Two-dimensional microscale engineering of protein-based nanoparticles for cell guidance

Hierarchical Quatsome-RGD Nanoarchitectonic Surfaces for Enhanced Integrin-Mediated Cell Adhesion

The synthesis and study of the tripeptide Arg-Gly-Asp (RGD), the binding site of different extracellular matrix proteins, e.g., fibronectin and vitronectin, has allowed the production of a wide range of cell adhesive surfaces. Although the surface density and spacing of the RGD peptide at the nanoscale have already shown a significant influence on cell adhesion, the impact of its hierarchical nanostructure is still rather unexplored. Accordingly, a versatile colloidal system named quatsomes, based on fluid nanovesicles formed by the self-assembling of cholesterol and surfactant molecules, has been devised as a novel template to achieve hierarchical nanostructures of the RGD peptide. To this end, RGD was anchored on the vesicle's fluid membrane of quatsomes, and the RGD-functionalized nanovesicles were covalently anchored to planar gold surfaces, forming a state of quasi-suspension, through a long poly(ethylene glycol) (PEG) chain with a thiol termination. An underlying self-assembled monolayer (SAM) of a shorter PEG was introduced for vesicle stabilization and to avoid unspecific cell adhesion. In comparison with substrates featuring a homogeneous distribution of RGD peptides, the resulting hierarchical nanoarchitectonic dramatically enhanced cell adhesion, despite lower overall RGD molecules on the surface. The new versatile platform was thoroughly characterized using a multitechnique approach, proving its enhanced performance. These findings open new methods for the hierarchical immobilization of biomolecules on surfaces using quatsomes as a robust and novel tissue engineering strategy.

Methods for Processing Protein Aggregates into Surfaces

The processing of inclusion bodies (IBs) into surfaces is of great interest for cell culture applications due to the combined physical and biological cues these particles provide. The arrangement of these IBs into defined and tunable micropatterns can be useful for basic research purposes regarding the mechanical properties needed for cell adhesion and migration, among other responses. There are several approaches that can be used when functionalizing a substrate with IBs, regarding both the strategy used and also the kind of surface-particle interaction. The interaction between surface and IB can be mainly of three types: physisorption, electrostatic or covalent. This interaction can be controlled by depositing an appropriate self-assembled monolayer (SAM) on top of a substrate as an interface. Furthermore, several strategies can be used to immobilize IBs on surfaces in various configurations, like random deposition, micrometric printed geometries or gradient patterns.

Methods for the Characterization of Protein Aggregates

The physicochemical characterization of protein aggregates yields an important contribution to further our understanding on many diseases for which the formation of protein aggregates is one of the pathological hallmarks. On the other hand, bacterial inclusion bodies (IBs) have recently been shown to be highly pure proteinaceous aggregates of a few hundred nanometers, produced by recombinant bacteria supporting the biological activities of the embedded polypeptides. Despite the wide spectrum of uses of IBs as functional and biocompatible materials upon convenient engineering, very few is known about their physicochemical properties.In this chapter we present methods for the characterization of protein aggregates as particulate materials relevant to their physicochemical and nanoscale properties.Specifically, we describe the use of dynamic light scattering (DLS) for sizing, nanoparticle tracking analysis for sizing and counting, and zeta potential measurements for the determination of colloidal stability. To study the morphology of protein aggregates we present the use of atomic force microscopy (AFM) and scanning electron microscopy (SEM). Cryo-transmission electron microscopy (cryo-TEM) will be used for the determination of the internal structuration. Moreover, wettability and nanomechanical characterization can be performed using contact angle (CA) and force spectroscopic AFM (FS-AFM) measurements of the proteinaceous nanoparticles, respectively. Finally, the 4'4-dithiodipyridine (DTDP) method is presented as a way of relatively quantifying accessible sulfhydryl groups in the structure of the nanoparticle .The physical principles of the methods are briefly described and examples are given to help clarify capabilities of each technique.

Polylactide, Processed by a Foaming Method Using Compressed Freon R134a, for Tissue Engineering

Fabricating polymeric scaffolds using cost-effective manufacturing processes is still challenging. Gas foaming techniques using supercritical carbon dioxide (scCO₂) have attracted attention for producing synthetic polymer matrices; however, the high-pressure requirements are often a technological barrier for its widespread use. Compressed 1,1,1,2-tetrafluoroethane, known as Freon R134a, offers advantages over CO₂ in manufacturing processes in terms of lower pressure and temperature conditions and the use of low-cost equipment. Here, we report for the first time the use of Freon R134a for generating porous polymer matrices, specifically polylactide (PLA). PLA scaffolds processed with Freon R134a exhibited larger pore sizes, and total porosity, and appropriate mechanical properties compared with those achieved by scCO₂ processing. PLGA scaffolds processed with Freon R134a were highly porous and showed a relatively fragile structure. Human mesenchymal stem cells (MSCs) attached to PLA scaffolds processed with Freon R134a, and their metabolic activity increased during culturing. In addition, MSCs displayed spread morphology on the PLA scaffolds processed with Freon R134a, with a well-organized actin cytoskeleton and a dense matrix of fibronectin fibrils. Functionalization of Freon R134a-processed PLA scaffolds with protein nanoparticles, used as bioactive factors, enhanced the scaffolds' cytocompatibility. These findings indicate that gas foaming using compressed Freon R134a could represent a cost-effective and environmentally friendly fabrication technology to produce polymeric scaffolds for tissue engineering approaches.

Coiled-Coil Based Inclusion Bodies and Their Potential Applications

The production of recombinant proteins using microbial cell factories is frequently associated with the formation of inclusion bodies (IBs). These proteinaceous entities can be sometimes a reservoir of stable and active protein, might display good biocompatibility, and are produced efficiently and cost-effectively. Thus, these submicrometric particles are increasingly exploited as functional biomaterials for biotechnological and biomedical purposes. The fusion of aggregation-prone sequences to the target protein is a successful strategy to sequester soluble recombinant polypeptides into IBs. Traditionally, the use of these IB-tags results in the formation of amyloid-like scaffolds where the protein of interest is trapped. This amyloid conformation might compromise the protein's activity and be potentially cytotoxic. One promising alternative to overcome these limitations exploits the coiled-coil fold, composed of two or more α-helices and widely used by nature to create supramolecular assemblies. In this review, we summarize the state-of-the-art of functional IBs technology, focusing on the coiled-coil-assembly strategy, describing its advantages and applications, delving into future developments and necessary improvements in the field.

Recent advances in luminescent materials for super-resolution imaging via stimulated emission depletion nanoscopy

Recent progress on STED fluorophores for super-resolution imaging and also their characteristics are outlined here, thus providing some guidelines to select proper probes and even develop new materials for super-resolution imaging via STED nanoscopy.

Stable anchoring of bacteria-based protein nanoparticles for surface enhanced cell guidance

In tissue engineering, biological, physical, and chemical inputs have to be combined to properly mimic cellular environments and successfully build artificial tissues which can be designed to fulfill different biomedical needs such as the shortage of organ donors or the development of in vitro disease models for drug testing. Inclusion body-like protein nanoparticles (pNPs) can simultaneously provide such physical and biochemical stimuli to cells when attached to surfaces. However, this attachment has only been made by physisorption. To provide a stable anchoring, a covalent binding of lactic acid bacteria (LAB) produced pNPs, which lack the innate pyrogenic impurities of Gram-negative bacteria like Escherichia coli, is presented. The reported micropatterns feature a robust nanoscale topography with an unprecedented mechanical stability. In addition, they are denser and more capable of influencing cell morphology and orientation. The increased stability and the absence of pyrogenic impurities represent a step forward towards the translation of this material to a clinical setting.

High-Throughput Cell Motility Studies on Surface-Bound Protein Nanoparticles with Diverse Structural and Compositional Characteristics

Eighty areas with different structural and compositional characteristics made of bacterial inclusion bodies formed by the fibroblast growth factor (FGF-IBs) were simultaneously patterned on a glass surface with an evaporation-assisted method that relies on the coffee-drop effect. The resulting surface patterned with these protein nanoparticles enabled to perform a high-throughput study of the motility of NIH-3T3 fibroblasts under different conditions including the gradient steepness, particle concentrations, and area widths of patterned FGF-IBs, using for the data analysis a methodology that includes "heat maps". From this analysis, we observed that gradients of concentrations of surface-bound FGF-IBs stimulate the total cell movement but do not affect the total net distances traveled by cells. Moreover, cells tend to move toward an optimal intermediate FGF-IB concentration (i.e., cells seeded on areas with high IB concentrations moved toward areas with lower concentrations and vice versa, reaching the optimal concentration). Additionally, a higher motility was obtained when cells were deposited on narrow and highly concentrated areas with IBs. FGF-IBs can be therefore used to enhance and guide cell migration, confirming that the decoration of surfaces with such IB-like protein nanoparticles is a promising platform for regenerative medicine and tissue engineering.

Bacterial inclusion bodies are industrially exploitable amyloids

Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.

Surface-Bound Gradient Deposition of Protein Nanoparticles for Cell Motility Studies

A versatile evaporation-assisted methodology based on the coffee-drop effect is described to deposit nanoparticles on surfaces, obtaining for the first time patterned gradients of protein nanoparticles (pNPs) by using a simple custom-made device. Fully controllable patterns with specific periodicities consisting of stripes with different widths and distinct nanoparticle concentration as well as gradients can be produced over large areas (∼10 cm²) in a fast (up to 10 mm²/min), reproducible, and cost-effective manner using an operational protocol optimized by an evolutionary algorithm. The developed method opens the possibility to decorate surfaces "a-la-carte" with pNPs enabling different categories of high-throughput studies on cell motility.

Artificial 3D Culture Systems for T Cell Expansion

Adoptive cell therapy, i.e., the extraction, manipulation, and administration of ex vivo generated autologous T cells to patients, is an emerging alternative to regular procedures in cancer treatment. Nevertheless, these personalized treatments require laborious and expensive laboratory procedures that should be alleviated to enable their incorporation into the clinics. With the objective to improve the ex vivo expansion of large amount of specific T cells, we propose the use of three-dimensional (3D) structures during their activation with artificial antigen-presenting cells, thus resembling the natural environment of the secondary lymphoid organs. Thus, the activation, proliferation, and differentiation of T cells have been analyzed when cultured in the presence of two 3D systems, Matrigel and a 3D polystyrene scaffold, showing an increase in cell proliferation compared to standard suspension systems.

Fabrication of BSA@AuNC-Based Nanostructures for Cell Fluoresce Imaging and Target Drug Delivery

Drug delivery which can offer efficient and localized drug transportation together with imaging capabilities is highly demanded in the development of cancer theranostic approaches. Herein, we report the construction of bovine serum albumin (BSA) gold nanoclusters (BSA@AuNCs) for cell fluoresce imaging and target drug delivery. BSA@AuNCs were modified with cyclic arginine-glycine-aspartate with the product RGD-BSA@AuNCs to enhance cell internalization of the nanoclusters. Furthermore, doxorubicin hydrochloride or doxorubicin (DOX), a widely used chemotherapy drug, was also used to modify RGD-BSA@AuNCs. The final design of the DOX/RGD-BSA@AuNC system was constructed through the disulfide bond. The physical microstructure and biological characterization of the BSA@AuNCs were realized through high-resolution transmission electron microscopy and confocal laser fluorescence microscopy. As the disulfide bonds were cleaved by glutathione in cancer cells, DOX-SH molecules were released from the nanosystem to inhibit the growth of cancer cells. The as-prepared DOX/RGD-BSA@AuNC system can be used not only to deliver drug but also to achieve the antitumor effect by in vivo imaging, demonstrating its promising applications in cancer treatment.

Improving Biomaterials Imaging for Nanotechnology: Rapid Methods for Protein Localization at Ultrastructural Level

The preparation of biological samples for electron microscopy is material- and time-consuming because it is often based on long protocols that also may produce artifacts. Protein labeling for transmission electron microscopy (TEM) is such an example, taking several days. However, for protein-based nanotechnology, high resolution imaging techniques are unique and crucial tools for studying the spatial distribution of these molecules, either alone or as components of biomaterials. In this paper, we tested two new short methods of immunolocalization for TEM, and compared them with a standard protocol in qualitative and quantitative approaches by using four protein-based nanoparticles. We reported a significant increase of labeling per area of nanoparticle in both new methodologies (H = 19.811; p < 0.001) with all the model antigens tested: GFP (H = 22.115; p < 0.001), MMP-2 (H = 19.579; p < 0.001), MMP-9 (H = 7.567; p < 0.023), and IFN-γ (H = 62.110; p < 0.001). We also found that the most suitable protocol for labeling depends on the nanoparticle's tendency to aggregate. Moreover, the shorter methods reduce artifacts, time (by 30%), residues, and reagents hindering, losing, or altering antigens, and obtaining a significant increase of protein localization (of about 200%). Overall, this study makes a step forward in the development of optimized protocols for the nanoscale localization of peptides and proteins within new biomaterials.

Bacterial Inclusion Bodies: Discovering Their Better Half

Bacterial inclusion bodies (IBs) are functional, non-toxic amyloids occurring in recombinant bacteria showing analogies with secretory granules of the mammalian endocrine system. The scientific interest in these mesoscale protein aggregates has been historically masked by their status as a hurdle in recombinant protein production. However, progressive understanding of how the cell handles the quality of recombinant polypeptides and the main features of their intriguing molecular organization has stimulated the interest in inclusion bodies and spurred their use in diverse technological fields. The engineering and tailoring of IBs as functional protein particles for materials science and biomedicine is a good example of how formerly undesired bacterial byproducts can be rediscovered as promising functional materials for a broad spectrum of applications.

Bacterial mimetics of endocrine secretory granules as immobilized in vivo depots for functional protein drugs

In the human endocrine system many protein hormones including urotensin, glucagon, obestatin, bombesin and secretin, among others, are supplied from amyloidal secretory granules. These granules form part of the so called functional amyloids, which within the whole aggregome appear to be more abundant than formerly believed. Bacterial inclusion bodies (IBs) are non-toxic, nanostructured functional amyloids whose biological fabrication can be tailored to render materials with defined biophysical properties. Since under physiological conditions they steadily release their building block protein in a soluble and functional form, IBs are considered as mimetics of endocrine secretory granules. We have explored here if the in vivo implantation of functional IBs in a given tissue would represent a stable local source of functional protein. Upon intratumoral injection of bacterial IBs formed by a potent protein ligand of CXCR4 we have observed high stability and prevalence of the material in absence of toxicity, accompanied by apoptosis of CXCR4⁺ cells and tumor ablation. Then, the local immobilization of bacterial amyloids formed by therapeutic proteins in tumors or other tissues might represent a promising strategy for a sustained local delivery of protein drugs by mimicking the functional amyloidal architecture of the mammals’ endocrine system.

Integrating mechanical and biological control of cell proliferation through bioinspired multieffector materials

In nature, cells respond to complex mechanical and biological stimuli whose understanding is required for tissue construction in regenerative medicine. However, the full replication of such bimodal effector networks is far to be reached. Engineering substrate roughness and architecture allows regulating cell adhesion, positioning, proliferation, differentiation and survival, and the external supply of soluble protein factors (mainly growth factors and hormones) has been long applied to promote growth and differentiation. Further, bioinspired scaffolds are progressively engineered as reservoirs for the in situ sustained release of soluble protein factors from functional topographies. We review here how research progresses toward the design of integrative, holistic scaffold platforms based on the exploration of individual mechanical and biological effectors and their further combination.

Functional protein aggregates: just the tip of the iceberg

An increasing number of both prokaryotic and eukaryotic cell types are being adapted as platforms for recombinant protein production. The overproduction of proteins in such expression systems leads to the formation of insoluble protein-based aggregates. Although these protein clusters have been poorly studied in most of the eukaryotic systems, aggregates formed in E. coli, named inclusion bodies (IBs), have been deeply characterized in the last decades. Contrary to the general belief, an important fraction of the protein embedded in IB is functional, showing promise in biocatalysis, regenerative medicine and cell therapy. Thus, the exploration of all these functional protein clusters would largely expand their potential in both pharma and biotech industry.

Methods for characterization of protein aggregates

Physicochemical characterization of protein aggregates is important on one hand, due to its large impact in understanding many diseases for which formation of protein aggregates is one of the pathological hallmarks. On the other hand, recently it has been observed that bacterial inclusion bodies (IBs) are also highly pure proteinaceous aggregates of a few hundred nanometers produced by recombinant bacteria supporting the biological activities of the embedded polypeptides. From this fact arises a wide spectrum of uses of IBs as functional and biocompatible materials upon convenient engineering but very few is known about their physicochemical properties. In this chapter we present methods for the characterization of protein aggregates as particulate materials relevant to their physicochemical and nanoscale properties. Specifically, we describe the use of infrared spectroscopy (IR) for the determination of the secondary structure, dynamic light scattering (DLS) for sizing, nanosight for sizing and counting, and Z-potential measurements for the determination of colloidal stability. To study their morphology we present the use of atomic force microscopy (AFM). Cryo-transmission electron microscopy will be used for the determination of the internal structuration. Moreover, wettability and nanomechanical characterization can be performed using contact angle (CA) and force spectroscopic AFM measurements of the proteinaceous nanoparticles, respectively. The physical principles of the methods are briefly described and examples of data for real samples and how that data is interpreted are given to help clarify capabilities of each technique.

Recombinant protein materials for bioengineering and nanomedicine

Proteins are essential macromolecules supporting life. Being efficient catalyzers and offering specific cross-molecular contacts, proteins are largely exploited in biotechnology and biomedicine as therapeutics, in industrial catalysis or as molecular reagents. Recombinant enzymes, hormones, immunogens and antibodies are produced aiming to different applications, on the basis of their ability to interact with or modify substrates or biological targets. In nature, proteins also perform task-specific architectonic roles, and they can organize in supramolecular complexes with intriguing physical properties such as elasticity and adhesiveness, and with regulatable stiffness, flexibility and mechanical strength. Proteins have recently gained interest as materials for bioengineering and nanomedicine as they can combine these features with functionality, biocompatibility and degradability in unusually versatile composites. We revise here the fundamental properties of the diverse categories of emerging protein materials resulting from biological synthesis and how they can be genetically re-designed to engineer the interplay between mechanical and biological properties in a medically oriented exploitable way.

Production of functional inclusion bodies in endotoxin-free Escherichia coli

Escherichia coli is the workhorse for gene cloning and production of soluble recombinant proteins in both biotechnological and biomedical industries. The bacterium is also a good producer of several classes of protein-based self-assembling materials such as inclusion bodies (IBs). Apart from being a relatively pure source of protein for in vitro refolding, IBs are under exploration as functional, protein-releasing materials in regenerative medicine and protein replacement therapies. Endotoxin removal is a critical step for downstream applications of therapeutic proteins. The same holds true for IBs as they are often highly contaminated with cell-wall components of the host cells. Here, we have investigated the production of IBs in a recently developed endotoxin-free E. coli strain. The characterization of IBs revealed this mutant as a very useful cell factory for the production of functional endotoxin-free IBs that are suitable for the use at biological interfaces without inducing endotoxic responses in human immune cells.

Investigation of the interfacial effects of small chemical-modified TiO2 nanotubes on 3T3 fibroblast responses

In order to gain insight into how interfacial effects influence cell responses, chemically modified anodized TiO2 nanotubes (ATNs) were used to simultaneously investigate the effects of nanoscale substrate structure and angstrom-scale chemicals on cell morphological change and cell growth. Two small chemicals were used to modify the ATNs, namely, 3-aminopropyltrimethoxysilane (APTMS) and 3-mercaptopropyltrimethoxysilane (MPTMS), resulting in APTMS-modified ATNs (APTMS-ATNs) and MPTMS-modified ATNs (MPTMS-ATNs), respectively. In our in vitro observation of NIH/3T3 fibroblasts, cells thrived on both unmodified and modified ATNs. Quantitative analyses of cell numbers exhibited that APTMS-ATNs effectively facilitated cell proliferation and directed cell orientation owing to full cell-substrate contact caused by positively charged amino groups (-NH3(+)) on the surface. In addition, scanning electron microscopy and fluorescence images showed different cell morphologies on APTMS-ATNs and MPTMS-ATNs. APTMS-ATNs resulted in flat spreading of fibroblasts, while MPTMS-ATNs resulted in fibroblasts with a three-dimensional solid shape and clear contours. The results indicate that the synergistic effects of nanotube surface topology and small chemical modification and, to a lesser extent, surface hydrophilicity, alter the interfacial interactions between cells and substrates, significantly affecting cell morphology, attachment, and growth. Using ATNs with different interfacial effects from various small chemicals, orientation of cells into various patterns can be achieved and investigation of cell fates, such as proliferation or stem cell differentiation, can be performed for future advanced medical or biological applications.

Thermoresponsive nanofabricated substratum for the engineering of three-dimensional tissues with layer-by-layer architectural control

Current tissue engineering methods lack the ability to properly recreate scaffold-free, cell-dense tissues with physiological structures. Recent studies have shown that the use of nanoscale cues allows for precise control over large-area 2D tissue structures without restricting cell growth or cell density. In this study, we developed a simple and versatile platform combining a thermoresponsive nanofabricated substratum (TNFS) incorporating nanotopographical cues and the gel casting method for the fabrication of scaffold-free 3D tissues. Our TNFS allows for the structural control of aligned cell monolayers which can be spontaneously detached via a change in culture temperature. Utilizing our gel casting method, viable, aligned cell sheets can be transferred without loss of anisotropy or stacked with control over individual layer orientations. Transferred cell sheets and individual cell layers within multilayered tissues robustly retain structural anisotropy, allowing for the fabrication of scaffold-free, 3D tissues with hierarchical control of overall tissue structure.