Amphiphilic Polysaccharide Nanogels as Artificial Chaperones in Cell-Free Protein Synthesis

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Reconstituted Cell-free Translation Systems for Exploring Protein Folding and Aggregation

Protein folding is crucial for achieving functional three-dimensional structures. However, the process is often hampered by aggregate formation, necessitating the presence of chaperones and quality control systems within the cell to maintain protein homeostasis. Despite a long history of folding studies involving the denaturation and subsequent refolding of translation-completed purified proteins, numerous facets of cotranslational folding, wherein nascent polypeptides are synthesized by ribosomes and folded during translation, remain unexplored. Cell-free protein synthesis (CFPS) systems are invaluable tools for studying cotranslational folding, offering a platform not only for elucidating mechanisms but also for large-scale analyses to identify aggregation-prone proteins. This review provides an overview of the extensive use of CFPS in folding studies to date. In particular, we discuss a comprehensive aggregation formation assay of thousands of Escherichia coli proteins conducted under chaperone-free conditions using a reconstituted translation system, along with its derived studies.

Pullulan based stimuli responsive and sub cellular targeted nanoplatforms for biomedical application: Synthesis, nanoformulations and toxicological perspective

With growing interest in polymers of natural origin, innumerable polysaccharides have gained attention for their biomedical application. Pullulan, one of the FDA approved nutraceuticals, possesses multiple unique properties which make them highly advantageous for biomedical applications. This present review encompasses the sources, production, properties and applications of pullulan. It highlights various pullulan based stimuli-responsive systems (temperature, pH, ultrasound, magnetic), subcellular targeted systems (mitochondria, Golgi apparatus/endoplasmic reticulum, lysosome, endosome), lipid-vesicular systems (solid-lipid nanoparticles, liposomes), polymeric nanofibres, micelles, inorganic (SPIONs, gold and silver nanoparticles), carbon-based nanoplatforms (carbon nanotubes, fullerenes, nanodiamonds) and quantum dots. This article also gives insight into different biomedical, therapeutic and diagnostic applications of pullulan viz., imaging, tumor targeting, stem cell therapy, gene therapy, vaccine delivery, cosmetic applications, protein delivery, tissue engineering, photodynamic therapy and chaperone-like activities. The review also includes the toxicological profile of pullulan which is helpful for the development of suitable delivery systems for clinical applications.

Nanogelation and Thermal Stabilization of Enzyme by Vitamin B6-Bearing Polysaccharide as Biocrosslinker

Nanogels containing a protein (carbonic anhydrase, CA) were prepared by cross-linking CA and pyridoxal (vitamin B₆)-bearing pullulan (PLPP) as a biocrosslinker via Schiff base formation. UV titration and high-performance liquid chromatography confirmed that CA was quantitatively complexed with PLPP in the presence of zinc ions. Dynamic light scattering and transmission electron microscopy showed that the nanogel diameter was about 20 nm. CA retained 90% of its native activity after complexation with PLPP. Moreover, the residual enzymatic activity of CA after heating and its long-term storage stability at room temperature were improved by complexation with PLPP. Enzyme nanogelation with PLPP is an efficient method for enzyme stabilization.

Nanogels as drug-delivery systems: a comprehensive overview

Nanogels have attracted considerable attention as nanoscopic drug carriers, particularly for site-specific or time-controlled delivery of bioactive mediators. A high diversity of polymer systems and the simple modification of their physicochemical features have provided multipurpose forms of nanogel preparations. Nanogels have outstandingly high stability, drug loading ability, biologic consistence, good permeation capability and can be responsive to environmental stimuli. Great potential has been shown by nanogels in many fields including delivery of genes, chemotherapy drugs, diagnosis, targeting of specific organs and several others. This review focuses mainly on different types of nanogels, methods of preparation including methods of drug loading, different modes of biodegradation mechanisms as well as main mechanisms of drug release from nanogels. Recent applications of nanogels are also briefly discussed and exemplified.

A Novel Method to Evaluate Ribosomal Performance in Cell-Free Protein Synthesis Systems

Cell-free protein synthesis (CFPS) systems were designed to produce proteins with a minimal set of purified components, thus offering the possibility to follow translation as well as protein folding. In order to characterize the performance of the ribosomes in such a system, it is crucial to separately quantify the two main components of productivity, namely the fraction of active ribosomes and the number of synthesizing cycles. Here, we provide a direct and highly reliable measure of ribosomal activity in any given CFPS system, introducing an enhanced-arrest peptide variant. We observe an almost complete stalling of ribosomes that produce GFPem (~95%), as determined by common centrifugation techniques and fluorescence correlation spectroscopy (FCS). Moreover, we thoroughly study the effect of different ribosomal modifications independently on activity and number of synthesizing cycles. Finally, employing two-colour coincidence detection and two-colour colocalisation microscopy, we demonstrate real-time access to key productivity parameters with minimal sample consumption on a single ribosome level.

Supramolecular Self-Assembly into Biofunctional Soft Nanotubes: From Bilayers to Monolayers

The inner and outer surfaces of bilayer-based lipid nanotubes can be hardly modified selectively by a favorite functional group. Monolayer-based nanotubes display a definitive difference in their inner and outer functionalities if bipolar wedge-shaped amphiphiles, so-called bolaamphiphiles, as a constituent of the monolayer membrane pack in a parallel fashion with a head-to-tail interface. To exclusively form unsymmetrical monolayer lipid membranes, we focus herein on the rational molecular design of bolaamphiphiles and a variety of self-assembly processes into tubular architectures. We first describe the importance of polymorph and polytype control and then discuss diverse methodologies utilizing a polymer template, multiple hydrogen bonds, binary and ternary coassembly, and two-step self-assembly. Novel biologically important functions of the obtained soft nanotubes, brought about only by completely unsymmetrical inner and outer surfaces, are discussed in terms of protein refolding, drug nanocarriers, lectin detection, a chiral inducer for achiral polymers, the tailored fabrication of polydopamine, and spontaneous nematic alignment.

Comprehensive study of liposome-assisted synthesis of membrane proteins using a reconstituted cell-free translation system

Membrane proteins play pivotal roles in cellular processes and are key targets for drug discovery. However, the reliable synthesis and folding of membrane proteins are significant problems that need to be addressed owing to their extremely high hydrophobic properties, which promote irreversible aggregation in hydrophilic conditions. Previous reports have suggested that protein aggregation could be prevented by including exogenous liposomes in cell-free translation processes. Systematic studies that identify which membrane proteins can be rescued from irreversible aggregation during translation by liposomes would be valuable in terms of understanding the effects of liposomes and developing applications for membrane protein engineering in the context of pharmaceutical science and nanodevice development. Therefore, we performed a comprehensive study to evaluate the effects of liposomes on 85 aggregation-prone membrane proteins from Escherichia coli by using a reconstituted, chemically defined cell-free translation system. Statistical analyses revealed that the presence of liposomes increased the solubility of >90% of the studied membrane proteins, and ultimately improved the yields of the synthesized proteins. Bioinformatics analyses revealed significant correlations between the liposome effect and the physicochemical properties of the membrane proteins.

Nano-cage-mediated refolding of insulin by PEG-PE micelle

Insulin aggregation has pronounced pharmaceutical implications and biological importance. Deposition of insulin aggregates is associated with type II diabetes and instability of pharmaceutical formulations. We present in this study the renaturation effect of PEG-PE micelle on dithiothreitol (DTT)-denatured insulin revealed by techniques including turbidity assay, circular dichroism (CD), thioflavinT (ThT) binding assay, bis-ANS binding assay, agarose gel electrophoresis and MALDI-TOF MS. The obtained results show that PEG-PE micelle having a hydrophilic nano-cage-like structure in which with a negative charge layer, can capture DTT-induced insulin A and B chains, and block their hydrophobic interaction, thereby preventing aggregation. The reduced insulin A and B chain in the nano-cage are capable of recognizing each other and form the native insulin with yields of ∼30% as measured by hypoglycemic activity analysis in mice. The observed insulin refolding assisted by PEG-PE micelle may be applicable to other proteins.

Conceptual and methodological advances in cell-free directed evolution

Although cell-free directed evolution methods have been used to engineer proteins for nearly two decades, selections on more complex phenotypes have largely remained in the domain of cell-based engineering approaches. Here, we review recent conceptual advances that now enable in vitro display of multimeric proteins, integral membrane proteins, and proteins with an expanded amino acid repertoire. Additionally, we discuss methodological improvements that have enhanced the accessibility, efficiency, and robustness of cell-free approaches. Coupling these advances with the in vitro advantages of creating exceptionally large libraries and precisely controlling all experimental conditions, cell-free directed evolution is poised to contribute significantly to our understanding and engineering of more complex protein phenotypes.

Micro- and nanogels with labile crosslinks – from synthesis to biomedical applications

We emphasize the synthetic strategies to produce micro-/nanogels and the importance of degradable linkers incorporated in the gel network.

Nanogel--an advanced drug delivery tool: Current and future

Nanogels are robust nanoparticles that could be used to deliver active drug compounds in controlled drug delivery applications. Nanogels drug delivery system is more effective and safer for both hydrophilic and hydrophobic drugs due to their chemical composition and formulations that are inappropriate for other formulations. Nanogels have enabled enlargement of functionalized nanoparticles, which act as a drug carriers that can be loaded with drugs and other active material to be released in a controlled manner at specific site. This review aims at providing general introduction on nanogels, recent synthesis methodology and their novel application in different fields.

Engine out of the chassis: cell-free protein synthesis and its uses

The translation machinery is the engine of life. Extracting the cytoplasmic milieu from a cell affords a lysate capable of producing proteins in concentrations reaching to tens of micromolar. Such lysates, derivable from a variety of cells, allow the facile addition and subtraction of components that are directly or indirectly related to the translation machinery and/or the over-expressed protein. The flexible nature of such cell-free expression systems, when coupled with high throughput monitoring, can be especially suitable for protein engineering studies, allowing one to bypass multiple steps typically required using conventional in vivo protein expression.

Functional expression and characterisation of membrane transport proteins

Membrane transporters set the framework organising the complexity of plant metabolism in cells, tissues and organisms. Their substrate specificity and controlled activity in different cells is a crucial part for plant metabolism to run pathways in concert. Transport proteins catalyse the uptake and exchange of ions, substrates, intermediates, products and cofactors across membranes. Given the large number of metabolites, a wide spectrum of transporters is required. The vast majority of in silico annotated membrane transporters in plant genomes, however, has not yet been functionally characterised. Hence, to understand the metabolic network as a whole, it is important to understand how transporters connect and control the metabolic pathways of plant cells. Heterologous expression and in vitro activity studies of recombinant transport proteins have highly improved their functional analysis in the last two decades. This review provides a comprehensive overview of the recent advances in membrane protein expression and functional characterisation using various host systems and transport assays.

Cyclodextrin-based nanogels for pharmaceutical and biomedical applications

Hydrophilic nanogels combine the advantages of hydrogels with certain advantages that are inherent in their nanoscale size. Similar to macrogels, nanogels can contain and protect drugs and regulate their release by incorporating high-affinity functional groups, stimuli-responsive conformations and biodegradable bonds into the polymer network. Similar to nanoparticles, nanogels can easily be administered in liquid form for parenteral drug delivery. The nanoscale size of nanogels gives them a high specific surface area that is available for further bioconjugation of active targeting agents. Biodistribution and drug release can be modulated through size adjustments. The incorporation of hydrophilic cyclodextrin (CD) moieties into the polymeric network of the nanogels provides them with a drug loading and release mechanism that is based on the formation of inclusion complexes without decreasing the hydrophilicity of the network. The covalent attachment of CD molecules to the chemically crosslinked networks may enable the CDs to display fully their ability to form complexes, while simultaneously preventing drug release upon media dilution. The preparation, characterization and advantages for pharmaceutical and biomedical applications of CD-based nanogels are reviewed in this article.

Cell-free protein synthesis: applications come of age

Cell-free protein synthesis has emerged as a powerful technology platform to help satisfy the growing demand for simple and efficient protein production. While used for decades as a foundational research tool for understanding transcription and translation, recent advances have made possible cost-effective microscale to manufacturing scale synthesis of complex proteins. Protein yields exceed grams protein produced per liter reaction volume, batch reactions last for multiple hours, costs have been reduced orders of magnitude, and reaction scale has reached the 100-liter milestone. These advances have inspired new applications in the synthesis of protein libraries for functional genomics and structural biology, the production of personalized medicines, and the expression of virus-like particles, among others. In the coming years, cell-free protein synthesis promises new industrial processes where short protein production timelines are crucial as well as innovative approaches to a wide range of applications.