Effect of urea on the hydration and aggregation of hydrophobic and amphiphilic solute models: Implications to protein aggregation

Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving?

Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes' preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where β-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.

Mechanistic Insights into Polyphenols' Aggregation Inhibition of α-Synuclein and Related Peptides

While several polyphenols were found to either inhibit or modulate the aggregation of proteins implicated in neurodegenerative diseases, such as Parkinson's disease (PD), discrepant action mechanisms have been reported. This, in addition to some polyphenols' pan-assay interference compounds' reputation, casts some doubts concerning their therapeutic relevance. Here, we studied, through molecular dynamics and enhanced sampling methods, the aggregation of 11-mer peptides from the non-amyloid-β component, an aggregation-prone domain of α-synuclein (α-syn) implicated in PD and other synucleinopathies, in neat water and aqueous solutions of resveratrol (RSV) and gallic acid (GA). Further, simulations of the complete protein were carried out in aqueous urea, RSV, and GA solutions. Our results show that peptide aggregation is not disrupted by either phenolic compound. Thus, instead, intrusion of RSV and GA in the inter-peptide region induces a peptide-peptide re-orientation, favoring terminal interactions that manifest in the formation of barrierless solvent-separated configurations. Moreover, although the (poly)phenols induce a pronounced peptide dewetting at high concentrations, β-sheet-rich regions, a hallmark of α-syn aggregation, are not disrupted. Thus, our results indicate that, if anything, RSV and GA delay or modulate peptide aggregation at high concentrations via the stabilization of solvent-separated conformations as opposed to aggregation inhibition. Structural analysis of the full protein, however, shows that the (poly)phenols induce more extended conformations of α-syn, similar to urea, possibly also influencing its aggregation propensity. However, opposite to urea, the (poly)phenols reduce α-syn's conformational space, likely due to steric effects and a slowdown of the solvent dynamics. These effects are concentration-dependent and possibly unattainable at therapeutic-relevant concentrations. These results suggest that the aggregation inhibition activity of RSV and GA in vitro should involve, instead, either the non-covalent binding to oligomeric intermediates or the stabilization of the monomer and/or oligomers through the formation of covalent bonds of the respective quinones with α-syn. In addition, the enhanced aggregation tendency of the peptides observed here could be associated with the formation of non-toxic oligomers, reported for some polyphenols.

Aggregation of a Parkinson's Disease-Related Peptide: When Does Urea Weaken Hydrophobic Interactions?

While the exact cause of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease is not completely understood, compelling evidence implicates the aggregation of specific proteins and peptides. Co-solvents can provide molecular insight into protein aggregation mechanisms and the chemical nature of potential aggregation inhibitors. Here, we study, through molecular simulations, the hydration and binding free energies of an amphiphilic peptide from the nonamyloid-β component (NAC), a key aggregation-prone domain of α-synuclein, in water and an 8 M aqueous urea solution. Isoleucine, glycine, and serine peptides of the same length are also studied to unravel the role of urea in the hydration and aggregation of hydrophobic and hydrophilic domains. A strong impact of urea in hindering the aggregation of the NAC subdomain is observed. A slightly weaker aggregation inhibition is observed for the Gly and Ser peptides, whereas a much lower aggregation inhibitory activity is found for the Ile peptide, seemingly contrasting with urea's protein unfolding mechanism. This behavior is shown to derive from a lower profusion of urea next to the hydrophobic side chains and the backbone of the Ile's peptide in the dimeric form. As a consequence, β-sheets, formed upon aggregation, remain nearly intact. Hydrophilic neighbor groups in the amphiphilic NAC subdomain, however, are shown to anchor enough urea to weaken hydrophobic interactions and disrupt β-sheet structures. Our results indicate that urea's activity is potentiated in amphiphilic domains and that potential drugs could disrupt hydrophobic β-sheet-rich regions while not binding primarily to hydrophobic amino acids.

Hydrophobic association and solvation of neopentane in urea, TMAO and urea-TMAO solutions

A detailed knowledge of hydrophobic association and solvation is crucial for understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using molecular dynamics simulations, it is found that the hydrophobic association of neopentane molecules is greater in a mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, 4 M TMAO solution and neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We find the association is even less in TMAO solution than pure water. From free energy calculations, it is revealed that the neopentane sized cavity creation in mixed urea-TMAO-water is most unfavorable and that causes the highest hydrophobic association. The cavity formation in urea solution is either more unfavorable or comparable to that in TMAO solution. Importantly, it is found that the population of neopentane-neopentane contact pair and the free energy contribution for the cavity formation step in TMAO solution are very sensitive towards the choice of TMAO force-fields. A careful construction of TMAO force-fields is important for studying the hydrophobic association. Interestingly it is observed that the total solute-solvent dispersion interaction energy contribution is always the most favorable in mixed urea-TMAO-water. The magnitude of this interaction energy is greater in urea solution relative to TMAO solution for two different force-fields of TMAO, whereas the lowest value is obtained in pure water. It is revealed that the extent of the overall hydrophobic association in osmolyte solutions is mainly governed by the cavity creation step and it nullifies the contribution coming from the solute-solvent interaction contribution.