Biofabricating Functional Soft Matter Using Protein Engineering to Enable Enzymatic Assembly

Electro-Biofabrication. Coupling Electrochemical and Biomolecular Methods to Create Functional Bio-Based Hydrogels

Twenty years ago, this journal published a review entitled "Biofabrication with Chitosan" based on the observations that (i) chitosan could be electrodeposited using low voltage electrical inputs (typically less than 5 V) and (ii) the enzyme tyrosinase could be used to graft proteins (via accessible tyrosine residues) to chitosan. Here, we provide a progress report on the coupling of electronic inputs with advanced biological methods for the fabrication of biopolymer-based hydrogel films. In many cases, the initial observations of chitosan's electrodeposition have been extended and generalized: mechanisms have been established for the electrodeposition of various other biological polymers (proteins and polysaccharides), and electrodeposition has been shown to allow the precise control of the hydrogel's emergent microstructure. In addition, the use of biotechnological methods to confer function has been extended from tyrosinase conjugation to the use of protein engineering to create genetically fused assembly tags (short sequences of accessible amino acid residues) that facilitate the attachment of function-conferring proteins to electrodeposited films using alternative enzymes (e.g., transglutaminase), metal chelation, and electrochemically induced oxidative mechanisms. Over these 20 years, the contributions from numerous groups have also identified exciting opportunities. First, electrochemistry provides unique capabilities to impose chemical and electrical cues that can induce assembly while controlling the emergent microstructure. Second, it is clear that the detailed mechanisms of biopolymer self-assembly (i.e., chitosan gel formation) are far more complex than anticipated, and this provides a rich opportunity both for fundamental inquiry and for the creation of high performance and sustainable material systems. Third, the mild conditions used for electrodeposition allow cells to be co-deposited for the fabrication of living materials. Finally, the applications have been expanded from biosensing and lab-on-a-chip systems to bioelectronic and medical materials. We suggest that electro-biofabrication is poised to emerge as an enabling additive manufacturing method especially suited for life science applications and to bridge communication between our biological and technological worlds.

One-pot synthesis of fibrillar-shaped functional nanomaterial using microbial transglutaminase

Recently, functional nanowire production using amyloids as a scaffold for protein immobilization has attracted attention. However, protein immobilization on amyloid fibrils often caused protein inactivation. In this study, we investigated protein immobilization using enzymatic peptide ligation to suppress protein inactivation during immobilization. We attempted to immobilize functional molecules such as green fluorescent protein (GFP) and Nanoluc to a transthyretin (TTR) amyloid using microbial transglutaminase (MTG), which links the glutamine side chain to the primary amine. Linkage between amyloid fibrils and functional molecules was achieved through the MTG substrate sequence, and the functional molecules-loaded nanowires were successfully fabricated. We also found that the synthetic process from amyloidization to functional molecules immobilization could be achieved in a single-step procedure.All rights reserved.

Unaided efficient transglutaminase cross-linking of whey proteins strongly impacts the formation and structure of protein alginate particles

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Microbial transglutaminase (MTG) cross-linked >70% β-lactoglobulin (β-Lg) at pH 8.5.

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Initial MTG catalyzed isopeptide bond formation caused partial unfolding of β-Lg.

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>75% of whey protein cross-linked, forming hetero-polymers containing β-Lg.

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50% less alginate is needed to form particles with cross-linked than with native β-Lg.

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Cross-linked β-Lg and alginate formed suspendable hydrophobically driven particles.

There is a dogma within whey protein modification, which dictates the necessity of pretreatment to enzymatic cross-linking of β-lactoglobulin (β-Lg). Here microbial transglutaminase (MTG) cross-linked whey proteins and β-Lg effectively in 50 mM NaHCO₃, pH 8.5, without pretreatment. Cross-linked β-Lg spanned 18 to >240 kDa, where 6 of 9 glutamines reacted with 8 of 15 lysines. The initial isopeptide bond formation caused loss of β-Lg native structure with t_1/2 = 3 h, while the polymerization occurred with t_1/2 = 10 h. Further, cross-linking effects on protein carbohydrate interaction have been overlooked, leaving a gap in understanding of these complex food matrices. Complexation with alginate showed that β-Lg cross-linking decreased onset of particle formation, hydrodynamic diameter, stoichiometry (β-Lg/alginate) and dissociation constant. The complexation was favored at higher temperatures (40 °C), suggesting that hydrophobic interactions were important. Thus, β-Lg was cross-linked without pretreatment and the resulting polymers gave rise to altered complexation with alginate.

Bioinspired Hydrogels as Platforms for Life-Science Applications: Challenges and Opportunities

Hydrogels, as interconnected networks (polymer mesh; physically, chemically, or dynamic crosslinked networks) incorporating a high amount of water, present structural characteristics similar to soft natural tissue. They enable the diffusion of different molecules (ions, drugs, and grow factors) and have the ability to take over the action of external factors. Their nature provides a wide variety of raw materials and inspiration for functional soft matter obtained by complex mechanisms and hierarchical self-assembly. Over the last decade, many studies focused on developing innovative and high-performance materials, with new or improved functions, by mimicking biological structures at different length scales. Hydrogels with natural or synthetic origin can be engineered as bulk materials, micro- or nanoparticles, patches, membranes, supramolecular pathways, bio-inks, etc. The specific features of hydrogels make them suitable for a wide variety of applications, including tissue engineering scaffolds (repair/regeneration), wound healing, drug delivery carriers, bio-inks, soft robotics, sensors, actuators, catalysis, food safety, and hygiene products. This review is focused on recent advances in the field of bioinspired hydrogels that can serve as platforms for life-science applications. A brief outlook on the actual trends and future directions is also presented.

Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation

The modification of intracellular metabolic pathways by metabolic engineering has generated many engineered strains with relatively high yields of various target products in the past few decades. However, the unpredictable accumulation of toxic products, the cell membrane barrier, and competition between the carbon flux of cell growth and product synthesis have severely retarded progress toward the industrial-scale production of many essential chemicals. On the basis of an in-depth understanding of intracellular metabolic pathways, scientists intend to explore more sustainable methods and construct a cell-free biosynthesis system in vitro. In this review, the synthesis and application of pyruvate as a platform compound is used as an example to introduce cell-free biosynthesis systems. We systematically summarize a proposed methodology workflow of cell-free biosynthesis systems, including pathway design, enzyme mining, enzyme modification, multienzyme assembly, and pathway optimization. Some new methods, such as machine learning, are also mentioned in this review.

From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures

The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

Electrobiofabrication: electrically based fabrication with biologically derived materials

While conventional material fabrication methods focus on form and strength to achieve function, the fabrication of material systems for emerging life science applications will need to satisfy a more subtle set of requirements. A common goal for biofabrication is to recapitulate complex biological contexts (e.g. tissue) for applications that range from animal-on-a-chip to regenerative medicine. In these cases, the material systems will need to: (i) present appropriate surface functionalities over a hierarchy of length scales (e.g. molecular features that enable cell adhesion and topographical features that guide differentiation); (ii) provide a suite of mechanobiological cues that promote the emergence of native-like tissue form and function; and (iii) organize structure to control cellular ingress and molecular transport, to enable the development of an interconnected cellular community that is engaged in cell signaling. And these requirements are not likely to be static but will vary over time and space, which will require capabilities of the material systems to dynamically respond, adapt, heal and reconfigure. Here, we review recent advances in the use of electrically based fabrication methods to build material systems from biological macromolecules (e.g. chitosan, alginate, collagen and silk). Electrical signals are especially convenient for fabrication because they can be controllably imposed to promote the electrophoresis, alignment, self-assembly and functionalization of macromolecules to generate hierarchically organized material systems. Importantly, this electrically based fabrication with biologically derived materials (i.e. electrobiofabrication) is complementary to existing methods (photolithographic and printing), and enables access to the biotechnology toolbox (e.g. enzymatic-assembly and protein engineering, and gene expression) to offer exquisite control of structure and function. We envision that electrobiofabrication will emerge as an important platform technology for organizing soft matter into dynamic material systems that mimic biology's complexity of structure and versatility of function.

Supramolecular chirality and crystallization from biocatalytic self-assembly in lipidic cubic mesophases

Biocatalytic self-assembly in a nanoconfined environment is widely used in nature to construct complex structures that endow special characteristics to life. There is tremendous interest in mimicking such bottom-up processes to fabricate functional materials. In this study, we have investigated a novel biomimetic scaffold based on lipidic cubic mesophases (LCMs), which provide a special nanoconfined environment for biocatalytic self-assembly and subsequent formation of organic crystals. (R)-Benzoin generated in situ from benzaldehyde in a reaction catalyzed by the enzyme benzaldehyde lyase (BAL) exhibits - when confined within LCMs - enhanced chirality compared to (R)-benzoin in solution or (R)-benzoin-doped LCMs. We infer that a metastable state is formed under kinetic control that displays enhanced supramolecular chirality. As they age, these metastable structures can further grow into thermodynamically stable crystals. The biomimetic, nanoconfined environment provided by the LCMs plays a key role in the development of supramolecular chirality and subsequent crystallization.

Coupling Self-Assembly Mechanisms to Fabricate Molecularly and Electrically Responsive Films

Biomacromolecules often possess information to self-assemble through low energy competing interactions which can make self-assembly responsive to environmental cues and can also confer dynamic properties. Here, we coupled self-assembling systems to create biofunctional multilayer films that can be cued to disassemble through either molecular or electrical signals. To create functional multilayers, we: (i) electrodeposited the pH-responsive self-assembling aminopolysaccharide chitosan, (ii) allowed the lectin Concanavalin A (ConA) to bind to the chitosan-coated electrode (presumably through electrostatic interactions), (iii) performed layer-by-layer self-assembly by sequential contacting with glycogen and ConA, and (iv) conferred biological (i.e., enzymatic) function by assembling glycoprotein (i.e., enzymes) to the ConA-terminated multilayer. Because the ConA tetramer dissociates at low pH, this multilayer can be triggered to disassemble by acidification. We demonstrate two approaches to induce acidification: (i) glucose oxidase can induce multilayer disassembly in response to molecular cues, and (ii) anodic reactions can induce multilayer disassembly in response to electrical cues.