Conformational Properties of Aß 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 ß (Aß) peptides in the brain. We have carried out atomistic molecular dynamics simulations to investigate the size-dependent conformational properties of aggregated Aß 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).

Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study.

Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.

Exploring the Heterogeneous Dynamical Environment at the Interface of Aß42 Peptide in Aqueous Ionic Liquid Solution.

In this study, we have investigated the heterogeneous dynamical environment around an ensemble of full-length amyloid-ß (Aß42) peptide monomers in binary aqueous solution containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4] as a co-solvent. Atomistic molecular dynamics (MD) simulations have been employed with the aim of understanding the effect of the IL on the distribution of water molecules and IL components around distinct segments of the peptide. As compared to pure aqueous medium, locally heterogeneous restricted water motions at the interface have been spotted in the presence of the IL. Our calculations revealed faster diffusion of water molecules hydrating hydrophilic segments (N-term and turn) as opposed to that around hydrophobic segments (hp1, hp2, and C-term). The extent of non-uniform restriction on the center-of-mass motions as well as the reorientation of water molecules and IL ions have been similarly affected in the binary IL-water solution. The effects of IL on the formation of hydrogen bond networks have been evident from the longer hydrogen bond relaxation time scales of peptide-water, with only a small fraction of peptide-anion hydrogen bonds contributing to the structural relaxation. Due to the size and shape factors, the increasingly sluggish dynamics of the IL components in the solvation shell can be attributed to a longer time scale for the onset of maximum dynamic heterogeneity. Interestingly, the water molecules around the polar segments of the peptide take longer to attain dynamic heterogeneity, which intensifies in the presence of IL. These calculations clearly suggest that electrostatic interaction plays a crucial role in water-mediated peptide-IL interaction, thereby shielding the surface from hydrophobic collapse and preventing possible further growth of the monomers into fibrils at higher peptide concentrations.

Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid ß Components of α-Synuclein.

Self-association of α-synuclein peptides into oligomeric species and ordered amyloid fibrils is associated with Parkinson's disease, a progressive neurodegenerative disorder. In particular, the peptide domain formed between the residues Glu-61 (or E61) and Val-95 (or V95) of α-synuclein, typically termed the "nonamyloid ß component" (NAC), is known to play critical roles in forming aggregated structures. In this work, we have employed molecular dynamics simulations to explore the conformational properties and relative stabilities of aggregated protofilaments of different orders, namely, tetramer (P(4)), hexamer (P(6)), octamer (P(8)), decamer (P(10)), dodecamer (P(12)), and tetradecamer (P(14)), formed by the NAC domains of α-synuclein. Besides, center-of-mass pulling and umbrella sampling simulation methods have also been employed to characterize the mechanistic pathway of peptide association/dissociation and the corresponding free energy profiles. Structural analysis showed that the disordered C-terminal loop and the central core regions of the peptide units lead to more flexible and distorted structures of the lower order protofilaments (P(4) and P(6)) as compared to the higher order ones. Interestingly, our calculation shows the presence of multiple distinctly populated conformational states for the lower order protofilament P(4), which may drive the oligomerization process along multiple pathways to form different polymorphic α-synuclein fibrillar structures. It is further observed that the nonpolar interaction between the peptides and the corresponding nonpolar solvation free energy play a dominant role in stabilizing the aggregated protofilaments. Importantly, our result showed that reduced cooperativity during the binding of a peptide unit beyond a critical size of the protofilament (P(12)) leads to less favorable binding free energy of a peptide.

Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies.

Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM+ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.

Exploring the Dynamic Heterogeneity at the Interface of a Protein in Aqueous Ionic Liquid Solutions.

Room temperature molecular dynamics (MD) simulations of the globular protein α-lactalbumin in aqueous solutions containing BMIM (1-butyl-3-methylimidazolium) based ionic liquids (ILs) with a series of Hofmeister anions have been carried out. In particular, effects of anions of different shapes/sizes and hydrophobic/hydrophilic characters, namely, thiocyanate (SCN-), dicyanamide (DCA-), methyl sulfate (MS-), triflate (TFO-), and bis(trifluoromethane) sulfonimide (TF2N-) on the heterogeneous dynamic environment at the interface around the protein have been explored. The calculations revealed exchange of population between water and IL cation-anion components beyond the first layer of bound water molecules at the protein surface. Further, increasingly restricted diffusivity of the IL components and water around the protein has been found to be associated with a longer time scale for the onset of dynamic heterogeneity at the interface. Restricted diffusivity of water molecules at the interface in the presence of the ILs has been found to be correlated with the longer time scale of structural relaxations of protein-water hydrogen bonds at the interface. More importantly, the time scale associated with the reorientations of the anions has been found to be anticorrelated with their translational diffusivity, with the effect being more at the interface as compared to the bulk IL solutions. It is demonstrated that the nonuniform ability of the anions to form hydrogen bonds with water due to their differential shapes and hydrophilic characters is the origin of such anticorrelation.

Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide.

It is believed that water around an intrinsically disordered protein or peptide (IDP) in an aqueous environment plays an important role in guiding its conformational properties and aggregation behavior. However, despite its importance, only a handful of studies exploring the correlation between the conformational motions of an IDP and the microscopic properties of water at its surface are reported. Attempts have been made in this work to study the dynamic properties of water present in the vicinity of α-synuclein, an IDP associated with Parkinson's disease (PD). Room temperature molecular dynamics (MD) simulations of eight α-synuclein1-95 peptides with a wide range of initial conformations have been carried out in aqueous media. The calculations revealed that due to solid-like caging motions, the translational and rotational mobility of water molecules near the surfaces of the peptide repeat unit segments R1 to R7 are significantly restricted. A small degree of dynamic heterogeneity in the hydration environment around the repeat units has been observed with water near the hydrophobic R6 unit exhibiting relatively more restricted diffusivity. The time scales involving the overall structural relaxations of peptide-water and water-water hydrogen bonds near the peptide have been found to be correlated with the time scale of diffusion of the interfacial water molecules. We believe that the relatively more hindered dynamic environment near R6 can help create water-mediated contacts centered around R6 between peptide monomers at a higher concentration, thereby enhancing the early stages of peptide aggregation.

Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein.

Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM+) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF6-), ethyl sulfate (ETS-), acetate (OAc-), chloride (Cl-), dicyanamide (DCA-), and nitrate (NO3-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.

Microscopic Understanding of the Effect of Ionic Liquid on Protein from Molecular Simulation Studies.

We have performed molecular dynamics (MD) simulations of the protein α-lactalbumin in aqueous solution containing the ionic liquid (IL) 1-butyl-3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) as the cosolvent at different concentrations. Attempts have been made to obtain quantitative understanding of the effects of the IL on the conformational features of the protein as well as the distributions of the IL and water around it. The calculations revealed enhanced rigidity of the protein with reduced conformational fluctuations and increasingly correlated local motions in the presence of the IL. Nonuniform relative population of the BMIM+ and BF4- ions at the protein surface with respect to that in the bulk solution has been observed. It is demonstrated that exchange of water by the IL around the protein results in rearrangement of the hydrogen bond network at the interface with breaking of protein-water hydrogen bonds and formation of protein-IL hydrogen bonds. Importantly, it is found that the protein forms increased number of stronger salt bridges in the presence of IL. This shows that the formation of a greater number of such stronger salt bridges is the origin behind the enhanced rigidity of the protein in the presence of the IL.