Understanding the microscopic origin behind heterogeneous properties of water confined in and around Aβ17-42 protofilaments

Conformational Properties of Aβ Peptide Oligomers in Aqueous Ionic Liquid Solution: Insights from Molecular Simulation Studies

Alzheimer's disease is a progressive irreversible neurological disorder with abnormal extracellular deposition of amyloid β (Aβ) peptides in the brain. We have carried out atomistic molecular dynamics simulations to investigate the size-dependent conformational properties of aggregated Aβ oligomers of different orders, namely, pentamer [O(5)], decamer [O(10)], and hexadecamer [O(16)] in aqueous solutions containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The calculations revealed reduced peptide conformational fluctuations in O(5) and O(10) in the presence of the IL. In contrast, the higher order oligomer [O(16)] has been found to exhibit greater structural distortion due to enhanced flexibilities of its peptide units in the presence of the IL. Based on the distributions of the solvent (water) and the cosolvent (IL) components, it is demonstrated that exchange of water by the IL ion pairs at the exterior surface of the oligomers primarily occurs beyond the first layer of surface-bound water molecules. Importantly, a reduced number of relatively weaker peptide salt bridges have been found in O(16) in binary water-IL solution as compared to the other two smaller-sized oligomers [O(5) and O(10)]. Such differential influence of the IL on peptide salt bridges results in less favorable binding free energies of peptide monomers to O(16), which leads to its greater structural distortion and reduced stability compared to those of O(5) and O(10).

Stability of the Aβ42 Peptide in Mixed Solutions of Denaturants and Proline

Amyloid β-peptide (Aβ) is responsible for the neuronal damage and death of a patient with Alzheimer's disease (AD). Aβ42 oligomeric forms are dominant neurotoxins and are related to neurodegeneration. Their different forms are related to various pathological conditions in the brain. We investigated Aβ42 peptides in different environments of proline, urea, and GdmCl solutions (in pure and mixed binary forms) through atomistic molecular dynamics simulations. Preferential exclusion from the protein surface and facile formation of a large number of weak molecular interactions are the driving forces for the osmolyte's action. We have focused on these interactions between peptide monomers and pure/mixed osmolytes and denaturants. Urea, as usual, denatures the peptide strongly compared to the GdmCl by accumulation around the peptide. GdmCl shows lesser build-up around protein in contrast to urea but is involved in destabilizing the salt bridge formation of Asp23 and Lys28. Proline as an osmolyte protects the peptide from aggregation when mixed with urea and GdmCl solutions. In mixed solutions of two denaturants and osmolyte plus denaturant, the peptide shows enhanced stability as compared to pure denaturant urea solution. The enhanced stability of peptides in proline may be attributed to its exclusion from the peptide surface and favoring salt bridge formation.

In Silico Studies to Predict the Role of Solvent in Guiding the Conformations of Intrinsically Disordered Peptides and Their Aggregated Protofilaments

The formation of amyloids due to the self-assembly of intrinsically disordered proteins or peptides is a hallmark for different neurodegenerative diseases. For example, amyloids formed by the amyloid beta (Aβ) peptides are responsible for the most devastating neuropathological disease, namely, Alzheimer's disease, while aggregation of α-synuclein peptides causes the etiology of another neuropathological disease, Parkinson's disease. Characterization of the intermediates and the final amyloid formed during the aggregation process is, therefore, crucial for microscopic understanding of the origin behind such diseases, as well as for the development of proper therapeutics to combat those. However, most of the research activities reported in this area have been directed toward examining the early stages of the aggregation process, including probing the conformational characteristics of the responsible protein/peptide in the monomeric state or in small oligomeric forms. This is because the small soluble oligomers have been found to be more deleterious than the final insoluble amyloids. This review discusses some of the recent findings obtained from our simulation studies on Aβ and α-synuclein monomers and small preformed Aβ aggregates. A molecular-level insight of the aggregation process with a special emphasis on the role of water in inducing the aggregation process has been provided.

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aβ misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aβ peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aβ₄₂ peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aβ peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aβ aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.

Importance of Solvent in Guiding the Conformational Properties of an Intrinsically Disordered Peptide

Aggregated form of α-synuclein in the brain has been found to be the major component of Lewy bodies that are hallmarks of Parkinson's disease (PD), the second most devastating neurodegenerative disorder. We have carried out room-temperature all-atom molecular dynamics (MD) simulations of an ensemble of widely different α-synuclein_1-95 peptide monomer conformations in aqueous solution. Attempts have been made to obtain a generic understanding of the local conformational motions of different repeat unit segments, namely R1-R7, of the peptide and the correlated properties of the solvent at the interface. The analyses revealed relatively greater rigidity of the hydrophobic R6 unit as compared to the other repeat units of the peptide. Besides, water molecules around R6 have been found to be less structured and weakly interacting with the peptide. These are important observations as the R6 unit with reduced conformational motions can act as the nucleation site for the aggregation process, while less structured weakly interacting water around it can become displaced easily, thereby facilitating the hydrophobic collapse of the peptide monomers and their association during the nucleation phase at higher concentrations. In addition, we demonstrated presence of doubly coordinated highly ordered as well as triply coordinated relatively disordered water molecules at the interface. We believe that while the ordered water molecules can favor water-mediated interactions between different peptide monomers, the randomly ordered ones on the other hand are likely to be expelled easily from the interface, thereby facilitating direct peptide-peptide interactions during the aggregation process.

Effect of TMAO and Urea on Dimers and Tetramers of Amyloidogenic Heptapeptides (23FGAILSS29)

Human islet amyloid polypeptide (hIAPP) (1-37) is an intrinsically disordered protein that is released with insulin by β-cells found in the pancreas. Under certain environmental conditions, hIAPP can aggregate, which leads to β-cell death. FGAILSS (23-29) residues of the hIAPP protein form β sheets, which may be toxic species in type 2 diabetes (T2D) patients. All-atom molecular dynamics (MD) simulations have been used to analyze the effect of two distinct types of osmolytes trimethylamine N-oxide (TMAO) and urea on two and four FGAILSS heptapeptides. TMAO leads the individual peptide toward an extended conformation with a higher radius of gyration and favors the formation of antiparallel β-sheets with an increase in its concentration. However, urea mostly shows compaction of individual peptides except at 4.0 M in the case of a tetramer but does not show aggregation behavior as a whole. TMAO leads both the dimer and tetramer toward the native state with an increase in its concentration. Moreover, both the dimer and tetramer show irregular behavior in urea. The tetramer in 4.0 M urea shows the maximum fraction of native contacts due to the formation of antiparallel β-sheets. This formation of antiparallel β-sheets favors the aggregation of peptides. TMAO forms a smaller number of hydrogen bonds with peptides as compared to urea as the exclusion of TMAO and accumulation of urea around the peptides have occurred in the first solvation shell (FSS). Principal component analysis (PCA) results suggest that the minima in the free energy landscape (FEL) plot are homogeneous for a particular conformation in TMAO with smaller basins, while in urea, the dimer shows minima mostly for extended conformations. For a 4.0 M urea concentration, the tetramer shows the minimum for antiparallel β-sheets, which indicates the aggregation behavior of the tetramer, and for a higher concentration, it shows minima with wider basins of extended conformations.