Surface- and Solution-Based Assembly of Amyloid Fibrils for Biomedical and Nanotechnology Applications

The contribution of individual residues of an aggregative hexapeptide derived from the human γD-crystallin to its amyloidogenicity

Human γD-crystallin protein is abundant in the lens and is essential for preserving lens transparency. With age the protein may lose its native structure resulting in the formation of cataract. We recently reported an aggregative peptide, ⁴¹Gly-Cys-Trp-Met-Leu-Tyr⁴⁶ from the human γD-crystallin, termed GDC6, exhibiting amyloidogenic properties in vitro. Here, we aimed to determine the contribution of each residue of the GDC6 to its amyloidogenicity. Molecular dynamic (MD) simulations revealed that the residues Trp, Leu, and Tyr played an important role in the amyloidogenicity of GDC6 by facilitating inter-peptide main-chain hydrogen bonds, and π-π interactions. MD predictions were further validated using single-, double- and triple-alanine-substituted GDC6 peptides in which their amyloidogenic propensity was individually evaluated using complementary biophysical techniques including Thioflavin T assay, turbidity assay, CD spectroscopy, and TEM imaging. Results revealed that the substitution of Trp, Leu, and Tyr together by Ala completely abolished aggregation of GDC6 in vitro, highlighting their importance in the amyloidogenicity of GDC6.

Collective Cell Migration in a Fibrous Environment: A Hybrid Multiscale Modelling Approach

The specific structure of the extracellular matrix (ECM), and in particular the density and orientation of collagen fibres, plays an important role in the evolution of solid cancers. While many experimental studies discussed the role of ECM in individual and collective cell migration, there are still unanswered questions about the impact of nonlocal cell sensing of other cells on the overall shape of tumour aggregation and its migration type. There are also unanswered questions about the migration and spread of tumour that arises at the boundary between different tissues with different collagen fibre orientations. To address these questions, in this study we develop a hybrid multi-scale model that considers the cells as individual entities and ECM as a continuous field. The numerical simulations obtained through this model match experimental observations, confirming that tumour aggregations are not moving if the ECM fibres are distributed randomly, and they only move when the ECM fibres are highly aligned. Moreover, the stationary tumour aggregations can have circular shapes or irregular shapes (with finger-like protrusions), while the moving tumour aggregations have elongate shapes (resembling to clusters, strands or files). We also show that the cell sensing radius impacts tumour shape only when there is a low ratio of fibre to non-fibre ECM components. Finally, we investigate the impact of different ECM fibre orientations corresponding to different tissues, on the overall tumour invasion of these neighbouring tissues.

Directionality of Macrophages Movement in Tumour Invasion: A Multiscale Moving-Boundary Approach

Invasion of the surrounding tissue is one of the recognised hallmarks of cancer (Hanahan and Weinberg in Cell 100: 57–70, 2000. 10.1016/S0092-8674(00)81683-9), which is accomplished through a complex heterotypic multiscale dynamics involving tissue-scale random and directed movement of the population of both cancer cells and other accompanying cells (including here, the family of tumour-associated macrophages) as well as the emerging cell-scale activity of both the matrix-degrading enzymes and the rearrangement of the cell-scale constituents of the extracellular matrix (ECM) fibres. The involved processes include not only the presence of cell proliferation and cell adhesion (to other cells and to the extracellular matrix), but also the secretion of matrix-degrading enzymes. This is as a result of cancer cells as well as macrophages, which are one of the most abundant types of immune cells in the tumour micro-environment. In large tumours, these tumour-associated macrophages (TAMs) have a tumour-promoting phenotype, contributing to tumour proliferation and spread. In this paper, we extend a previous multiscale moving-boundary mathematical model for cancer invasion, by considering also the multiscale effects of TAMs, with special focus on the influence that their directional movement exerts on the overall tumour progression. Numerical investigation of this new model shows the importance of the interactions between pro-tumour TAMs and the fibrous ECM, highlighting the impact of the fibres on the spatial structure of solid tumour.

Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration

An overview of recent advances in computational investigation of peptide–lipid interactions in neurodegeneration – Alzheimer's, Parkinson's and Huntington's disease.

Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones

Amyloids are highly organized cross β-sheet protein nanofibrils that are associated with both diseases and functions. Thermodynamically amyloids are stable structures as they represent the lowest free energy state that proteins can attain. However, recent studies suggest that amyloid fibrils can be dissociated by a change in environmental parameters such as pH and ionic strength. This reversibility of amyloids can not only be associated with disease, but function as well. In disease-associated amyloids, fibrils can act as reservoirs of cytotoxic oligomers. Recently, in higher organisms such as mammals, hormones were found to be stored in amyloid-like state, where these were reported to act as a reservoir of functional monomers. These hormone amyloids can dissociate to monomers upon release from the secretory granules, and subsequently bind to their respective receptors and perform their functions. In this book chapter, we describe in detail how these protein nanofibrils represent the densest possible peptide packing and are suitable for long-term storage. Thus, mimicking the feature of amyloids to release functional monomers, it is possible to formulate amyloid-based peptide/protein drugs, which can be used for sustained release.

Amyloids Are Novel Cell-Adhesive Matrices

Amyloids are highly ordered peptide/protein aggregates traditionally associated with multiple human diseases including neurodegenerative disorders. However, recent studies suggest that amyloids can also perform several biological functions in organisms varying from bacteria to mammals. In many lower organisms, amyloid fibrils function as adhesives due to their unique surface topography. Recently, amyloid fibrils have been shown to support attachment and spreading of mammalian cells by interacting with the cell membrane and by cell adhesion machinery activation. Moreover, similar to cellular responses on natural extracellular matrices (ECMs), mammalian cells on amyloid surfaces also use integrin machinery for spreading, migration, and differentiation. This has led to the development of biocompatible and implantable amyloid-based hydrogels that could induce lineage-specific differentiation of stem cells. In this chapter, based on adhesion of both lower organisms and mammalian cells on amyloid nanofibrils, we posit that amyloids could have functioned as a primitive extracellular matrix in primordial earth.

Chemically and thermally stable silica nanowires with a β-sheet peptide core for bionanotechnology

BACKGROUND

A series of amyloidogenic peptides based on the sequence KFFEAAAKKFFE template the silica precursor, tetraethyl orthosilicate to form silica-nanowires containing a cross-β peptide core.

RESULTS

Investigation of the stability of these fibres reveals that the silica layers protect the silica-nanowires allowing them to maintain their shape and physical and chemical properties after incubation with organic solvents such as 2-propanol, ethanol, and acetonitrile, as well as in a strong acidic solution at pH 1.5. Furthermore, these nanowires were thermally stable in an aqueous solution when heated up to 70 °C, and upon autoclaving. They also preserved their conformation following incubation up to 4 weeks under these harsh conditions, and showed exceptionally high physical stability up to 1000 °C after ageing for 12 months. We show that they maintain their β-sheet peptide core even after harsh treatment by confirming the β-sheet content using Fourier transform infrared spectra. The silica nanowires show significantly higher chemical and thermal stability compared to the unsiliconised fibrils.

CONCLUSIONS

The notable chemical and thermal stability of these silica nanowires points to their potential for use in microelectromechanics processes or fabrication for nanotechnological devices.

Cell Adhesion on Amyloid Fibrils Lacking Integrin Recognition Motif

Amyloids are highly ordered, cross-β-sheet-rich protein/peptide aggregates associated with both human diseases and native functions. Given the well established ability of amyloids in interacting with cell membranes, we hypothesize that amyloids can serve as universal cell-adhesive substrates. Here, we show that, similar to the extracellular matrix protein collagen, amyloids of various proteins/peptides support attachment and spreading of cells via robust stimulation of integrin expression and formation of integrin-based focal adhesions. Additionally, amyloid fibrils are also capable of immobilizing non-adherent red blood cells through charge-based interactions. Together, our results indicate that both active and passive mechanisms contribute to adhesion on amyloid fibrils. The present data may delineate the functional aspect of cell adhesion on amyloids by various organisms and its involvement in human diseases. Our results also raise the exciting possibility that cell adhesivity might be a generic property of amyloids.

Back to the oligomeric state: pH-induced dissolution of concanavalin A amyloid-like fibrils into non-native oligomers

Changes in solution pH may result in modifications of energy landscape shape making readily accessible or more favourable native or oligomeric intermediate minima with respect to the fibrillar one.

Correlation between nanomechanics and polymorphic conformations in amyloid fibrils

Amyloid fibrils occur in diverse morphologies, but how polymorphism affects the resulting mechanical properties is still not fully appreciated. Using formalisms from the theory of elasticity, we propose an original way of averaging the second area moment of inertia for non-axisymmetric fibrils, which constitutes the great majority of amyloid fibrils. By following this approach, we derive theoretical expressions for the bending properties of the most common polymorphic forms of amyloid fibrils (twisted ribbons, helical ribbons, and nanotubes), and we benchmark the predictions to experimental cases. These results not only allow an accurate estimation of the amyloid fibrils' elastic moduli but also bring insight into the structure-property relationships in the nanomechanics of amyloid systems, such as in the closure of helical ribbons into nanotubes.

Stability and cytotoxicity of crystallin amyloid nanofibrils

Previous work has identified crystallin proteins extracted from fish eye lenses as a cheap and readily available source for the self-assembly of amyloid nanofibrils. However, before exploring potential applications, the biophysical aspects and safety of this bionanomaterial need to be assessed so as to ensure that it can be effectively and safely used. In this study, crude crystallin amyloid fibrils are shown to be stable across a wide pH range, in a number of industrially relevant solvents, at both low and high temperatures, and in the presence of proteases. Crystallin nanofibrils were compared to well characterised insulin and whey protein fibrils using Thioflavin T assays and TEM imaging. Cell cytotoxicity assays suggest no adverse impact of both mature and fragmented crystallin fibrils on cell viability of Hec-1a endometrial cells. An IR microspectroscopy study supports long-term structural integrity of crystallin nanofibrils.

Proteins and peptides as biological nanowires: towards biosensing devices

The current landscape of nanotechnology is such that attention is being given to those materials that self-assemble, as a mode of "bottom-up" fabrication of nanomaterials. The field of nanotubes and nanowires has long been dominated by carbon nanotubes and inorganic materials. However in more recent years, the search for materials with desirable properties, such as self-assembly, has unsurprisingly led to the biological world, where functional nanoscale biomolecular assemblies are in abundance.Potential has been seen for a number of these assemblies to be translated into functional nanomaterials. The early days of bionanotechnology saw a lot of attention given to DNA molecules as nanowires, and proteins and peptides have now also been seen to have promise in this area. With most of the biological structures investigated having low conductivity in the native state, the use of biomolecules as templates for the formation of metallic and semiconductor nanowires has been the direction taken.This chapter will discuss the use of various biomolecules and biomolecular assemblies as nanowires, with a particular emphasis on proteins, beginning with an introduction into the field of nanotubes and nanowires. Many applications are now recognized for nanowires, but for brevity, this chapter will focus solely on their use as biosensors, using glucose sensors as a case study.

Biodegradable nanocomposites of amyloid fibrils and graphene with shape-memory and enzyme-sensing properties

Graphene has exceptional mechanical and electronic properties, but its hydrophobic nature is a disadvantage in biologically related applications. Amyloid fibrils are naturally occurring protein aggregates that are stable in solution or under highly hydrated conditions, have well-organized supramolecular structures and outstanding strength. Here, we show that graphene and amyloid fibrils can be combined to create a new class of biodegradable composite materials with adaptable properties. This new composite material is inexpensive, highly conductive and can be degraded by enzymes. Furthermore, it can reversibly change shape in response to variations in humidity, and can be used in the design of biosensors for quantifying the activity of enzymes. The properties of the composite can be fine-tuned by changing the graphene-to-amyloid ratio.