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13 pages, 5908 KiB

Open AccessArticle

Modulation of Insulin Amyloid Fibrillization in Imidazolium-Based Ionic Liquids with Hofmeister Series Anions

by Vladimir Vanik, Zuzana Bednarikova, Gabriela Fabriciova, Steven S.-S. Wang, Zuzana Gazova and Diana Fedunova

Int. J. Mol. Sci. 2023, 24(11), 9699; https://doi.org/10.3390/ijms24119699 - 2 Jun 2023

Cited by 2 | Viewed by 1647

Abstract

Amyloid fibrils have immense potential to become the basis of modern biomaterials. The formation of amyloid fibrils in vitro strongly depends on the solvent properties. Ionic liquids (ILs), alternative solvents with tunable properties, have been shown to modulate amyloid fibrillization. In this work, [...] Read more.

Amyloid fibrils have immense potential to become the basis of modern biomaterials. The formation of amyloid fibrils in vitro strongly depends on the solvent properties. Ionic liquids (ILs), alternative solvents with tunable properties, have been shown to modulate amyloid fibrillization. In this work, we studied the impact of five ILs with 1-ethyl-3-methylimidazolium cation [EMIM⁺] and anions of Hofmeisterseries hydrogen sulfate [HSO₄⁻], acetate [AC⁻], chloride [Cl⁻], nitrate [NO₃⁻], and tetrafluoroborate [BF₄⁻] on the kinetics of insulin fibrillization and morphology, and the structure of insulin fibrils when applying fluorescence spectroscopy, AFM and ATR-FTIR spectroscopy. We found that the studied ILs were able to speed up the fibrillization process in an anion- and IL-concentration-dependent manner. At an IL concentration of 100 mM, the efficiency of the anions at promoting insulin amyloid fibrillization followed the reverse Hofmeister series, indicating the direct binding of ions with the protein surface. At a concentration of 25 mM, fibrils with different morphologies were formed, yet with similar secondary structure content. Moreover, no correlation with the Hofmeister ranking was detected for kinetics parameters. IL with the kosmotropic strongly hydrated [HSO₄⁻] anion induced the formation of large amyloid fibril clusters, while the other kosmotropic anion [AC⁻] along with [Cl⁻] led to the formation of fibrils with similar needle-like morphologies to those formed in the IL-free solvent. The presence of the ILs with the chaotropic anions [NO₃⁻] and [BF₄⁻] resulted in longer laterally associated fibrils. The effect of the selected ILs was driven by a sensitive balance and interplay between specific protein–ion and ion–water interactions and non-specific long-range electrostatic shielding. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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17 pages, 3330 KiB

Open AccessArticle

Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study

by Nojood Altwaijry, Ghaliah S. Almutairi, Mohd Shahnawaz Khan, Gouse M. Shaik and Majed S. Alokail

Int. J. Mol. Sci. 2023, 24(4), 3112; https://doi.org/10.3390/ijms24043112 - 4 Feb 2023

Cited by 2 | Viewed by 2053

Abstract

Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest [...] Read more.

Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL–CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE⁹⁸, GLN⁵⁷, ASP⁵², TRP¹⁰⁸, TRP⁶³, TRP⁶³, ILE⁵⁸, and ALA¹⁰⁷ residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of −6.58 kcal mol⁻¹. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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14 pages, 3182 KiB

Open AccessArticle

Roles of Tryptophan and Charged Residues on the Polymorphisms of Amyloids Formed by K-Peptides of Hen Egg White Lysozyme Investigated through Molecular Dynamics Simulations

by Husnul Fuad Zein and Thana Sutthibutpong

Int. J. Mol. Sci. 2023, 24(3), 2626; https://doi.org/10.3390/ijms24032626 - 30 Jan 2023

Viewed by 1641

Abstract

Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that [...] Read more.

Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that amyloid models with antiparallel configurations possessed greater stability and compactness than those with parallel configurations. Then, peptide chain stretching and ordering were measured through the end-to-end distance and the order parameter, for which the amyloid models consisting of K-peptides and the STDY-K-peptides at pH 2 displayed a higher level of chain stretching and ordering. After that, the molecular mechanics energy decomposition and the radial distribution function (RDF) clearly displayed the importance of Trp62 to the K-peptide and the STDY-K-peptide models at pH 2. Moreover, the results also displayed how the negatively charged Asp52 disrupted the interaction networks and prevented the amyloid formation from STDY-K-peptide at pH 7. Finally, this study provided an insight into the interplay between pH conditions and molecular interactions underlying the formation of amyloid fibrils from short peptides contained within the HEWL. This served as a basis of understanding towards the design of other amyloids for biomaterial applications. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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11 pages, 3678 KiB

Open AccessArticle

Amyloid Formation in Nanoliter Droplets

by Da Yeon Cheong, Wonseok Lee, Insu Park, Jinsung Park and Gyudo Lee

Int. J. Mol. Sci. 2022, 23(10), 5480; https://doi.org/10.3390/ijms23105480 - 13 May 2022

Cited by 4 | Viewed by 2595

Abstract

Processes that monitor the nucleation of amyloids and characterize the formation of amyloid fibrils are vital to medicine and pharmacology. In this study, we observe the nucleation and formation of lysozyme amyloid fibrils using a facile microfluidic system to generate nanoliter droplets that [...] Read more.

Processes that monitor the nucleation of amyloids and characterize the formation of amyloid fibrils are vital to medicine and pharmacology. In this study, we observe the nucleation and formation of lysozyme amyloid fibrils using a facile microfluidic system to generate nanoliter droplets that can control the flow rate and movement of monomer-in-oil emulsion droplets in a T-junction microchannel. Using a fluorescence assay, we monitor the nucleation and growth process of amyloids based on the volume of droplets. Using the microfluidic system, we demonstrate that the lag phase, which is vital to amyloid nucleation and growth, is reduced at a lower droplet volume. Furthermore, we report a peculiar phenomenon of high amyloid formation at the edge of a bullet-shaped droplet, which is likely due to the high local monomer concentration. Moreover, we discovered that amyloid fibrils synthesized in the nanoliter droplets are shorter and thicker than fibrils synthesized from a bulk solution via the conventional heating method. Herein, a facile procedure to observe and characterize the nucleation and growth of amyloid fibrils using nanoliter droplets is presented, which is beneficial for investigating new features of amyloid fibril formation as an unconventional synthetic method for amyloid fibrils. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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13 pages, 4994 KiB

Open AccessArticle

Lysozyme Amyloid Fibril Structural Variability Dependence on Initial Protein Folding State

by Kamile Mikalauskaite, Mantas Ziaunys and Vytautas Smirnovas

Int. J. Mol. Sci. 2022, 23(10), 5421; https://doi.org/10.3390/ijms23105421 - 12 May 2022

Cited by 12 | Viewed by 2693

Abstract

Amyloid fibril formation is associated with several amyloidoses, including neurodegenerative Alzheimer’s or Parkinson’s diseases. The process of such fibrillar structure formation is still not fully understood, with new mechanistic insights appearing on a regular basis. This, in turn, has limited the development of [...] Read more.

Amyloid fibril formation is associated with several amyloidoses, including neurodegenerative Alzheimer’s or Parkinson’s diseases. The process of such fibrillar structure formation is still not fully understood, with new mechanistic insights appearing on a regular basis. This, in turn, has limited the development of potential anti-amyloid compounds, with only a handful of effective cures or treatment modalities available. One of the multiple amyloid aggregation factors that requires further examination is the ability of proteins to form multiple, structurally distinct aggregates, based on the environmental conditions. In this work, we examine how the initial folding state affects the fibrilization of lysozyme—an amyloidogenic protein, often used in protein aggregation studies. We show that there is a correlation between the initial state of the protein and the aggregate formation lag time, rate of elongation, resulting aggregate structural variability and dye-binding properties, as well as formation lag time and rate of elongation. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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17 pages, 2211 KiB

Open AccessArticle

Effect of 1-Ethyl-3-methylimidazolium Tetrafluoroborate and Acetate Ionic Liquids on Stability and Amyloid Aggregation of Lysozyme

by Diana Fedunova, Andrea Antosova, Jozef Marek, Vladimir Vanik, Erna Demjen, Zuzana Bednarikova and Zuzana Gazova

Int. J. Mol. Sci. 2022, 23(2), 783; https://doi.org/10.3390/ijms23020783 - 11 Jan 2022

Cited by 11 | Viewed by 2771

Abstract

Amyloid fibrils draw attention as potential novel biomaterials due to their high stability, strength, elasticity or resistance against degradation. Therefore, the controlled and fast fibrillization process is of great interest, which raises the demand for effective tools capable of regulating amyloid fibrillization. Ionic [...] Read more.

Amyloid fibrils draw attention as potential novel biomaterials due to their high stability, strength, elasticity or resistance against degradation. Therefore, the controlled and fast fibrillization process is of great interest, which raises the demand for effective tools capable of regulating amyloid fibrillization. Ionic liquids (ILs) were identified as effective modulators of amyloid aggregation. The present work is focused on the study of the effect of 1-ethyl-3-methyl imidazolium-based ILs with kosmotropic anion acetate (EMIM-ac) and chaotropic cation tetrafluoroborate (EMIM-BF₄) on the kinetics of lysozyme amyloid aggregation and morphology of formed fibrils using fluorescence and CD spectroscopy, differential scanning calorimetry, AFM with statistical image analysis and docking calculations. We have found that both ILs decrease the thermal stability of lysozyme and significantly accelerate amyloid fibrillization in a dose-dependent manner at concentrations of 0.5%, 1% and 5% (v/v) in conditions and time-frames when no fibrils are formed in ILs-free solvent. The effect of EMIM-BF₄ is more prominent than EMIM-ac due to the different specific interactions of the anionic part with the protein surface. Although both ILs induced formation of amyloid fibrils with typical needle-like morphology, a higher variability of fibril morphology consisting of a different number of intertwining protofilaments was identified for EMIM-BF_4. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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13 pages, 3406 KiB

Open AccessArticle

Polymorphism of Alpha-Synuclein Amyloid Fibrils Depends on Ionic Strength and Protein Concentration

by Mantas Ziaunys, Andrius Sakalauskas, Kamile Mikalauskaite and Vytautas Smirnovas

Int. J. Mol. Sci. 2021, 22(22), 12382; https://doi.org/10.3390/ijms222212382 - 17 Nov 2021

Cited by 29 | Viewed by 3021

Abstract

Protein aggregate formation is linked with multiple amyloidoses, including Alzheimer‘s and Parkinson‘s diseases. Currently, the understanding of such fibrillar structure formation and propagation is still not sufficient, the outcome of which is a lack of potent, anti-amyloid drugs. The environmental conditions used during [...] Read more.

Protein aggregate formation is linked with multiple amyloidoses, including Alzheimer‘s and Parkinson‘s diseases. Currently, the understanding of such fibrillar structure formation and propagation is still not sufficient, the outcome of which is a lack of potent, anti-amyloid drugs. The environmental conditions used during in vitro protein aggregation assays play an important role in determining both the aggregation kinetic parameters, as well as resulting fibril structure. In the case of alpha-synuclein, ionic strength has been shown as a crucial factor in its amyloid aggregation. In this work, we examine a large sample size of alpha-synuclein aggregation reactions under thirty different ionic strength and protein concentration combinations and determine the resulting fibril structural variations using their dye-binding properties, secondary structure and morphology. We show that both ionic strength and protein concentration determine the structural variability of alpha-synuclein amyloid fibrils and that sometimes even identical conditions can result in up to four distinct types of aggregates. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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Review

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13 pages, 596 KiB

Open AccessReview

Micro- and Nanoplastics’ Effects on Protein Folding and Amyloidosis

by Joseph Windheim, Laura Colombo, Nora C. Battajni, Luca Russo, Alfredo Cagnotto, Luisa Diomede, Paolo Bigini, Elena Vismara, Ferdinando Fiumara, Silvia Gabbrielli, Alfonso Gautieri, Gemma Mazzuoli-Weber, Mario Salmona and Luca Colnaghi

Int. J. Mol. Sci. 2022, 23(18), 10329; https://doi.org/10.3390/ijms231810329 - 7 Sep 2022

Cited by 25 | Viewed by 4635

Abstract

A significant portion of the world’s plastic is not properly disposed of and, through various processes, is degraded into microscopic particles termed micro- and nanoplastics. Marine and terrestrial faunae, including humans, inevitably get in contact and may inhale and ingest these microscopic plastics [...] Read more.

A significant portion of the world’s plastic is not properly disposed of and, through various processes, is degraded into microscopic particles termed micro- and nanoplastics. Marine and terrestrial faunae, including humans, inevitably get in contact and may inhale and ingest these microscopic plastics which can deposit throughout the body, potentially altering cellular and molecular functions in the nervous and other systems. For instance, at the cellular level, studies in animal models have shown that plastic particles can cross the blood–brain barrier and interact with neurons, and thus affect cognition. At the molecular level, plastics may specifically influence the folding of proteins, induce the formation of aberrant amyloid proteins, and therefore potentially trigger the development of systemic and local amyloidosis. In this review, we discuss the general issue of plastic micro- and nanoparticle generation, with a focus on their effects on protein folding, misfolding, and their possible clinical implications. Full article

(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation 2.0)

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