Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme

Pillai, Visakh; Kumari, Pallavi; Kolagatla, Srikanth; Sakai, Victoria García; Rudić, Svemir; Rodriguez, Brian J.; Rubini, Marina; Tych, Katarzyna M.; Benedetto, Antonio

doi:10.1021/acs.jpclett.2c01505

Cited by 10 publications

(9 citation statements)

References 58 publications

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“…Toxicity is, however, also a synonym of affinity, and this have stimulated, in turn, a series of biological and chemical-physical investigations aimed at using the ability of ILs to interact with biosystems to develop applications in bio-nanomedicine and bio-nanotechnology (Egorova et al 2017 ; Benedetto and Ballone 2018 ; Banerjee et al 2018 ; Tanner et al 2020 ; Curreri et al 2021 ; Kumari et al 2021a ; Pillai et al 2022a ; Hu et al 2023 ). For example, it has been shown that the oral delivery of a choline-based IL prevents the absorption of fat molecules through intestinal tissue in rats (Nurunnabi et al 2019 ).…”

Section: Ionic Liquidsmentioning

confidence: 99%

Ionic liquids meet lipid bilayers: a state-of-the-art review

Benedetto

2023

Biophys Rev

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In the past 25 years, a vast family of complex organic salts known as room-temperature ionic liquids (ILs) has received increasing attention due to their potential applications. ILs are composed by an organic cation and either an organic or inorganic anion, and possess several intriguing properties such as low vapor pressure and being liquid around room temperature. Several biological studies flagged their moderate-to-high (cyto)-toxicity. Toxicity is, however, also a synonym of affinity, and this boosted a series of biophysical and chemical-physical investigations aimed at exploiting ILs in bio-nanomedicine, drug-delivery, pharmacology, and bio-nanotechnology. Several of these investigations focused on the interaction between ILs and lipid membranes, aimed at determining the microscopic mechanisms behind their interaction. This is the focus of this review work. These studies have been carried out on a variety of different lipid bilayer systems ranging from 1-lipid to 5-lipids systems, and also on cell-extracted membranes. They have been carried out at different chemical-physical conditions and by the use of a number of different approaches, including atomic force microscopy, neutron and X-ray scattering, dynamic light scattering, differential scanning calorimetry, surface quartz microbalance, nuclear magnetic resonance, confocal fluorescence microscopy, and molecular dynamics simulations. The aim of this “2023 Michèle Auger Award” review work is to provide the reader with an up-to-date overview of this fascinating research field where “ILs meet lipid bilayers (aka biomembranes),” with the aim to boost it further and expand its cross-disciplinary edges towards novel high-impact ideas/applications in pharmacology, drug delivery, biomedicine, and bio-nanotechnology.

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Section: Ionic Liquidsmentioning

confidence: 99%

Ionic liquids meet lipid bilayers: a state-of-the-art review

Benedetto

2023

Biophys Rev

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“…The presence of a trace amount of π-stacking-forming toluene solvent in chloroform cannot induce self-assembly . The impact of aqueous ionic liquid (IL) solution on peptide or protein aggregation has received considerable attention. − Adding water to HB-forming IL, ethylammonium nitrate (EAN), triggers self-assembling into nanofibrils, different from the no visible structure found in pure ILs . Introduction of water in 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM] + [BF 4 ] − ) induces self-assembly into nanotubes, and no ordered structure is observed in pure IL …”

Section: Introductionmentioning

confidence: 99%

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids

Ge,

Wang,

Zhu

et al. 2023

J. Chem. Theory Comput.

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Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]− solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P–P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL–water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.

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“…Anions such as phosphate and sulfate promoted aggregation, whereas mesylate anion suppressed it due to a competitive anion−water interaction guiding the self-assembly. 17 Very recently, 23 atomic force microscopy have revealed that protic ILs shows a strong influence on the thickness of growth on lysozyme amyloids under different IL concentrations in presence of water. They even conjectured 24 the nanostructuring of protic ILs and the heterogeneous distributions of the ions and water in space using computer simulation study.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution

et al. 2023

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In this study, we have investigated the heterogeneous dynamical environment around an ensemble of full-length amyloid-β (Aβ 42 ) peptide monomers in binary aqueous solution containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF 4 ] 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 (Nterm 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.

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Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme

Cited by 10 publications

References 58 publications

Ionic liquids meet lipid bilayers: a state-of-the-art review

Ionic liquids meet lipid bilayers: a state-of-the-art review

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution

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Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme

Cited by 10 publications

References 58 publications

Ionic liquids meet lipid bilayers: a state-of-the-art review

Ionic liquids meet lipid bilayers: a state-of-the-art review

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ42 Peptide in Aqueous Ionic Liquid Solution

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Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ₄₂ Peptide in Aqueous Ionic Liquid Solution