Facet-Dependent Interactions of Islet Amyloid Polypeptide with Gold Nanoparticles: Implications for Fibril Formation and Peptide-Induced Lipid Membrane Disruption

Insights into the mechanism of peptide fibril growth on gold surface

Understanding the formation of β-fibrils over the gold surface is of paramount interest in nano-bio-medicinal Chemistry. The intricate mechanism of self-assembly of neurofibrillogenic peptides and their growth over the gold surface remains elusive, as experiments are limited in unveiling the microscopic dynamic details, in particular, at the early stage of the peptide aggregation. In this work, we carried out equilibrium molecular dynamics and enhanced sampling simulations to elucidate the underlying mechanism of the growth of an amyloid-forming sequence of tau fragments over the gold surface. Our results disclose that the collective intermolecular interactions between the peptide chains and peptides with the gold surface facilitate the peptide adsorption, followed by integration, finally leading to the fibril formation.

On the interactions of peptides with gold nanoparticles: effects of sequence and size

Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous media. In the present study, we use all-atom molecular dynamic (MD) simulations to study the interactions of ten short peptides (namely A3, AgBP1, AgBP2, AuBP1, AuBP2, GBP1, Midas2, Pd4, Z1, and Z2) with different gold nanoparticles (of different diameters ranging from 2 to 8 nm). Our MD simulation results imply that the gold nanoparticles have a remarkable effect on the stability and conformational properties of peptides. Moreover, the size of the gold nanoparticles and the type of peptide amino acid sequences play important roles in the stability of the peptide-AuNP complexes. Our results reveal that some amino acids such as Tyr, Phe, Met, Lys, Arg, and Gln have direct contact with the metal surface in comparison with Gly, Ala, Pro, Thr, and Val residues. The peptide adsorption on the surface of the gold nanoparticles is favorable from the energetic viewpoint, in which the van der Waals (vdW) interactions between the peptides and metal surface can be considered as one of the driving forces for the complexation process. The calculated Gibbs binding energies indicate that AuNPs have more sensitivity against the GBP1 peptide in the presence of different peptides. Overall, the results of this study can provide new insight into the peptide interaction with the gold nanoparticles from the molecular viewpoint, which can be important for designing new biomaterials based on the peptides and gold nanoparticles.Communicated by Ramaswamy H. Sarma.

Interfacial effect on the ability of peptide-modified gold nanoclusters to inhibit hIAPP fibrillation and cytotoxicity

Deposit of amyloid peptides in the cells is related to various amyloidosis diseases. A variety of nanomaterials have been developed to resist amyloid deposit. Most of the research on the inhibition of nanomaterials against amyloid aggregation are undertaken in solution, while the membranes that may mediate fibrillar aggregation and affect interaction of inhibitors with amyloid peptides in biotic environment are little taken into account. In this study, we synthesized three kinds of gold nanoclusters modified with cysteine (C@AuNCs), glutathione (GSH@AuNCs) and a peptide derived from the core region of hIAPP fibrillation (C-HL-8P@AuNCs), and investigated their inhibitory activities against hIAPP fibrillation in the absence and presence of lipid vesicles (POPC/POPG 4:1 LUVs) by the experiments of ThT fluorescence kinetics, AFM and CD. We also explored the inhibitions of hIAPP-induced membrane damage and cytotoxicity by peptide@AuNCs using fluorescent dye leakage and cell viability assays. Our study revealed that the inhibitory efficiency of these peptide@AuNCs against hIAPP fibrillation follows C-HL-8P@AuNCs≅GSH@AuNCs>C@AuNCs in lipid-free solution and C-HL-8P@AuNCs≫GSH@AuNCs>C@AuNCs in lipid membrane environment. Compared with the results obtained in lipid-free solution, the inhibitions of hIAPP fibrillation observed in lipid membrane environment were more associated with the inhibitions of hIAPP-induced damages of lipid vesicles and INS-1 cells (C-HL-8P@AuNCs≫GSH@AuNCs>C@AuNCs). An additional hydrophobic interaction with the homologous core region of hIAPP, which is only provided by C-HL-8P@AuNCs and largely suppressed in lipid-free solution, enhanced in the membrane environment and therefore made C-HL-8P@AuNCs much more powerful than GSH@AuNCs and C@AuNCs in the inhibitions of hIAPP fibrillation and cytotoxicity.

Aggregation of an Amyloidogenic Peptide on Gold Surfaces

Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation depends on both the protein structure and the surface chemistry, with the different molecular and oligomer structures adopted by proteins on surfaces likely to be crucial. In this paper, the aggregation of the model amyloidogenic peptide, Aβ(16-22), corresponding to a hydrophobic segment of the amyloid beta protein on a gold surface is studied using molecular dynamics simulation. Previous simulations of this peptide on gold surfaces have shown that it adopts conformations on surfaces that are quite different from those in bulk solution. These simulations show that this then leads to significant differences in the oligomer structures formed in solution and on gold surfaces. In particular, oligomers formed on the surface are low in beta-strands so are unlike the structures formed in bulk solution. When oligomers formed in solution adsorb onto gold surfaces they can then restructure themselves. This can then help explain the inhibition of Aβ(16-22) fibrillation by gold surfaces and nanoparticles seen experimentally.

ISOTHERMAL TITRATION CALORIMETRY (ITC) AS A PROMISING TOOL IN PHARMACEUTICAL NANOTECHNOLOGY

Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. Taking into account the relevance of ITC, we conducted, therefore, an integrative revision of the literature, from 2000 to 2023, on the main purposes of using this technique in pharmaceutical nanotechnology. The search were carried out in the Pubmed, Sciencedirect, Web of Science, and Scifinder databases using the descriptors "Nanoparticles", "Isothermal Titration Calorimetry", and "ITC". We have observed that the ITC technique has been increasingly used in pharmaceutical nanotechnology, seeking to understand the interaction mechanisms in the formation of nanoparticles. Additionally, to understand the behavior of nanoparticles with biological materials (proteins, DNA, cell membranes, among others), thereby helping to understand the behavior of nanocarriers in vivo studies. As a contribution, we intended to reveal the importance of ITC in the laboratory routine, which is itself a quick and easy technique to obtain relevant results that help to optimize the nanosystems formulation process.

Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy

As nanomaterials become more prevalent in both industry and medicine, it is crucial to fully understand their health risks. One area of concern is the interaction of nanoparticles with proteins, including their ability to modulate the uncontrolled aggregation of amyloid proteins associated with diseases, such as Alzheimer's disease and type II diabetes, and potentially extend the lifetime of cytotoxic soluble oligomers. This work demonstrates that two-dimensional infrared spectroscopy and ¹³C¹⁸O isotope labeling can be used to follow the aggregation of human islet amyloid polypeptide (hIAPP) in the presence of gold nanoparticles (AuNPs) with single-residue structural resolution. 60 nm AuNPs were found to inhibit hIAPP, tripling the aggregation time. Furthermore, calculating the actual transition dipole strength of the backbone amide I' mode reveals that hIAPP forms a more ordered aggregate structure in the presence of AuNPs. Ultimately, such studies can provide insight into how mechanisms of amyloid aggregation are altered in the presence of nanoparticles, furthering our understanding of protein-nanoparticle interactions.

Charge and hydrophobicity of amyloidogenic protein/peptide templates regulate the growth and morphology of gold nanoparticles

Biomolecules are known to interact with metals and produce nanostructured hybrid materials with diverse morphologies and functions. In spite of the great advancement in the principles of biomimetics for designing complex nano-bio structures, the interplay between the physical properties of biomolecules such as sequence, charge, and hydrophobicity with predictable morphology of the resulting nanomaterials is largely unknown. Here, using various amyloidogenic proteins/peptides and their corresponding fibrils in combination with different pH, we show defined principle for gold nanocrystal growth into triangular and supra-spheres with high prediction. Using a combination of different biophysical and structural techniques, we establish the mechanism of nucleation and crystal growth of gold nanostructures and show the effective isolation of intact nanostructures from amyloid templates using protein digestion. This study will significantly advance our design principle for bioinspired materials for specific functions with great predictability.

Nanoparticles and Nanocolloidal Carbon: Will They Be the Next Antidiabetic Class That Targets Fibrillation and Aggregation of Human Islet Amyloid Polypeptide in Type 2 Diabetes?

Nanotechnology is revolutionizing human medicine. Nanoparticles (NPs) are currently used for treating various cancers, for developing vaccines, and for imaging, and other promises offered by NPs might come true soon. Due to the interplay between NPs and proteins, there is more and more evidence supporting the role of NPs for treating amyloid-based diseases. NPs can induce some conformational changes of the adsorbed protein molecules via various molecular interactions, leading to inhibition of aggregation and fibrillation of several and different amyloid proteins. Though an in depth understanding of such interactions between NPs and amyloid structures is still lacking, the inhibition of protein aggregation by NPs represents a new generation of innovative and effective medicines to combat metabolic diseases such as type 2 diabetes (T2D). Here, we lay out advances made in the field of T2D notably for optimizing protein aggregation inhibition strategies. This Account covers discussions about the current understanding of β-cells, the insulin producing cells within the pancreas, under diabetic conditions, notably increased glucose and fatty acid levels, and the implication of these conditions on the formation of human islet amyloid polypeptide (hIAPP) amylin oligomers and aggregates. Owing to the great potential of carbon nanostructures to interfere with protein aggregation, an important part of this Account will be devoted to the state of the art of therapeutic options in the form of emerging nanomaterials-based amyloidosis inhibitors. Our group has recently made some substantial progress in this regard by investigating the impact of glucose and fatty acid concentrations on hIAPP aggregation and β-cell toxicity. Furthermore, the great potential of carbon nanocolloids in reversing hIAPP aggregation under diabetic conditions will be highlighted as the approach has been validated on β-cell cultures from rats. We hope that this Account will evoke new ideas and concepts in this regard. We give some lead references below on pancreatic β-cell aspects and carbon quantum dots for managing diabetics and nanomedicine related aspects, a topic of interest in our laboratory.

Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation

The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer's and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parameters determine interfacial effects, we focus here on the role of nanoparticle (NP) size and curvature. We used thioflavin T (ThT) fluorescence assays to demonstrate the size-dependent effects of NPs on amyloid fibril formation for the peptides Aβ₄₀, NNFGAIL, GNNQQNY and VQIYVK. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of all peptides except NNFGAIL, larger 20 nm gold NPs (AuNP-20) tended to accelerate or not influence peptide aggregation. Differences in the NP effects for the peptides resulted from the different peptide properties (size, tendency to aggregate) and associated surface binding affinities. Additional dynamic light scattering (DLS), electron microscopy, and atomic force microscopy (AFM) experiments with the Aβ₄₀ peptide confirmed size-dependent NP effects on peptide aggregation, and also suggested a structural influence on the formed fibrils. NPs can serve as a surface for the adsorption of peptide monomers and enable nucleation to oligomers and fibril formation. However, molecular dynamics (MD) simulations showed that peptide oligomers were less stable at smaller NPs. High surface curvatures destabilized prefibrillar structures, which provides a possible explanation for inhibitory effects on fibril growth, provided that peptide-NP surface binding was relevant for fibril formation. These mechanistic insights can support the design of future nanostructured materials.

Influencing factors and characterization methods of nanoparticles regulating amyloid aggregation

Human disorders associated with amyloid aggregation, such as Alzheimer's disease and Parkinson's disease, afflict the lives of millions worldwide. When peptides and proteins in the body are converted to amyloids, which have a tendency to aggregate, the toxic oligomers produced during the aggregation process can trigger a range of diseases. Nanoparticles (NPs) have been found to possess surface effects that can modulate the amyloid aggregation process and they have potential application value in the treatment of diseases related to amyloid aggregation and fibrillary tangles. In this review, we discuss recent progress relating to studies of nanoparticles that regulate amyloid aggregation. The review focuses on the factors influencing this regulation, which are important as guidelines for the future design of NPs for the treatment of amyloid aggregation. We describe the characterization methods that have been utilized so far in such studies. This review provides research information and characterization methods for the rational design of NPs, which should result in therapeutic strategies for amyloid diseases.

Compact Peptoid Molecular Brushes for Nanoparticle Stabilization

Controlling the interfaces and interactions of colloidal nanoparticles (NPs) via tethered molecular moieties is crucial for NP applications in engineered nanomaterials, optics, catalysis, and nanomedicine. Despite a broad range of molecular types explored, there is a need for a flexible approach to rationally vary the chemistry and structure of these interfacial molecules for controlling NP stability in diverse environments, while maintaining a small size of the NP molecular shell. Here, we demonstrate that low-molecular-weight, bifunctional comb-shaped, and sequence-defined peptoids can effectively stabilize gold NPs (AuNPs). The generality of this robust functionalization strategy was also demonstrated by coating of silver, platinum, and iron oxide NPs with designed peptoids. Each peptoid (PE) is designed with varied arrangements of a multivalent AuNP-binding domain and a solvation domain consisting of oligo-ethylene glycol (EG) branches. Among designs, a peptoid (PE5) with a diblock structure is demonstrated to provide a superior nanocolloidal stability in diverse aqueous solutions while forming a compact shell (∼1.5 nm) on the AuNP surface. We demonstrate by experiments and molecular dynamics simulations that PE5-coated AuNPs (PE5/AuNPs) are stable in select organic solvents owing to the strong PE5 (amine)-Au binding and solubility of the oligo-EG motifs. At the vapor-aqueous interface, we show that PE5/AuNPs remain stable and can self-assemble into ordered 2D lattices. The NP films exhibit strong near-field plasmonic coupling when transferred to solid substrates.

Inhibiting protein aggregation with nanomaterials: The underlying mechanisms and impact factors

Protein aggregation is correlated with the onset and progression of protein misfolding diseases (PMDs). Inhibiting the generation of toxic aggregates of misfolded proteins has been proposed as a therapeutic approach for PMDs. Due to their unique properties, nanomaterials have been extensively investigated for their ability to inhibit protein aggregation and have shown great potential in the diagnosis and treatment of PMDs. However, the precise mechanisms by which nanomaterials interact with amyloidogenic proteins and the factors influencing these interactions remain poorly understood. Consequently, developing a rational design strategy for nanomaterials that target specific proteins in PMDs has been challenging. In this review, we elucidate the effects of nanomaterials on protein aggregation and describe the mechanisms through which nanomaterials interfere with protein aggregation. The major factors impacting protein-nanomaterial interaction such as size, charge, concentration, surface modification and morphology that can be rationally addressed to achieve the desired effects of nanomaterials on protein aggregation are summarized. The prospects and challenges to the clinical application of nanomaterials for the treatment of PMDs are also discussed.

Therapeutic Strategies and Nano-Drug Delivery Applications in Management of Aging Alzheimer's Disease

Alzheimer's disease (AD) is a neurodegenerative disorder in which the death of brain cells causes memory loss and cognitive decline. Existing drugs only suppress symptoms or delay further deterioration but do not address the cause of the disease. In spite of screening numerous drug candidates against various molecular targets of AD, only a few candidates, such as acetylcholinesterase inhibitors, are currently utilized as an effective clinical therapy. Currently, nano-based therapies can make a difference, providing new therapeutic options by helping drugs to cross the blood-brain barrier and enter the brain more effectively. The main aim of this review was to highlight advances in research on the development of nano-based therapeutics for improved treatment of AD.

Chirality Transfer from Sub-Nanometer Biochemical Molecules to Sub-Micrometer Plasmonic Metastructures: Physiochemical Mechanisms, Biosensing, and Bioimaging Opportunities

Determining the structural chirality of biomolecules is of vital importance in bioscience and biomedicine. Conventional methods for characterizing molecular chirality, e.g., circular dichroism (CD) spectroscopy, require high-concentration specimens due to the weak electronic CD signals of biomolecules such as amino acids. Artificially designed chiral plasmonic metastructures exhibit strong intrinsic chirality. However, the significant size mismatch between metastructures and biomolecules makes the former unsuitable for chirality-recognition-based molecular discrimination. Fortunately, constructing metallic architectures through molecular self-assembly allows chirality transfer from sub-nanometer biomolecules to sub-micrometer, intrinsically achiral plasmonic metastructures by means of either near-field interaction or chirality inheritance, resulting in hybrid systems with CD signals orders of magnitude larger than that of pristine biomolecules. This exotic property provides a new means to determine molecular chirality at extremely low concentrations (ideally at the single-molecule level). Herein, three strategies of chirality transfer from sub-nanometer biomolecules to sub-micrometer metallic metastructures are analyzed. The physiochemical mechanisms responsible for chirality transfer are elaborated and new fascinating opportunities for employing plasmonic metastructures in chirality-based biosensing and bioimaging are outlined.

Investigating the effect of sugar-terminated nanoparticles on amyloid fibrillogenesis of β-lactoglobulin

In vivo tissue deposition of fibrillar protein aggregates is the cause of several degenerative diseases. Evidence suggests that interfering with the pathology-associated amyloid fibrillogenesis by inhibitory molecules is envisaged as the primary therapeutic strategy. Amyloid fibril formation of proteins has been demonstrated to be influenced by nanoparticles/nanomaterials. As compared with their molecular form counterpart, this work examined the effect of sucrose-terminated nanoparticles on the in vitro amyloid fibrillogenesis and structural properties of β-lactoglobulin at pH 2.0 and 80 °C. ThT binding and electron microscopy results demonstrated that sucrose-terminated nanoparticles were able to suppress β-lactoglobulin fibrillogenesis in a concentration-dependent fashion. Importantly, sucrose-terminated nanoparticles showed better β-lactoglobulin fibril-inhibiting ability than sucrose molecules. ANS fluorescence and right-angle light scattering results showed reduced solvent exposure and decreased aggregation, respectively, in the β-lactoglobulin samples upon treatment with sucrose-terminated nanoparticles. Moreover, fluorescence quenching analyses revealed that the static quenching mechanism and formation of a non-fluorescent fluorophore-nanoparticle complex are involved in the nanoparticle-β-lactoglobulin interaction. We believe that the results from this study may suggest that the nanoparticle form of biocompatible sugar-related osmolytes may serve as effective inhibiting/suppressing agents toward protein fibrillogenesis.

Effect of surface chemistry on islet amyloid polypeptide conformation

The formation of dense, linear arrays (fibrils) by biomolecules is the hallmark of a number of degenerative diseases, such as Alzheimer's and type-2 diabetes. Protein fibrils have also attracted interest as building blocks for new materials. It has long been recognized that surfaces can affect the fibrillation process. Recent work on the model fibril forming protein human islet amyloid polypeptide (hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the rate of fibril formation is lower than on other surfaces. To understand this, replica exchange molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on surfaces of different hydrophobicities. The hydrophobic surface stabilizes α-helical structures which are significantly different to those found on the hydrophilic surface and in bulk solution. There is also a greatly reduced conformational ensemble on the hydrophobic surface due to long-lived contacts between hydrophobic residues on the protein and the surface. This new microscopic information will help us determine the mechanism of the enhancement of fibril formation on surfaces and provides new insight into the effect of nanointerfaces and protein conformation.

Nontoxic Black Phosphorus Quantum Dots Inhibit Insulin Amyloid Fibrillation at an Ultralow Concentration

Amyloid are protein aggregates formed by cross β structures assemblies. Inhibiting amyloid aggregation or facilitating its disassembly are considered to be two major effective therapeutic strategies in diseases involving peptide or protein fibrillation such Alzheimer's disease or diabetes. Using thioflavin-T fluorescence, far-UV circular dichroism spectroscopy, and atomic force microscopy, we found nontoxic and biocompatible black phosphorus quantum dots (BPQDs) appear to have an exceptional capacity to inhibit insulin aggregation and to disassemble formed mature fibrils, even at an ultralow concentration (100 ng/mL). The inhibition of fibrillation persists at all stages of insulin aggregation and increases PC12 cells survival when exposed to amyloid fibrils. Molecular dynamics simulations suggest that BPQDs are able to stabilize the α-helix structure of insulin and obliterate the β-sheet structure to promote the fibril formation. These characteristics make BPQDs be promising candidate in preventing amyloidosis, disease treatment, as well as in the storage and processing of insulin.

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BPQDs inhibit insulin amyloid fibrillation at an ultralow concentration

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BPQDs can depolymerize protofibrils and even mature fibers

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BPQDs inhibit aggregation mainly by van der Waals' force and hydrophobic interaction

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BPQDs are biocompatible and can reduce insulin fibrils-induced cytotoxicity

Shape-controlled synthesis and in situ characterisation of anisotropic Au nanomaterials using liquid cell transmission electron microscopy

Understanding the mechanisms behind crystal nucleation and growth is a fundamental requirement for the design and production of bespoke nanomaterials with controlled sizes and morphologies. Herein, we select gold (Au) nanoparticles as the model system for our study due to their representative applications in biology, electronics and optoelectronics. We investigate the radiation-induced in situ growth of gold (Au) particles using liquid cell transmission electron microscopy (LCTEM) and study the growth kinetics of non-spherical Au structures. Under controlled electron fluence, liquid flow rate and Au3+ ion supply, we show the favoured diffusion-limited growth of multi-twinned nascent Au seed particles into branched structures when using thin liquid cells (100 nm and 250 nm) in LCTEM, whereas faceted structures (e.g., spheres, rods, and prisms) formed when using a 1 μm thick liquid cell. In addition, we observed that anisotropic Au growth could be modulated by Au-binding amyloid fibrils, which we ascribe to their capability to regulate Au3+ ion diffusion and mass transfer in solution. We anticipate that this study will provide new perspectives on the shape-controlled synthesis of anisotropic metallic nanomaterials using LCTEM.

Effects of Gold Nanospheres and Nanocubes on Amyloid-β Peptide Fibrillation

Direct exposure or intake of engineered nanoparticles (ENPs) to the human body will trigger a series of complicated biological consequences. Especially, ENPs could either up- or downregulate peptide fibrillation, which is associated with various degenerative diseases like Alzheimer's and Parkinson's diseases. This work reports the effects of gold nanoparticles (AuNPs) with different shapes on the aggregation of an amyloid-β peptide (Aβ(1-40)) involved in Alzheimer's disease. Two kinds of AuNPs were investigated, i.e., gold nanospheres (AuNSs, ∼20 nm in diameter) and gold nanocubes (AuNCs, ∼20 nm in edge length). It was found that AuNPs play a catalytic role in peptide nucleation through interfacial adsorption of Aβ(1-40). AuNSs with hybrid facets have higher affinity to Aβ(1-40) because of the higher degree of surface atomic unsaturation than the {100}-faceted AuNCs. Therefore, AuNSs exert a more significant acceleration effect on the fibrillation process of Aβ(1-40) than AuNCs. Besides, a shape-dependent secondary structure transformation of Aβ(1-40) with different AuNPs was observed using Fourier transform infrared spectroscopy. The variation of peptide-NP and peptide-peptide interactions caused by the shape alteration of AuNPs influences the equilibrium of inter- and intramolecular hydrogen bonds, which is believed to be responsible for the shape-dependent secondary structure transformation. The study offers further understanding on the complicated NP-mediated Aβ aggregation and also facilitates further development on designing and synthesizing task-specific AuNPs for amyloid disease diagnosis and therapy.

Metal-dependent inhibition of amyloid fibril formation: synergistic effects of cobalt-tannic acid networks

Metal-phenolic networks (MPNs) have received widespread interest owing to their modular incorporation of functional metal ions and phenolic ligands. However, the interaction between MPNs and biomolecules is still relatively unexplored. Herein, we studied the effects of MPN-coated gold nanoparticles on amyloid fibril formation (which is associated with Alzheimer's disease) as a function of the metal ion in the MPN systems. All coated particles examined inhibited amyloid formation, with cobalt(ii) MPN-coated particles exhibiting the highest inhibition activity (90%). Molecular dynamics simulations and quantum mechanics calculations suggested that the geometry of the exposed cobalt coordination site in the cobalt-tannic acid networks facilitates its interactions with histidine and methionine residues in the amyloid beta peptides. Furthermore, the unique structure of cobalt MPNs may enable a wider variety of biomedical applications.

The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations

Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.

Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles

Society is increasingly exposed to nanoparticles as they are ubiquitous in nature and introduced as man-made air pollutants and as functional ingredients in cosmetic products as well as in nanomedicine. Nanoparticles differ in size, shape and material properties. In addition to their intended function, the side effects on biochemical processes in organisms remain unclear. Nanoparticles can significantly influence the nucleation and aggregation process of peptides. The development of several neurodegenerative diseases, such as Alzheimer's disease, is related to the aggregation of peptides into amyloid fibrils. However, there is no comprehensive or universal mechanism to predict or explain apparent acceleration or inhibition of these aggregation processes. In this work, selected studies and possible mechanisms for amyloid peptide nucleation and aggregation, in the presence of nanoparticles, are highlighted. These studies are discussed in the context of recent data from our group on the role of gold nanoparticles in amyloid peptide aggregation using experimental methods and large-scale molecular dynamics simulations. A complex interplay of the surface properties of the nanoparticles, the properties of the peptides, as well as the resulting forces between both the nanoparticles and the peptides, appear to determine whether amyloid peptide aggregation is influenced, catalysed or inhibited by the presence of nanoparticles.

Fibrous Protein Self-Assembly in Biomimetic Materials

Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA. The structural materials that arise from biological self-assembly can display remarkable mechanical properties, often as a result of hierarchical structure on the nano- and microscales, and much research has been devoted to mimicking and exploiting these properties for a variety of end uses. This work presents a review of a range of studies in which biological functions are effectively reproduced through the design of self-assembling fibrous protein systems.

Exploring the Mechanism of Inhibition of Au Nanoparticles on the Aggregation of Amyloid-β(16-22) Peptides at the Atom Level by All-Atom Molecular Dynamics

The abnormal self-assembly of the amyloid-β peptide into toxic β-rich aggregates can cause Alzheimer’s disease. Recently, it has been shown that small gold nanoparticles (AuNPs) inhibit Aβ aggregation and fibrillation by slowing down the nucleation process in experimental studies. However, the effects of AuNPs on Aβ oligomeric structures are still unclear. In this study, we investigate the conformation of Aβ(16-22) tetramers/octamers in the absence and presence of AuNPs using extensive all-atom molecular-dynamics simulations in explicit solvent. Our studies demonstrate that the addition of AuNPs into Aβ(16-22) solution prevents β-sheet formation, and the inhibition depends on the concentration of Aβ(16-22) peptides. A detailed analysis of the Aβ(16-22)/Aβ(16-22)/water/AuNPs interactions reveals that AuNPs inhibit the β-sheet formation resulting from the same physical forces: hydrophobic interactions. Overall, our computational study provides evidence that AuNPs are likely to inhibit Aβ(16-22) and full-length Aβ fibrillation. Thus, this work provides theoretical insights into the development of inorganic nanoparticles as drug candidates for treatment of AD.