloid beta [Aβ] and tau) and other co-factors have been identified as causes of AD, which may indicate some of the mechanism at work in the early stages of AD. Today, one of the primary techniques used to help delay or prevent AD in the early stages involves alleviating the unwanted effects of oxidative stress on Aβ clearance. 4-Hydroxynonenal (HNE), a product of lipid peroxidation caused by oxidative stress, plays a key role in the adduction of the degrading proteases. This HNE employs a mechanism which decreases catalytic activity. This process ultimately impairs Aβ clearance. The degradation of HNE-modified proteins helps to alleviate the unwanted effects of oxidative stress. Having a clear understanding of the mechanisms associated with the degradation of the HNE-modified proteins is essential for the development of strategies and for alleviating the unwanted effects of oxidative stress. The strategies which could be employed to decrease the effects of oxidative stress include enhancing antioxidant activity, as well as the use of nanozymes and/or specific inhibitors. One area which shows promise in reducing oxidative stress is protein design. However, more research is needed to improve the effectiveness and accuracy of this technique. This paper discusses the interplay of potential pathological factors and AD. In particular, it focuses on the effect of oxidative stress on the expression of the Aβ-degrading proteases through adduction of the degrading proteases caused by HNE. The paper also elucidates other strategies that can be used to alleviate the unwanted effects of oxidative stress on Aβ clearance. To improve the effectiveness and accuracy of protein design, we explain the application of quantum mechanical/molecular mechanical approach.

An S-Shaped Aβ42 Cross-β Hexamer Embedded into a Lipid Bilayer Reveals Membrane Disruption and Permeability

The interactions of amyloid oligomers with membranes are known to contribute to cellular toxicity. Numerous in vitro experimental studies reported on the insertion of oligomers of different sizes that can induce cell membrane disruption, extract lipids, and form ion-permeable transmembrane pores. The current repertoire of amyloid-beta (Aβ) membrane-inserted folds that was subject to high-resolution structure NMR spectroscopy and computer simulations is devoid of any cross-β fibrillar structure. In this study, we explored the dynamics of an S-shaped Aβ42 cross-β hexamer model inserted into a lipid bilayer membrane by two atomistic molecular dynamics simulations. The initial model is characterized by the hydrophobic residues at the central hydrophobic core (residues 17-21, CHC) and the C-terminus (residues 30-42) embedded into the membrane. We observed major structural secondary, tertiary, and quaternary rearrangements leading to two distinct species, hexamer and two trimers, accompanied by membrane disruption and water permeation. The simulations show that some configurations, but not the majority, have the CHC and C-terminus hydrophobic residues exposed to the solvent. Overall, our computational results offer new perspectives to understand the relationship between Aβ42 assemblies and membrane permeability.

Differential effects of DTT on HEWL amyloid fibrillation and fibril morphology at different pH

Proteins can transform from their native state to a state having fibrillar aggregates characterized by cross β sheet structure. The fibrillar aggregates are known as amyloid and have been linked to several disorders. Disulfide bonds in proteins are one of the important factors that determine the propensity of aggregation. Hen Egg White Lysozyme (HEWL) was used by us as a model protein to decipher the role disulfide bonds play in the amyloid fibril formation and fibril morphology by using Dithiothreitol (DTT) as reducing agent at pH 2.7 and pH 7.4. We found that DTT can have different effects on HEWL amyloid depending on pH and the buffer used for preparing the amyloid fibrils. Our studies highlight the critical role of non-native disulfide bonds in amyloidogenesis and how disruption of these bonds can greatly affect the fibrillation process. Overall, these studies throw light on the fibrillation mechanism and can be explored further in designing effective inhibitors against amyloidosis.

Recent Advances in Molecular Dynamics Simulations of Tau Fibrils and Oligomers

The study of tau protein aggregation and interactions with other molecules or solvents using molecular dynamics simulations (MDs) is of interest to many researchers to propose new mechanism-based therapeutics for neurodegenerative diseases such as Alzheimer's disease, Pick's disease, chronic traumatic encephalopathy, and other tauopathies. In this review, we present recent MD simulation studies of tau oligomers and fibrils such as tau-NPK, tau-PHF, tau-K18, and tau-R3-R4 monomers and dimers. All-atom simulations by replica exchange MDs and coarse-grained MDs in lipid bilayers and in solution were used. The simulations revealed different mechanisms in the binding of tau in bilayers and in solutions, depending on the peptide size. Phosphorylation is also an important factor in MD simulations. The use of steered MDs was also included to simulate the dissociation of tau fibrils. The exponential improvement in the computing power of computers has led to an increasing number of scientists and engineers using a cost-effective, high-performance computing platform to study how the tau protein interacts and the effects of changing its structure, such as the phosphorylation of tau fibrils.

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

How Cu(II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations

We report accelerated molecular dynamics simulations of α-Synuclein and its complex with two Cu(II) ions bound to experimentally determined binding sites. Adding two Cu(II) ions, one bound to the N-terminal region and one to the C-terminus, decreases size and flexibility of the peptide while introducing significant new contacts within and between N-terminus and non-Aβ component (NAC). Cu(II) ions also alter the pattern of secondary structure within the peptide, inducing more and longer-lasting elements of secondary structure such as β-strands and hairpins. Free energy surfaces, obtained from reweighting the accelerated molecular dynamics boost potential, further demonstrate the restriction on size and flexibility that results from binding of copper ions.

New Insights into the Structural and Binding Properties on Aβ Mature Fibrils Due to Histidine Protonation Behaviors

Histidine tautomeric behaviors have been considered origin factors for controlling the structure and aggregation properties of misfolding peptides. Except for tautomeric behaviors, histidine protonation behaviors definitely have the same capacities due to the net charge changes and the various N/N-H orientations on imidazole rings. However, such phenomena are still unknown. In the current study, Aβ mature fibrils substituted with various protonation states were performed by molecular dynamics simulations to investigate the structure and binding properties. Our results show that all kinds of protonation states can increase the ΔG1 stability and decrease ΔG2 and ΔG3 stabilities. A significantly higher averaged β-sheet content was detected in (εεp), (εpp), and (ppp) fibrils in one, two, and three protonation stages, respectively. Impressively, we found that the substituted fibril with specific protonated states can control the N-terminus structural properties. Further analysis confirmed that H6 and H13 are more important than H14 since the H-bond donor and receptor cooperate among C1/C3/C8_H6, C1/C3/C8_H13, and C1/C3/C8_E11. Furthermore, the mechanism of protonation behaviors was discussed. The current study is helpful for understanding the histidine protonation behaviors on one, two, and three protonation stages, which provides new horizons for exploring the origin of protein folding and misfolding.

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution

Introduction: Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.

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.

Modeling structural interconversion in Alzheimers' amyloid beta peptide with classical and intrinsically disordered protein force fields

A comprehensive understanding of the aggregation mechanism in amyloid beta 42 (Aβ42) peptide is imperative for developing therapeutic drugs to prevent or treat Alzheimer's disease. Because of the high flexibility and lack of native tertiary structures of Aβ42, molecular dynamics (MD) simulations may help elucidate the peptide's dynamics with atomic details and collectively improve ensembles not seen in experiments. We applied microsecond-timescale MD simulations to investigate the dynamics and conformational changes of Aβ42 by using a newly developed Amber force field (ff14IDPSFF). We compared the ff14IDPSFF and the regular ff14SB force field by examining the conformational changes of two distinct Aβ42 monomers in explicit solvent. Conformational ensembles obtained by simulations depend on the force field and initial structure, Aβ42^α-helix or Aβ42^β-strand. The ff14IDPSFF sampled a high ratio of disordered structures and diverse β-strand secondary structures; in contrast, ff14SB favored helicity during the Aβ42^α-helix simulations. The conformations obtained from Aβ42^β-strand simulations maintained a balanced content in the disordered and helical structures when simulated by ff14SB, but the conformers clearly favored disordered and β-sheet structures simulated by ff14IDPSFF. The results obtained with ff14IDPSFF qualitatively reproduced the NMR chemical shifts well. In-depth peptide and cluster analysis revealed some characteristic features that may be linked to early onset of the fibril-like structure. The C-terminal region (mainly M35-V40) featured in-registered anti-parallel β-strand (β-hairpin) conformations with tested systems. Our work should expand the knowledge of force field and structure dependency in MD simulations and reveals the underlying structural mechanism-function relationship in Aβ42 peptides. Communicated by Ramaswamy H. Sarma.

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.

Curcumin Interacts with α-Synuclein Condensates To Inhibit Amyloid Aggregation under Phase Separation

The amyloid aggregation of α-synuclein (α-Syn) is highly associated with Parkinson's disease (PD). Discovering α-Syn amyloid inhibitors is one of the strategies for PD therapies. Recent studies suggested that α-Syn undergoes phase separation to accelerate amyloid aggregation. Molecules modulating α-Syn phase separation or transition have the potential to regulate amyloid aggregation. Here, we discovered that curcumin, a small natural molecule, interacts with α-Syn during phase separation. Our study showed that curcumin neither affects the formation of α-Syn condensates nor influences the initial morphology of α-Syn condensates. However, curcumin decreases the fluidity of α-Syn inside the condensates and efficiently inhibits α-Syn from turning into an amyloid. It also inhibits the amyloid aggregations of PD disease-related α-Syn E46K and H50Q mutants under phase separation. Furthermore, curcumin can destabilize preformed α-Syn amyloid aggregates in the condensates. Together, our findings demonstrate that curcumin regulates α-Syn amyloid formation during protein phase separation and reveal that α-Syn amyloid aggregation under phase separation can be modulated by small molecules.

Impact of A2T and D23N mutations on C99 homodimer conformations

The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.

Molecular Dynamics Simulations of the Tau Amyloid Fibril Core Dimer at the Surface of a Lipid Bilayer Model: I. In Alzheimer's Disease

A tau R3-R4 domain spanning residues 306-378 was shown to form an amyloid fibril core of a full-length tau in the brain of patients with Alzheimer's disease. Recently, we studied the dynamics of a tau R3-R4 monomer at the surface of a lipid bilayer model and revealed deep insertion of the amino acids spanning the PHF6 motif (residues 306-311) and its flanking residues. Here, we explore the membrane-associated conformational ensemble of a tau R3-R4 dimer by means of atomistic molecular dynamics. Similar to the monomer simulation, the R3-R4 dimer has the propensity to form β-hairpin-like conformation. Unlike the monomer, the dimer shows insertion of the C-terminal R4 region and transient adsorption of the PHF6 motif. Taken together, these results reveal the multiplicity of adsorption and insertion modes of tau into membranes depending on its oligomer size.

Inhibition Mechanisms of (-)-Epigallocatechin-3-gallate and Genistein on Amyloid-beta 42 Peptide of Alzheimer's Disease via Molecular Simulations

The misfolding and self-assembly of amyloid-beta (Aβ) peptides are one of the most important factors contributing to Alzheimer's disease (AD). This study aims to reveal the inhibition mechanisms of (-)-epigallocatechin-3-gallate (EGCG) and genistein on the conformational changes of Aβ42 peptides by using molecular docking and molecular dynamics (MD) simulation. The results indicate that both EGCG and genistein have inhibitory effects on the conformational transition of Aβ42 peptide. EGCG and genistein reduce the ratio of β-sheet secondary structures of Aβ42 peptide while inducing random coil structures. In terms of hydrophobic interactions in the central hydrophobic core of Aβ42 peptide, the binding affinities of EGCG are significantly larger in comparison with that of genistein. Our findings illustrate the inhibition mechanisms of EGCG and genistein on the Aβ42 peptides and prove that EGCG is a very promising inhibitor in impeding the conformational change of Aβ42 peptide.

Single-Particle Resolution of Copper-Associated Annular α-Synuclein Oligomers Reveals Potential Therapeutic Targets of Neurodegeneration

Metal ions stabilize protein–protein interactions and can modulate protein aggregation. Here, using liquid-based atomic force microscopy and molecular dynamics simulations, we study the concentration-dependent effect of Cu²⁺ ions on the aggregation pathway of α-synuclein (α-Syn) proteins, which play a key role in the pathology of Parkinson’s disease. The full spectrum of α-Syn aggregates in the presence and absence of Cu²⁺ ions from monomers to mature fibrils was resolved and quantified at the gold–water interface. Raman spectroscopy confirmed the atomic force microscopy (AFM) findings on the heterogeneity in aggregated states of α-Syn. The formation of annular oligomers was exclusively detected upon incubating α-Syn with Cu²⁺ ions. Our findings emphasize the importance of targeting annular α-Syn protein oligomers for therapeutic intervention and their potential role as biomarkers for early detection and monitoring progression of neurodegeneration.

α-Synuclein phase separation and amyloid aggregation are modulated by C-terminal truncations

The aggregation of α-synuclein (α-Syn) is a key pathological hallmark of Parkinson's disease (PD). α-Syn undergoes liquid-liquid phase separation (LLPS) to drive amyloid aggregation. How the LLPS of α-Syn is regulated remains largely unknown. Here, we discovered that the C-terminal region modulates α-Syn phase separation through electrostatic interactions. The wild-type (WT) and PD disease-related truncated α-Syn can co-exist in the condensates. The truncated α-Syn could dramatically promote WT α-Syn phase separation. Further studies demonstrated that the truncated α-Syn accelerated WT α-Syn turning to amyloid aggregates by modulation of phase separation. Together, our findings disclose the role of the C-terminal domain in the LLPS of α-Syn and pave the path for understanding the mechanism of truncated α-Syn in PD pathology.

Molecular Dynamics Simulations of the Tau R3-R4 Domain Monomer in the Bulk Solution and at the Surface of a Lipid Bilayer Model

The aggregation of the tau protein plays a significant role in Alzheimer's disease, and the tau R3-R4 domain spanning residues 306-378 was shown to form the amyloid fibril core of a full-length tau. The conformations of the tau R3-R4 monomer in the bulk solution and at the surface of membranes are unknown. In this study, we address these questions by means of atomistic molecular dynamics. The simulations in the bulk solution show a very heterogeneous ensemble of conformations with low β and helical contents. The tau R3-R4 monomer has the propensity to form transient β-hairpins within the R3 repeat and between the R3 and R4 repeats and parallel β-sheets spanning the R3 and R4 repeats. The simulations also show that the surface of the membrane does not induce β-sheet insertion and leads to an ensemble of structures very different from those in the bulk solution. They also reveal the dynamical properties of the membrane-bound state of the tau R3-R4 monomer, enabling insertion of the residues 306-318 and 376-378.

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.

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

We propose the replica permutation with solute tempering (RPST) by combining the replica-permutation method (RPM) and the replica exchange with solute tempering (REST). Temperature permutations are performed among more than two replicas in RPM, whereas temperature exchanges are performed between two replicas in the replica-exchange method (REM). The temperature transition in RPM occurs more efficiently than in REM. In REST, only the temperatures of the solute region, the solute temperatures, are exchanged to reduce the number of replicas compared to REM. Therefore, RPST is expected to be an improved method taking advantage of these methods. For comparison, we applied RPST, REST, RPM, and REM to two amyloid-β(16–22) peptides in explicit water. We calculated the transition ratio and the number of tunneling events in the temperature space and the number of dimerization events of amyloid-β(16–22) peptides. The results indicate that, in RPST, the number of replicas necessary for frequent random walks in the temperature and conformational spaces is reduced compared to the other three methods. In addition, we focused on the dimerization process of amyloid-β(16–22) peptides. The RPST simulation with a relatively small number of replicas shows that the two amyloid-β(16–22) peptides form the intermolecular antiparallel β-bridges due to the hydrophilic side-chain contact between Lys and Glu and hydrophobic side-chain contact between Leu, Val, and Phe, which stabilizes the dimer of the peptides.

Calcium promotes α-synuclein liquid-liquid phase separation to accelerate amyloid aggregation

α-Synuclein (α-Syn) is an aggregation-prone protein whose accumulation in Lewy bodies leads to neurodegenerative diseases like Parkinson's disease (PD). Calcium plays a critical role in neurons, and calcium dysregulation is one of the risk factors of PD. It is known that Ca²⁺ interacts with α-Syn and affects its assembly. However, how Ca²⁺ regulates α-Syn aggregation remains unclear. Here, we reported that Ca²⁺ accelerates α-Syn amyloid aggregation through the modulation of protein phase separation. We observed that Ca²⁺ promotes the formation of α-Syn liquid droplets but does not change the protein fluidity inside the droplets. Further studies showed Ca²⁺-involved α-Syn droplets are still able to fuse. A metal chelator eliminated Ca²⁺-induced enlargement of α-Syn droplets, suggesting the influence of Ca²⁺ on α-Syn assembly could be reversed at the stage of liquid-liquid phase separation (LLPS). Interestingly, our data showed Ca²⁺ still promoted α-Syn phase separation in the presence of the lipid membranes. In addition, Ca²⁺/α-syn droplets could efficiently recruit lipid vesicles to the surface of these condensates. Our findings demonstrate that Ca²⁺ facilitates α-Syn phase separation to accelerate amyloid aggregation and pave the path for understanding the implications of Ca²⁺ in α-Syn accumulation and PD.

Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers

Alzheimer’s disease displays aggregates of the amyloid-beta (Aβ) peptide in the brain, and there is increasing evidence that cholesterol may contribute to the pathogenesis of the disease. Though many experimental and theoretical studies have focused on the interactions of Aβ oligomers with membrane models containing cholesterol, an understanding of the effect of free cholesterol on small Aβ42 oligomers is not fully established. To address this question, we report on replica exchange with a solute tempering simulation of an Aβ42 trimer with cholesterol and compare it with a previous replica exchange molecular dynamics simulation. We show that the binding hot spots of cholesterol are rather complex, involving hydrophobic residues L17–F20 and L30–M35 with a non-negligible contribution of loop residues D22–K28 and N-terminus residues. We also examine the effects of cholesterol on the trimers of the disease-causing A21G and disease-protective A2T mutations by molecular dynamics simulations. We show that these two mutations moderately impact cholesterol-binding modes. In our REST2 simulations, we find that cholesterol is rarely inserted into aggregates but rather attached as dimers and trimers at the surface of Aβ42 oligomers. We propose that cholesterol acts as a glue to speed up the formation of larger aggregates; this provides a mechanistic link between cholesterol and Alzheimer’s disease.

Structure optimization of the toxic conformation model of amyloid β42 by intramolecular disulfide bond formation

Amyloid β (Aβ) oligomers play a critical role in the pathology of Alzheimer's disease. Recently, we reported that a conformation-restricted Aβ42 with an intramolecular disulfide bond through cysteine residues at positions 17/28 formed stable oligomers with potent cytotoxicity. To further optimize this compound as a toxic conformer model, we synthesized three analogs with a combination of cysteine  and homocysteine at positions 17/28.  The analogs with Cys-Cys, Cys-homoCys, or homoCys-Cys, but not the homoCys-homoCys analog, exhibited potent cytotoxicity against SH-SY5Y and THP-1 cells even  at 10 nM. In contrast, the cytotoxicity of conformation-restricted analogs at positions 16/29 or 18/27 was significantly weaker than that of wild-type Aβ42. Furthermore, a thioflavin-T assay, non-denaturing gel electrophoresis, and morphological study suggested that the majority of these conformation-restricted analogs existed in an oligomeric state in cell culture medium, indicating that the toxic conformation of Aβ42, rather than the oligomeric state, is essential to induce cytotoxicity.

Insights into the Interactions that Trigger the Primary Nucleation of Polymorphic α-Synuclein Dimers

Parkinson's disease is associated with the accumulation of α-synuclein (AS) aggregates that include polymorphic AS oligomers and polymorphic fibrils. There have been advances in solving the polymorphic state of AS fibrils, both by experimental techniques and molecular modeling tools. Yet, the polymorphic AS oligomers are now considered as the neurotoxic species, thus current and future studies making efforts to solve their structures at the molecular level. Importantly, it is crucial to explore the specific interactions between AS monomers within the dimer that stabilize the dimer and yield nucleation. Herein, we present a first work that probes at the molecular level the specific interactions between monomers in polymorphic AS dimers are derived from AS fibrils by applying molecular modeling tools. Our work reveals that both N-terminal and the non-amyloidogenic component domains play a role in the dimerization of all polymorphic AS dimers. In addition, helices along the N-terminal of AS monomers impede the contacts between AS monomers, thus preventing the nucleation or the dimerization of AS. This work provides insights into several mechanisms of the production of polymorphic AS dimers. Thus, the findings obtained in this work may assist in developing new therapeutic strategies for inhibiting the formation of the early-stage neurotoxic AS dimers.

Disordered regions tune order in chromatin organization and function

Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.

Anatomy and Formation Mechanisms of Early Amyloid-β Oligomers with Lateral Branching: Graph Network Analysis on Large-Scale Simulations

Oligomeric amyloid-β aggregates (AβOs) effectively trigger Alzheimer's disease-related toxicity, generating great interest in understanding their structures and formation mechanisms. However, AβOs are heterogeneous and transient, making their structure and formation difficult to study. Here, we performed graph network analysis of tens of microsecond massive simulations of early amyloid-β (Aβ) aggregations at near-atomic resolution to characterize AβO structures with sizes up to 20-mers. We found that AβOs exhibit highly curvilinear, irregular shapes with occasional lateral branches, consistent with recent cryo-electron tomography experiments. We also found that Aβ40 oligomers were more likely to develop branches than Aβ42 oligomers, explaining an experimental observation that only Aβ40 was trapped in network-like aggregates and exhibited slower fibrillization kinetics. Moreover, AβO architecture dissection revealed that their curvilinear appearance is related to the local packing geometries of neighboring peptides and that Aβ40's greater branching ability originates from specific C-terminal interactions at branching interfaces. Finally, we demonstrate that whether Aβ oligomerization causes oligomers to elongate or to branch depends on the sizes and shapes of colliding aggregates. Collectively, this study provides bottom-up structural information for understanding early Aβ aggregation and AβO toxicity.

Graph network analysis on large-scale simulations uncovers the differential branching behaviours of large Aβ40 and Aβ42 oligomers.

Dynamic protein structures in normal function and pathologic misfolding in systemic amyloidosis

Dynamic and disordered regions in native proteins are often critical for their function, particularly in ligand binding and signaling. In certain proteins, however, such regions can contribute to misfolding and pathologic deposition as amyloid fibrils in vivo. For example, dynamic and disordered regions can promote amyloid formation by destabilizing the native structure, by directly triggering the aggregation, by promoting protein condensation, or by acting as sites of early proteolytic cleavage that favor a release of aggregation-prone fragments or facilitate fibril maturation. At the same time, enhanced dynamics in the native protein state accelerates proteolytic degradation that counteracts amyloid accumulation in vivo. Therefore, the functional need for dynamic protein regions must be balanced against their inherently labile nature. How exactly this balance is achieved and how is it shifted upon amyloidogenic mutations or post-translational modifications? To illustrate possible scenarios, here we review the beneficial and pathologic roles of dynamic and disordered regions in the native states of three families of human plasma proteins that form amyloid precursors in systemic amyloidoses: immunoglobulin light chain, apolipoproteins, and serum amyloid A. Analysis of structure, stability and local dynamics of these diverse proteins and their amyloidogenic variants exemplifies how disordered/dynamic regions can provide a functional advantage as well as an Achilles heel in pathologic amyloid formation.

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.

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis

Cytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neurotoxic species causing neuronal cell death. However, understanding the structural and molecular insights of these oligomers are very challenging due to the heterogeneity and transient nature of the species. In this review, we discuss the recent advancements in understanding the formation and role of α-Syn oligomers in PD pathogenesis. We also summarize the different types of α-Syn oligomeric species and potential mechanisms to exert neurotoxicity. Finally, we address the possible ways to target α-Syn as a promising approach against PD and the possible future directions.

Manganese promotes α-synuclein amyloid aggregation through the induction of protein phase transition

α-Synuclein (α-Syn) is the major protein component of Lewy bodies, a key pathological feature of Parkinson’s disease (PD). The manganese ion Mn²⁺ has been identified as an environmental risk factor of PD. However, it remains unclear how Mn²⁺ regulates α-Syn aggregation. Here, we discovered that Mn²⁺accelerates α-Syn amyloid aggregation through the regulation of protein phase separation. We found that Mn²⁺ not only promotes α-Syn liquid-to-solid phase transition but also directly induces soluble α-Syn monomers to form solid-like condensates. Interestingly, the lipid membrane is integrated into condensates during Mn²⁺-induced α-Syn phase transition; however, the preformed Mn²⁺/α-syn condensates can only recruit lipids to the surface of condensates. In addition, this phase transition can largely facilitate α-Syn amyloid aggregation. Although the Mn²⁺-induced condensates do not fuse, our results demonstrated that they could recruit soluble α-Syn monomers into the existing condensates. Furthermore, we observed that a manganese chelator reverses Mn²⁺-induced α-Syn aggregation during the phase transition stage. However, after maturation, α-Syn aggregation becomes irreversible. These findings demonstrate that Mn²⁺ facilitates α-Syn phase transition to accelerate the formation of α-Syn aggregates and provide new insights for targeting α-Syn phase separation in PD treatment.

A mechanistic survey of Alzheimer's disease

Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.

Differential effect of polyol and sugar osmolytes on the refolding of homologous alpha amylases: A comparative study

Polyol and sugar osmolytes are known to enhance the stability of proteins, however, their role in assisting protein folding is not well understood. We asked whether these osmolytes have the same effect during refolding of a pair of thermophilic and mesophilic proteins. Herein, we have chosen α-amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) as thermophilic like and mesophilic counterparts respectively, having similar structures but differing thermostability. The effect of a series of polyols with varying number of -OH groups from 2 to 6 (Ethylene glycol, glycerol, erythritol, xylitol and sorbitol) and sugars (trehalose and sucrose) has been studied on the refolding of BLA and BAA. Our study demonstrates that glycerol, sorbitol and trehalose are the efficient cosolvents for BAA refolding, while comparatively less effective for BLA. Urea induced destabilization of BLA and BAA is differently compensated by polyol and sugar osmolytes during refolding. This suggests that the early species formed during BLA and BAA refolding are differently susceptible towards urea, indicating differential nature of their refolding pathways. Addition of trehalose at different times during refolding showed that the presence of trehalose is essential at the early stages of refolding. It is one of the first systematic study wherein the comparative effect of polyol and sugar assisted refolding of thermophilic and mesophilic protein has been carried out. The study highlights the differential effect of protein-osmolyte interactions during refolding of thermophilic and mesophilic proteins which may have implications in protein formulations, refolding and inhibition of aggregation.