Differentially Instructive Extracellular Protein Micro-nets

Hyperspectral Mapping of Human Primary and Stem Cells at Cell-Matrix Interfaces

Extracellular matrices interface with cells to promote cell growth and tissue development. Given this critical role, matrix mimetics are introduced to enable biomedical materials ranging from tissue engineering scaffolds and tumor models to organoids for drug screening and implant surface coatings. Traditional microscopy methods are used to evaluate such materials in their ability to support exploitable cell responses, which are expressed in changes in cell proliferation rates and morphology. However, the physical imaging methods do not capture the chemistry of cells at cell-matrix interfaces. Herein, we report hyperspectral imaging to map the chemistry of human primary and embryonic stem cells grown on matrix materials, both native and artificial. We provide the statistical analysis of changes in lipid and protein content of the cells obtained from infrared spectral maps to conclude matrix morphologies as a major determinant of biochemical cell responses. The study demonstrates an effective methodology for evaluating bespoke matrix materials directly at cell-matrix interfaces.

Extracellular matrix type 0: From ancient collagen lineage to a versatile product pipeline - JellaGel™

Extracellular matrix type 0 is reported. The matrix is developed from a jellyfish collagen predating mammalian forms by over 0.5 billion years. With its ancient lineage, compositional simplicity, and resemblance to multiple collagen types, the matrix is referred to as the extracellular matrix type 0. Here we validate the matrix describing its physicochemical and biological properties and present it as a versatile, minimalist biomaterial underpinning a pipeline of commercialised products under the collective name of JellaGelTM. We describe an extensive body of evidence for folding and assembly of the matrix in comparison to mammalian matrices, such as bovine collagen, and its use to support cell growth and development in comparison to known tissue-derived products, such as Matrigel™. We apply the matrix to co-culture human astrocytes and cortical neurons derived from induced pluripotent stem cells and visualise neuron firing synchronicity with correlations indicative of a homogenous extracellular material in contrast to the performance of heterogenous commercial matrices. We prove the ability of the matrix to induce spheroid formation and support the 3D culture of human immortalised, primary, and mesenchymal stem cells. We conclude that the matrix offers an optimal solution for systemic evaluations of cell-matrix biology. It effectively combines the exploitable properties of mammalian tissue extracts or top-down matrices, such as biocompatibility, with the advantages of synthetic or bottom-up matrices, such as compositional control, while avoiding the drawbacks of the two types, such as biological and design heterogeneity, thereby providing a unique bridging capability of a stem extracellular matrix.

Amyloid-β Inspired Short Peptide Amphiphile Facilitates Synthesis of Silver Nanoparticles as Potential Antibacterial Agents

An amyloid-β inspired biocompatible short peptide amphiphile (sPA) molecule was used for controlled and targeted delivery of bioactive silver nanoparticles via transforming sPA nanostructures. Such sPA-AgNPs hybrid structures can be further used to develop antibacterial materials to combat emerging bacterial resistance. Due to the excellent antibacterial activity of silver, the growth of clinically relevant bacteria was inhibited in the presence of AgNPs-sPA hybrids. Bacterial tests demonstrated that the high biocompatibility and low cytotoxicity of the designed sPA allow it to work as a model drug delivery agent. It therefore shows great potential in locally addressing bacterial infections. The results of our study suggest that these nanodevices have the potential to trap and then engage in the facile delivery of their chemical payload at the target site, thereby working as potential delivery materials. This system has potential therapeutic value for the treatment of microbiota triggered progression of neurodegenerative diseases.

Atomic force microscopy to elucidate how peptides disrupt membranes

Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.

Cellular Metrology: Scoping for a Value Proposition in Extra- and Intracellular Measurements

The symptomatic irreproducibility of data in biomedicine and biotechnology prompts the need for higher order measurements of cells in their native and near-native environments. Such measurements may support the adoption of new technologies as well as the development of research programs across different sectors including healthcare and clinic, environmental control and national security. With an increasing demand for reliable cell-based products and services, cellular metrology is poised to help address current and emerging measurement challenges faced by end-users. However, metrological foundations in cell analysis remain sparse and significant advances are necessary to keep pace with the needs of modern medicine and industry. Herein we discuss a role of metrology in cell and cell-related R&D activities to underpin growing international measurement capabilities. Relevant measurands are outlined and the lack of reference methods and materials, particularly those based on functional cell responses in native environments, is highlighted. The status quo and current challenges in cellular measurements are discussed in the light of metrological traceability in cell analysis and applications (e.g., a functional cell count). An emphasis is made on the consistency of measurement results independent of the analytical platform used, high confidence in data quality vs. quantity, scale of measurements and issues of building infrastructure for end-users.

Transition metal ions induced secondary structural transformation in a hydrophobized short peptide amphiphile

Transition metal ions mediate the secondary structural transformation of hydrophobized sPA and can be applied to the design and development of stimuli-responsive nanomaterials.

Peptide Tectonics: Encoded Structural Complementarity Dictates Programmable Self-Assembly

Programmable self-assembly of peptides into well-defined nanostructures represents one promising approach for bioinspired and biomimetic synthesis of artificial complex systems and functional materials. Despite the progress made over the past two decades in the development of strategies for precise manipulation of the self-assembly of peptides, there is a remarkable gap between current peptide assemblies and biological systems in terms of structural complexity and functions. Here, the concept of peptide tectonics for the creation of well-defined nanostructures predominately driven by the complementary association at the interacting interfaces of tectons is introduced. Peptide tectons are defined as peptide building blocks exhibiting structural complementarity at the interacting interfaces of commensurate domains and undergoing programmable self-assembly into defined supramolecular structures promoted by complementary interactions. Peptide tectons are categorized based on their conformational entropy and the underlying mechanism for the programmable self-assembly of peptide tectons is highlighted focusing on the approaches for incorporating the structural complementarity within tectons. Peptide tectonics not only provides an alternative perspective to understand the self-assembly of peptides, but also allows for precise manipulation of peptide interactions, thus leading to artificial systems with advanced complexity and functions and paves the way toward peptide-related functional materials resembling natural systems.

Transition Metal Ion-Mediated Tyrosine-Based Short-Peptide Amphiphile Nanostructures Inhibit Bacterial Growth

We report the design and synthesis of a biocompatible small-peptide-based compound for the controlled and targeted delivery of encapsulated bioactive metal ions through transformation of the internal nanostructures of its complexes. A tyrosine-based short-peptide amphiphile (sPA) was synthesized and observed to self-assemble into β-sheet-like secondary structures. The self-assembly of the designed sPA was modulated by application of different bioactive transition-metal ions, as was confirmed by spectroscopic and microscopic techniques. These bioactive metal-ion-conjugated sPA hybrid structures were further used to develop antibacterial materials. As a result of the excellent antibacterial activity of zinc ions the growth of clinically relevant bacteria such as Escherichia coli was inhibited in the presence of zinc⋅sPA conjugate. Bacterial testing demonstrated that, due to high biocompatibility with bacterial cells, the designed sPA acted as a metal ion delivery agent and might therefore show great potential in locally addressing bacterial infections.

Imaging Protein Fibers at the Nanoscale and In Situ

Protein self-assembly offers a rich repertoire of tools and technologies. However, despite significant progress in this area, a deterministic measure of the phenomenon, which might lead to predictable relationships between protein components, assembly mechanisms, and ultimately function, is lacking. Often the challenge relates to the choice of the most informative and precise measurements that can link the chemistry of the building blocks with the resulting assembly, ideally in situ and in real time. Using the example of protein fibrillogenesis-a self-assembly process fundamental to nearly every aspect of biological organization, from viral assembly to tissue restoration-this chapter demonstrates how protein self-assembly can be visually and precisely measured while providing measurement protocols applicable to other self-assembly systems.

Antimicrobial peptide capsids of de novo design

The spread of bacterial resistance to antibiotics poses the need for antimicrobial discovery. With traditional search paradigms being exhausted, approaches that are altogether different from antibiotics may offer promising and creative solutions. Here, we introduce a de novo peptide topology that—by emulating the virus architecture—assembles into discrete antimicrobial capsids. Using the combination of high-resolution and real-time imaging, we demonstrate that these artificial capsids assemble as 20-nm hollow shells that attack bacterial membranes and upon landing on phospholipid bilayers instantaneously (seconds) convert into rapidly expanding pores causing membrane lysis (minutes). The designed capsids show broad antimicrobial activities, thus executing one primary function—they destroy bacteria on contact.

With the growing threat of antibiotic resistance, unconventional approaches to antimicrobial discovery are needed. Here, the authors present a peptide topology that mimics virus architecture and assembles into antimicrobial capsids that disrupt bacterial membranes upon contact.

Peptide-Based Polymer-Polyoxometalate Supramolecular Structure with a Differed Antimicrobial Mechanism

Because of the increasing prevalence of multidrug resistance feature, several investigations have been so far reported regarding the antibiotic alternative supramolecular bioactive agents made of hybrid assemblies. In this regard, it is well-established that combinational therapy inherited by assembled supramolecular structures can improve the bioactivity to some extent, but their mode of action has not been studied in detail. We provide first direct evidence that the improved mechanism of action of antimicrobial supra-amphiphilic nanocomposites differs largely from their parent antimicrobial peptide-based polymers. For the construction of a hybrid combinational system, we have synthesized side-chain peptide-based antimicrobial polymers via RAFT polymerization and exploited their cationic nature to decorate supra-amphiphilic nanocomposites via interaction with anionic polyoxometalates. Because of cooperative antimicrobial properties of both the polymer and polyoxometalate, the nanocomposites show an enhanced antimicrobial activity with a different antimicrobial mechanism. The cationic stimuli-responsive peptide-based polymers attack bacteria via membrane disruption mechanism, whereas free radical-mediated cell damage is the likely mechanism of polymer-polyoxometalate-based supra-amphiphilic nanocomposites. Thus, our study highlights the different antimicrobial mechanism of combinational systems in detail, which improves our understanding of enhanced antimicrobial efficacy.

Fabrication of a biomimetic ZeinPDA nanofibrous scaffold impregnated with BMP-2 peptide conjugated TiO2 nanoparticle for bone tissue engineering

A biomimetic Zein polydopamine based nanofiber scaffold was fabricated to deliver bone morphogenic protein-2 (BMP-2) peptide conjugated titanium dioxide nanoparticles in a sustained manner for investigating its osteogenic differentiation potential. To prolong its retention time at the target site, BMP-2 peptide has been conjugated to titanium dioxide nanoparticles owing to its high surface to volume ratio. The effect of biochemical cues from BMP-2 peptide and nanotopographical stimulation of electrospun Zein polydopamine nanofiber were examined for its enhanced osteogenic expression of human fetal osteoblast cells. The sustained delivery of bioactive signals, improved cell adhesion, mineralization, and differentiation could be attributed to its highly interconnected nanofibrous matrix with unique material composition. Further, the expression of osteogenic markers revealed that the fabricated nanofibrous scaffold possess better cell-biomaterial interactions. These promising results demonstrate the potential of the composite nanofibrous scaffold as an effective biomaterial substrate for bone regeneration.

Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition

Self-assembly of small biomolecules is a prevalent phenomenon that is increasingly being recognised to hold the key to building complex structures from simple monomeric units. Small peptides, in particular ultrashort peptides containing up to seven amino acids, for which our laboratory has found many biomedical applications, exhibit immense potential in this regard. For next-generation applications, more intricate control is required over the self-assembly processes. We seek to find out how subtle moiety variation of peptides can affect self-assembly and nanostructure formation. To this end, we have selected a library of 54 tripeptides, derived from systematic moiety variations from seven tripeptides. Our study reveals that subtle structural changes in the tripeptides can exert profound effects on self-assembly, nanostructure formation, hydrogelation, and even phase transition of peptide nanostructures. By comparing the X-ray crystal structures of two tripeptides, acetylated leucine-leucine-glutamic acid (Ac-LLE) and acetylated tyrosine-leucine-aspartic acid (Ac-YLD), we obtained valuable insights into the structural factors that can influence the formation of supramolecular peptide structures. We believe that our results have major implications on the understanding of the factors that affect peptide self-assembly. In addition, our findings can potentially assist current computational efforts to predict and design self-assembling peptide systems for diverse biomedical applications.

CREIM: Coffee Ring Effect Imaging Model for Monitoring Protein Self-Assembly in Situ

Protein self-assembly is fundamental to nanotechnology. Self-assembling structures are produced under static in vitro conditions typically forming over hours. In contrast, hydrodynamic intracellular environments employ far shorter time scales to compartmentalize highly concentrated protein solutions. Herein, we exploit the radial capillary flow within a drying sessile droplet (the coffee ring effect) to emulate dynamic native environments and monitor an archetypal protein assembly in situ using high-speed super-resolution imaging. We demonstrate that the assembly can be empirically driven to completion within minutes to seconds without apparent changes in supramolecular morphology. The model offers a reliable tool for the diagnosis and engineering of self-assembling systems under nonequilibrium conditions.

Membrane association of the bacterial riboregulator Hfq and functional perspectives

Hfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption. Precisely, AFM images of lipid bilayers in contact with Hfq C-terminus fibrils show the emergence of holes with a size dependent on the time of interaction. Cryo-TEM observations also show that liposomes are in contact with clusters of fibrils, with occasional deformation of the vesicles and afterward the apparition of a multitude of tiny vesicles in the proximity of the fibrils, suggesting peptide-induced breakage of the liposomes. Finally, circular dichroism spectroscopy demonstrated a change in the secondary structure of Hfq C-terminus upon interaction with liposomes. Altogether, these results show an unexpected property of Hfq and suggest a possible new role for the protein, exporting sRNA outside of the bacterial cell.

Linear and orthogonal peptide templating of silicified protein fibres

Biomineralisation is essential for biology. Specialist proteins use peptide motifs that catalyse mineral deposition into nano-to-microscale inorganic materials. Unlike in native proteins, the motifs incorporated into self-assembled fibres can persistently propagate on the microscopic scale enabling empirically defined silica nanostructures. Herein we show that the two main modes of motif templating - linear and orthogonal - in self-assembling, fibre-forming peptide sequences effectively silicify protein fibres. We show that the mere charge and morphology of protein fibres are not sufficient for silica deposition, but it is the synergy between fibrillogenesis and silica-specific motifs regularly spaced in fibres that ensures silica templating, regardless of the relative orientation of the motifs.

Nano-mechanical single-cell sensing of cell-matrix contacts

Extracellular protein matrices provide a rigidity interface exhibiting nano-mechanical cues that guide cell growth and proliferation. Cells sense such cues using actin-rich filopodia extensions which encourage favourable cell-matrix contacts to recruit more actin-mediated local forces into forming stable focal adhesions. A challenge remains in identifying and measuring these local cellular forces and in establishing empirical relationships between them, cell adhesion and filopodia formation. Here we investigate such relationships using a micromanipulation system designed to operate at the time scale of focal contact dynamics, with the sample frequency of a force probe being 0.1 ms, and to apply and measure forces at nano-to-micro Newton ranges for individual mammalian cells. We explore correlations between cell biomechanics, cell-matrix attachment forces and the spread areas of adhered cells as well as their relative dependence on filopodia formation using synthetic protein matrices with a proven ability to induce enhanced filopodia numbers in adherent cells. This study offers a basis for engineering exploitable cell-matrix contacts in situ at the nanoscale and single-cell levels.

Structurally plastic peptide capsules for synthetic antimicrobial viruses

A conceptual design for artificial antimicrobial viruses is described. The design emulates viral assembly and function to create self-assembling peptide capsules that promote efficient gene delivery and silencing in mammalian cells. Unlike viruses, however, the capsules are antimicrobial, which allows them to exhibit a dual biological function: gene transport and antimicrobial activity. Unlike other antimicrobials, the capsules act as pre-concentrated antimicrobial agents that elicit rapid and localised membrane-disrupting responses by converting into individual pores at their precise landing positions on membranes. The concept holds promise for engineering virus-like scaffolds with biologically tuneable properties.

Advances in Functional Assemblies for Regenerative Medicine

The ability to synthesise bioresponsive systems and selectively active biochemistries using polymer-based materials with supramolecular features has led to a surge in research interest directed towards their development as next generation biomaterials for drug delivery, medical device design and tissue engineering.

Formation of functional super-helical assemblies by constrained single heptad repeat

Inspired by the key role of super-helical motifs in molecular self-organization, several tandem heptad repeat peptides were used as building blocks to form well-ordered supramolecular nano-assemblies. However, the need for stable helical structures limits the length of the smallest described units to three heptad repeats. Here we describe the first-ever self-assembling single heptad repeat module, based on the ability of the non-coded α-aminoisobutyric acid to stabilize very short peptides in helical conformation. A conformationally constrained peptide comprised of aromatic, but not aliphatic, residues, at the first and fourth positions formed helical fibrillar assemblies. Single crystal X-ray analysis of the peptide demonstrates super-helical packing in which phenylalanine residues formed an ‘aromatic zipper' arrangement at the molecular interface. The modification of the minimal building block with positively charged residues results in tight DNA binding ascribed to the combined factors of helicity, hydrophobicity and charge. The design of these peptides defines a new direction for assembly of super-helical nanostructures by minimal molecular elements.

Advances in bionanotechnology demand an increased portfolio of assemblies beyond those currently available. Here, the authors design a crystallographically characterized super-helical sequence composed of single heptad repeats which, through derivatisation, offers vast potential applications.

Peptide self-assembly for nanomaterials: the old new kid on the block

Peptide self-assembly is an increasingly attractive tool for nanomaterials. Perfected in biology peptide self-assembling systems have impacted on nearly any conceivable nanomaterial type. However, with all the information available to us commercialisation of peptide materials remains in its infancy. In an attempt to better understand the reasons behind this shortcoming we categorise peptide self-assembled materials in relation to their non-peptide counterparts. A particular emphasis is placed on the versatility of peptide self-assembly in terms of modularity, responsiveness and functional diversity, which enables direct comparisons with more traditional material chemistries.

Dynamic biointerfaces: from recognition to function

The transformation of recognition signals into regulating macroscopic behaviors of biological entities (e.g., biomolecules and cells) is an extraordinarily challenging task in engineering interfacial properties of artificial materials. Recently, there has been extensive research for dynamic biointerfaces driven by biomimetic techniques. Weak interactions and chirality are two crucial routes that nature uses to achieve its functions, including protein folding, the DNA double helix, phospholipid membranes, photosystems, and shell and tooth growths. Learning from nature inspires us to design dynamic biointerfaces, which usually take advantage of highly selective weak interactions (e.g., synergetic chiral H-bonding interactions) to tailor their molecular assemblies on external stimuli. Biomolecules can induce the conformational transitions of dynamic biointerfaces, then drive a switching of surface characteristics (topographic structure, wettability, etc.), and eventually achieve macroscopic functions. The emerging progresses of dynamic biointerfaces are reviewed and its role from molecular recognitions to biological functions highlighted. Finally, a discussion is presented of the integration of dynamic biointerfaces with the basic biochemical processes, possibly solving the big challenges in life science.

Supramolecular amphipathicity for probing antimicrobial propensity of host defence peptides

Supramolecular amphipathicity exposes antimicrobial propensity of host defence peptides.

Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains

Synthetic collagen mimetic peptides are used to probe the role of hydrophobic forces in mediating protein self-assembly. Higher order association is an integral property of natural collagens, which assemble into fibers and meshes that comprise the extracellular matrix of connective tissues. The unique triple-helix fold fully exposes two-thirds of positions in the protein to solvent, providing ample opportunities for engineering interaction sites. Inclusion of just a few hydrophobic groups in a minimal peptide promotes a rich variety of self-assembly behaviors, resulting in hundred-nanometer to micron size nanodiscs and nanofibers. Morphology depends primarily on the length of hydrophobic domains. Peptide discs contain lipophilic domains capable of sequestering small hydrophobic dyes. Combining multiple peptide types result in composite structures of discs and fibers ranging from stars to plates-on-a-string. These systems provide valuable tools to shed insight into the fundamental principles underlying hydrophobicity-driven higher order protein association that will facilitate the design of self-assembling systems in biomaterials and nanomedical applications.

Cicada-inspired cell-instructive nanopatterned arrays

Biocompatible surfaces hold key to a variety of biomedical problems that are directly related to the competition between host-tissue cell integration and bacterial colonisation. A saving solution to this is seen in the ability of cells to uniquely respond to physical cues on such surfaces thus prompting the search for cell-instructive nanoscale patterns. Here we introduce a generic rationale engineered into biocompatible, titanium, substrates to differentiate cell responses. The rationale is inspired by cicada wing surfaces that display bactericidal nanopillar patterns. The surfaces engineered in this study are titania (TiO2) nanowire arrays that are selectively bactericidal against motile bacteria, while capable of guiding mammalian cell proliferation according to the type of the array. The concept holds promise for clinically relevant materials capable of differential physico-mechanical responses to cellular adhesion.