De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Leveraging Protein-Ligand and DNA Interactions to Control Hydrogel Mechanics

Biomacromolecules can serve as molecularly precise building blocks for hydrogel materials, dictating material properties that depend on the chemical identity and interactions of the individual components. Herein, we introduce biomolecular hydrogels where ligand-functionalized DNA sequences form the hydrogel backbone and multivalent protein-ligand interactions form supramolecular cross-links. In these hydrogels, we can independently leverage the programmable rigidity of DNA (i.e., single-stranded vs double-stranded DNA) and defined protein-ligand binding affinities spanning >10 orders of magnitude to modulate the gel stiffness, stress relaxation, and shear thinning. We learn that (1) double-stranded networks have stiffness values up to 3 orders of magnitude greater than single-stranded networks and exhibit thermoresponsiveness and (2) the protein-ligand binding affinities and dissociation rate constants determine the network topologies and stress relaxation rates of the hydrogels. Finally, the hydrogels exhibit cytocompatibility and cell-type-specific degradation, where cells can migrate through the gels via interactions between the gels and their ligand-binding receptors. Together, this work demonstrates that varying the local chemical interactions of the hydrogel backbone and the supramolecular binding affinity of dynamic cross-links leads to cytocompatible hydrogels with tunable viscoelastic properties for applications in drug delivery and tissue engineering.

Employing the SpyTag-SpyCatcher Reaction for the Modification of Supramolecular Polymers with Functional Proteins

Supramolecular assemblies hold great potential as biomaterials for several biomedical applications. The modification of supramolecular biomaterials is needed to achieve controlled bioactive functions. Supramolecular ureidopyrimidinone (UPy) monomers have been shown to assemble into long supramolecular polymers that can be functionalized with bioactive peptides and visualized as UPy-fibers. So far, the introduction of biological functionality has been limited to small molecules and peptides. Here, we describe a general method based on SpyTag-SpyCatcher chemistry for conjugating full-length proteins with biologically relevant functions to μm-long UPy fibers via native peptide bond formation, yielding 100% conversion in a 5:95 mol % coassembly of UPy-SpyTag with UPy-glycinamide. The conjugation of monoclonal antibodies is performed using photo-cross-linkable protein G domains. We demonstrate intact fibers and colocalization of antibodies and UPy-fibers using biophysical and imaging methods and achieve recruitment of supramolecular assemblies to the surface of mammalian cells via the EGFR-specific antibody Cetuximab. The approach introduced here represents a robust and widely applicable postassembly modification method that shows promise in the functionalization of future biomaterials.

Can Electroactive Tracer Molecules Reveal Viscoelastic Structure by Measuring Non-Fickian Diffusion?

We find that viscous and viscoelastic fluids are distinguishable by gauging Non-Fickian diffusion of dissolved electroactive molecules. Typically, such fluids are differentiated by measuring the mean-squared-displacement <Δr2> of embedded tracer particles (~1 μm) diffusing over time (t). From the relationship <Δr2>=6Dtα (D=particle diffusivity), log plots of <Δr2>vs.tα reveal regimes encoded in the slope α. For Fickian diffusion α=1, whereas α<1 and α>1, indicate Non-Fickian sub- and super-diffusion, respectively. Here, we electrolyzed redox reporters as molecular tracers in selected fluids. The current (I) relationship I ∝ ${\propto }$ v1/2 (v=scan-rate) was recast as I2vs.1/tα to introduce α as Non-Fickian quantifier in log plots. When viscosity increased at high concentration of small-molecules, D for the redox reporter declined but α remained constant at ~1 (Fickian). In contrast, both D and α(<1) decreased in viscoelastic hydrogels confirming a molecular sub-diffusive regime. These results agree with particle microrheology on the same fluid types using optical methods that are inapplicable to molecules. By quantifying Non-Fickian diffusion of electroactive molecular tracers, our method can uncover diffusion-structure relationships to identify regulators in neurodegenerative liquid-solid transitions of protein aggregates. Unlike tracer particles, the diffusivity of tracer molecules is controlled by the applied potential and electrode size.

Self-Assembling Peptide-Co-PPIX Complex Catalyzes Photocatalytic Hydrogen Evolution and Forms Hydrogels

The sustainable production of carbon-free fuels such as hydrogen is an important goal in the search for alternative energy sources. Herein, we report a peptide-based system for light-driven hydrogen evolution from water under neutral conditions. The M1 peptide is an ABC triblock polymer featuring two coiled-coil alpha-helical regions flanking a water-soluble, polyanionic, intrinsically disordered region. M1 formed a hydrogel at high concentrations upon binding to cobalt protoporphyrin IX. This process is driven by the terminal regions, which coordinate the metalloporphyrin through histidine residues and form helical oligomers interconnected by flexible, intrinsically disordered regions, resulting in network formation. Co-M1 catalyzes hydrogen production upon irradiation in the presence of a photosensitizer and a sacrificial electron donor; the activity of Co-M1 is eight times higher than that of free Co-PPIX.

Advances in designed bionanomolecular assemblies for biotechnological and biomedical applications

Recent advances in protein engineering have revolutionized the design of bionanomolecular assemblies for functional therapeutic and biotechnological applications. This review highlights the progress in creating complex protein architectures, encompassing both finite and extended assemblies. AI tools, including AlphaFold, RFDiffusion, and ProteinMPNN, have significantly enhanced the scalability and success of de novo designs. Finite assemblies, like nanocages and coiled-coil-based structures, enable precise molecular encapsulation or functional protein domain presentation. Extended assemblies, including filaments and 2D/3D lattices, offer unparalleled structural versatility for applications such as vaccine development, responsive biomaterials, and engineered cellular scaffolds. The convergence of artificial intelligence-driven design and experimental validation promises strong acceleration of the development of tailored protein assemblies, offering new opportunities in synthetic biology, materials science, biotechnology, and biomedicine.

3D-Printed Protein-Based Bioplastics with Tunable Mechanical Properties Using Glycerol or Hyperbranched Poly(glycerol)s as Plasticizers

Protein-based materials can be engineered to derive utility from the structures and functions of the incorporated proteins. Modern methods of protein engineering bring promise of unprecedented control over molecular and network design, which will enable new and improved functionalities in materials that incorporate proteins as functional building blocks. For these advantages to be fully realized, there is a need for robust methods for producing protein-based networks, as well as methods for tuning their mechanical properties. Light-based 3D-printing techniques afford high-resolution fabrication capability with unparalleled design freedom in an inexpensive and decentralized capacity. This work features 3D-printed serum albumin-based bioplastics with mechanical properties modulated through the incorporation of glycerol or hyperbranched poly(glycerol)s (HPGs) as plasticizers. These materials capitalize upon important features of serum albumin, including its low intrinsic viscosity, high aqueous solubility, and relatively low cost. The incorporation of glycerol or HPGs of different sizes resulted in softer and more ductile bioplastics than those obtained natively without additives. These bioplastics showed shape-memory behavior and could be used to fabricate functional objects. These materials are accessible, possess minimal chemical hazards, and can be used for fabricating rigid and strong as well as soft and ductile parts using inexpensive commercial 3D printers.

Proteins for Hyperelastic Materials

Meticulous engineering and the yielded hyperelastic performance of structural proteins represent a new frontier in developing next-generation functional biomaterials. These materials exhibit outstanding and programmable mechanical properties, including elasticity, resilience, toughness, and active biological characteristics, such as degradability and tissue repairability, compared with their chemically synthetic counterparts. However, there are several critical issues regarding the preparation approaches of hyperelastic protein-based materials: limited natural sequence modules, non-hierarchical assembly, and imbalance between compressive and tensile elasticity, leading to unmet demands. Therefore, it is pivotal to develop an alternative strategy for biofabricating hyperelastic materials. Herein, the molecular design, engineering, and property regulation of hyperelastic structural proteins are overviewed. First, methodologies for deeper exploration of mechanical modules, including machine learning-aided de novo design, random mutations of natural sequences, and multiblock fusion techniques, are actively introduced. These methodologies facilitate the generation of elastomeric protein modules and demonstrate enhanced structural and functional versatility. Subsequently, assembly tactics of hyperelastic proteins (i.e., physical modulation, genetic adaptations, and chemical modifications) are reviewed, yielding hierarchically ordered structures. Finally, advances in biophysical techniques for more nuanced characterization of protein ensembles are discussed, unveiling the tuning mechanisms of protein elasticity across scales. Future developments in structural hyperelastic protein-based biomaterials are also envisioned.

Capturing the impact of protein unfolding on the dynamic assembly of protein networks

The rapid assembly of molecular or nanoscale building blocks into extended arrays is crucial to the construction of functional networks in vivo and in vitro and depends on various factors. One factor seldom considered is the dynamic changes of the building block shape. Folded protein building blocks offer a unique system to investigate dynamic shape changes due to their intrinsic ability to change from a compact and specific folded structure to an extended unfolded structure in response to a perturbation such as force. Here, we use photochemically crosslinked folded protein hydrogels constructed from force labile protein building blocks as a model dynamic shape-changing network system and characterise them by combining time-resolved rheology and small-angle X-ray scattering (SAXS). This approach probes both the load-bearing network structures, using rheology, and network architectures, using SAXS, thereby providing a crosslength scale understanding of the network formation. We propose a triple assembly model for the structural evolution of networks constructed from force labile protein building block consisting of: primary formation where monomeric folded proteins create the preliminary protein network scaffold; a subsequent secondary formation phase, where larger oligomers of protein diffuse to join the preliminary network scaffold; and finally in situ unfolding and relaxation which leads to the mature network structure of connected larger and denser fractal-like clusters. The time-resolved SAXS data provides evidence that protein unfolding occurs on the edges of the fractal-like clusters, resulting in a population of unfolded proteins in the space between clusters. Identifying the key stages of assembly in protein networks constructed from force labile proteins provides a greater understanding of the importance of protein unfolding in hierarchical biomechanics in vivo and creates future opportunities to develop bespoke biomaterials for novel biomedical applications.

In situ forming and self-crosslinkable protein hydrogels for localized cancer therapy and topical wound healing

Proteins, inherently biocompatible and biodegradable, face a challenge in forming stable hydrogels without external chemical crosslinkers. Here, we construct a ring-shaped trimeric SpyTag-fused Proliferating Cell Nuclear Antigen Protein (ST-PCNA) as a core protein building block, and a dumbbell-shaped tandem dimeric SpyCatcher (SC-SC) as a bridging component. Self-crosslinked PCNA/SC-SC Protein (2SP) hydrogels are successfully formed by simply mixing the solutions of ST-PCNA and SC-SC, without chemical crosslinkers. During their formation by mixing, various cargo molecules, including anti-cancer drugs, photosensitizers, and functional proteins, are efficiently incorporated, producing cargo@2SP hydrogels. Most of the entrapped cargo molecules gradually release as the hydrogels erode. Anti-cancer drug- or photosensitizer-incorporated 2SP hydrogels are successfully formed through localized injection beneath the 4 T1 tumor in mice. The localized gradual release of drugs in physiological microenvironment substantially suppresses tumor growth, and highly localized photosensitizers retained in the 2SP hydrogels raises the local temperature above 45 °C upon laser irradiation, resulting in a significant suppression of tumor growth. Additionally, the topical administration of growth factor proteins-incorporated 2SP hydrogels to the incision wound area effectively regenerates the skin, with rapid reconstruction of extracellular matrix. The injectable and self-crosslinkable 2SP hydrogels developed here offer promise as novel biocompatible scaffolds for local therapy.

Design of a Genetically Programmable and Customizable Protein Scaffolding System for the Hierarchical Assembly of Robust, Functional Macroscale Materials

Inspired by the properties of natural protein-based biomaterials, protein nanomaterials are increasingly designed with natural or engineered peptides or with protein building blocks. Few examples describe the design of functional protein-based materials for biotechnological applications that can be readily manufactured, are amenable to functionalization, and exhibit robust assembly properties for macroscale material formation. Here, we designed a protein-scaffolding system that self-assembles into robust, macroscale materials suitable for in vitro cell-free applications. By controlling the coexpression in Escherichia coli of self-assembling scaffold building blocks with and without modifications for covalent attachment of cross-linking cargo proteins, hybrid scaffolds with spatially organized conjugation sites are overproduced that can be readily isolated. Cargo proteins, including enzymes, are rapidly cross-linked onto scaffolds for the formation of functional materials. We show that these materials can be used for the in vitro operation of a coimmobilized two-enzyme reaction and that the protein material can be recovered and reused. We believe that this work will provide a versatile platform for the design and scalable production of functional materials with customizable properties and the robustness required for biotechnological applications.

Megamolecule Self-Assembly Networks: A Combined Computational and Experimental Design Strategy

This work describes the use of computational strategies to design megamolecule building blocks for the self-assembly of lattice networks. The megamolecules are prepared by attaching four Cutinase-SnapTag fusion proteins (CS fusions) to a four-armed linker, followed by functionalizing each fusion with a terpyridine linker. This functionality is designed to participate in a metal-mediated self-assembly process to give networks. This article describes a simulation-guided strategy for the design of megamolecules to optimize the peptide linker in the fusion protein to give conformations that are best suited for self-assembly and therefore streamlines the typically time-consuming and labor-intensive experimental process. We designed 11 candidate megamolecules and identified the most promising linker, (EAAAK)2, along with the optimal experimental conditions through a combination of all-atom molecular dynamics, enhanced sampling, and larger-scale coarse-grained molecular dynamics simulations. Our simulation findings were validated and found to be consistent with the experimental results. Significantly, this study offers valuable insight into the self-assembly of megamolecule networks and provides a novel and general strategy for large biomolecular material designs by using systematic bottom-up coarse-grained simulations.

Engineered Protein Hydrogels as Biomimetic Cellular Scaffolds

The biochemical and biophysical properties of the extracellular matrix (ECM) play a pivotal role in regulating cellular behaviors such as proliferation, migration, and differentiation. Engineered protein-based hydrogels, with highly tunable multifunctional properties, have the potential to replicate key features of the native ECM. Formed by self-assembly or crosslinking, engineered protein-based hydrogels can induce a range of cell behaviors through bioactive and functional domains incorporated into the polymer backbone. Using recombinant techniques, the amino acid sequence of the protein backbone can be designed with precise control over the chain-length, folded structure, and cell-interaction sites. In this review, the modular design of engineered protein-based hydrogels from both a molecular- and network-level perspective are discussed, and summarize recent progress and case studies to highlight the diverse strategies used to construct biomimetic scaffolds. This review focuses on amino acid sequences that form structural blocks, bioactive blocks, and stimuli-responsive blocks designed into the protein backbone for highly precise and tunable control of scaffold properties. Both physical and chemical methods to stabilize dynamic protein networks with defined structure and bioactivity for cell culture applications are discussed. Finally, a discussion of future directions of engineered protein-based hydrogels as biomimetic cellular scaffolds is concluded.

Bond-centric modular design of protein assemblies

We describe a modular bond-centric approach to protein nanomaterial design inspired by the rich diversity of chemical structures that can be generated from the small number of atomic valencies and bonding interactions. We design protein building blocks with regular coordination geometries and bonding interactions that enable the assembly of a wide variety of closed and opened nanomaterials using simple geometrical principles. Experimental characterization confirms successful formation of more than twenty multi-component polyhedral protein cages, 2D arrays, and 3D protein lattices, with a high (10-50 %) success rate and electron microscopy data closely matching the corresponding design models. Because of the modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable systems.

Advancing Synthetic Hydrogels through Nature-Inspired Materials Chemistry

Synthetic extracellular matrix (ECM) mimics that can recapitulate the complex biochemical and mechanical nature of native tissues are needed for advanced models of development and disease. Biomedical research has heavily relied on the use of animal-derived biomaterials, which is now impeding their translational potential and convoluting the biological insights gleaned from in vitro tissue models. Natural hydrogels have long served as a convenient and effective cell culture tool, but advances in materials chemistry and fabrication techniques now present promising new avenues for creating xenogenic-free ECM substitutes appropriate for organotypic models and microphysiological systems. However, significant challenges remain in creating synthetic matrices that can approximate the structural sophistication, biochemical complexity, and dynamic functionality of native tissues. This review summarizes key properties of the native ECM, and discusses recent approaches used to systematically decouple and tune these properties in synthetic matrices. The importance of dynamic ECM mechanics, such as viscoelasticity and matrix plasticity, is also discussed, particularly within the context of organoid and engineered tissue matrices. Emerging design strategies to mimic these dynamic mechanical properties are reviewed, such as multi-network hydrogels, supramolecular chemistry, and hydrogels assembled from biological monomers.

Genetically Encoded XTEN-based Hydrogels with Tunable Viscoelasticity and Biodegradability for Injectable Cell Therapies

While direct cell transplantation holds great promise in treating many debilitating diseases, poor cell survival and engraftment following injection have limited effective clinical translation. Though injectable biomaterials offer protection against membrane-damaging extensional flow and supply a supportive 3D environment in vivo that ultimately improves cell retention and therapeutic costs, most are created from synthetic or naturally harvested polymers that are immunogenic and/or chemically ill-defined. This work presents a shear-thinning and self-healing telechelic recombinant protein-based hydrogel designed around XTEN - a well-expressible, non-immunogenic, and intrinsically disordered polypeptide previously evolved as a genetically encoded alternative to PEGylation to "eXTENd" the in vivo half-life of fused protein therapeutics. By flanking XTEN with self-associating coil domains derived from cartilage oligomeric matrix protein, single-component physically crosslinked hydrogels exhibiting rapid shear thinning and self-healing through homopentameric coiled-coil bundling are formed. Individual and combined point mutations that variably stabilize coil association enables a straightforward method to genetically program material viscoelasticity and biodegradability. Finally, these materials protect and sustain viability of encapsulated human fibroblasts, hepatocytes, embryonic kidney (HEK), and embryonic stem-cell-derived cardiomyocytes (hESC-CMs) through culture, injection, and transcutaneous implantation in mice. These injectable XTEN-based hydrogels show promise for both in vitro cell culture and in vivo cell transplantation applications.

PhoCoil: An Injectable and Photodegradable Single-component Recombinant Protein Hydrogel for Localized Therapeutic Cell Delivery

Hydrogel biomaterials offer great promise for 3D cell culture and therapeutic delivery. Despite many successes, challenges persist in that gels formed from natural proteins are only marginally tunable while those derived from synthetic polymers lack intrinsic bioinstructivity. Towards the creation of biomaterials with both excellent biocompatibility and customizability, recombinant protein-based hydrogels have emerged as molecularly defined and user-programmable platforms that mimic the proteinaceous nature of the extracellular matrix. Here, we introduce PhoCoil, a dynamically tunable recombinant hydrogel formed from a single protein component with unique multi-stimuli responsiveness. Physical crosslinking through coiled-coil interactions promotes rapid shear-thinning and self-healing behavior, rendering the gel injectable, while an included photodegradable motif affords on-demand network dissolution via visible light. PhoCoil gel photodegradation can be spatiotemporally and lithographically controlled in a dose-dependent manner, through complex tissue, and without harm to encapsulated cells. We anticipate that PhoCoil will enable new applications in tissue engineering and regenerative medicine.