Ion Effect and Metal-Coordinated Cross-Linking for Multiscale Design of Nereis Jaw Inspired Mechanomutable Materials

AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein

We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions in Nvjp-1 are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.

Stimuli-Responsive Protein Hydrogels: Their Design, Properties, and Biomedical Applications

Protein-based hydrogels are considered ideal biomaterials due to their high biocompatibility, diverse structure, and their improved bioactivity and biodegradability. However, it remains challenging to mimic the native extracellular matrices that can dynamically respond to environmental stimuli. The combination of stimuli-responsive functionalities with engineered protein hydrogels has facilitated the development of new smart hydrogels with tunable biomechanics and biological properties that are triggered by cyto-compatible stimuli. This review summarizes the recent advancements of responsive hydrogels prepared from engineered proteins and integrated with physical, chemical or biological responsive moieties. We underscore the design principles and fabrication approaches of responsive protein hydrogels, and their biomedical applications in disease treatment, drug delivery, and tissue engineering are briefly discussed. Finally, the current challenges and future perspectives in this field are highlighted.

A study across scales to unveil microstructural regimes in the multivalent metal driven self-assembly of cellulose nanocrystals

Understanding the behaviour of self-assembled systems, from nanoscale building blocks to bulk materials, is a central theme for the rational design of high-performance materials. Herein, we revealed, at different length scales, how the self-assembly of TEMPO-oxidised cellulose nanocrystals (TOCNCs) into rod fractal gels is directed by the complexation of Fe3+ ions on the surface of colloidal particles. Different specificities in Fe3+ binding on the TOCNC surface and conformational changes of the nanocellulose chain were unveiled by paramagnetic NMR spectroscopy. The macroscopic properties of systems presenting different concentrations of TOCNCs and Fe3+ ions were investigated by rheology and microscopy, demonstrating the tunability of the self-assembly of cellulose nanorods driven by Fe3+ complexation. Near-atomistic coarse-grained molecular dynamics simulations were developed to gain microscopic insight into the behaviour of this colloidal system. We found that the formation of different self-assembled architectures is driven by metal-nanocellulose complexation combined with the attenuation of electrostatic repulsion and water structuration around cellulose, leading to different microstructural regimes, from isolated nanorods to disconnected rod fractal clusters and rod fractal gels. These findings lay the foundation to unlock the full potential of cellulose nanocrystals as sustainable building blocks to develop self-assembled materials with defined structural control for a range of advanced applications.

Protein-Based Biological Materials: Molecular Design and Artificial Production

Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.

Molecular Dynamics Investigation into pH Dependent Metal Binding of the Intrinsically Disordered Worm Jaw Protein, Nvjp-1

Sclerotization of the Nereis virens jaw is mediated by metal binding to the histidine-rich jaw protein, Nvjp-1. Previous studies showed that the mechanical properties of Nvjp-1 hydrogels could be modulated with zinc binding as well as the associated anion. Here, we show that the mechanical properties of Nvjp-1 hydrogels can be modulated by pH and that zinc binding to Nvjp-1 is stable at both acidic and alkaline pH conditions. To probe the mechanism of Zn²⁺ binding to Nvjp-1 at different pH conditions, we utilized all atom molecular dynamics simulations employing a polarizable force field. At low pH conditions, polar residues predominantly interacted with Zn²⁺, with at most two residues interacting with a given zinc ion. Surprisingly, little to no Zn²⁺ binding was observed with the abundant Nvjp-1 acidic residues, which form salt-bridges with the protonated histidines to effectively block their binding to Zn²⁺ ions. As the pH was shifted to alkaline conditions, Zn²⁺ binding residues reconfigured to form additional coordination bonds with histidine, resulting in a reduction in the radius of gyration that correlated with hydrogel sclerotization. Furthermore, acetate ions were shown to facilitate the capture of zinc ions through association with protonated histidines at low pH, freeing acidic residues to interact with Zn²⁺ ions and increasing the number of Zn²⁺ ions that diffuse into the Nvjp-1 interior. Thus, these studies provide valuable molecular insights into how amino acid residues in Nvjp-1 manage metal salt binding and coordination in hydrogels as a function of the pH and ionic environments.

Effect of Divalent Metal Cations on the Conformation, Elastic Behavior, and Controlled Release of a Photocrosslinked Protein Engineered Hydrogel

We investigate the effect of Zn²⁺, Cu²⁺, and Ni²⁺ coordination on the conformation, mechanical properties, contraction, and small-molecule drug encapsulation and release of a photocrosslinked protein-engineered hydrogel, CEC-D. The treatment of the CEC-D hydrogel with divalent metal (M²⁺) results in significant conformational changes where a loss in structure is observed with Zn²⁺, while both Cu²⁺ and Ni²⁺ induce a blueshift. The relationship of M²⁺ to mechanical properties illustrates a trend, while the CEC-D hydrogel in the presence of 2 mM Cu²⁺ reveals the highest increase in G' to 14.4 ± 0.7 kPa followed by 9.7 ± 0.9 kPa by addition of 2 mM Zn²⁺, and a decrease to 1.1 ± 0.2 kPa is demonstrated in the presence of 2 mM Ni²⁺. A similar observation in M²⁺ responsiveness emerges where CEC-D hydrogels contract into a condensed state of 2.6-fold for Cu²⁺, 2.4-fold for Zn²⁺, and 1.6-fold for Ni²⁺. Furthermore, CEC-D hydrogels coordinated with M²⁺ demonstrate control over the encapsulation and release of the small molecule curcumin. The trend of release is opposite of the mechanical and contraction properties with a 70.0 ± 5.3% release with Ni²⁺, 64.2 ± 1.2% release with Zn²⁺, and 42.3 ± 11.3 release with Cu²⁺. Taken together, these results indicate that the CEC-D hydrogel tuned by M²⁺ is a promising drug delivery platform with tunable physicochemical properties.

Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry

Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.

Disulfide Crosslinked Hydrogels Made From the Hydra Stinging Cell Protein, Minicollagen-1

Minicollagens from cnidarian nematocysts are attractive potential building blocks for the creation of strong, lightweight and tough polymeric materials with the potential for dynamic and reconfigurable crosslinking to modulate functionality. In this study, the Hydra magnipapillata minicollagen-1 isoform was recombinantly expressed in bacteria, and a high throughput purification protocol was developed to generate milligram levels of pure protein without column chromatography. The resulting minicollagen-1 preparation demonstrated spectral properties similar to those observed with collagen and polyproline sequences as well as the ability to self-assemble into oriented fibers and bundles. Photo-crosslinking with Ru(II)( bpy ) 3 2 + was used to create robust hydrogels that were analyzed by mechanical testing. Interestingly, the minicollagen-1 hydrogels could be dissolved with reducing agents, indicating that ruthenium-mediated photo-crosslinking was able to induce disulfide metathesis to create the hydrogels. Together, this work is an important first step in creating minicollagen-based materials whose properties can be manipulated through static and reconfigurable post-translational modifications.

Metallogels: Availability, Applicability, and Advanceability

Introducing metal components into gel matrices provides an effective strategy to develop soft materials with advantageous properties such as: optical activity, conductivity, magnetic response activity, self-healing activity, catalytic activity, etc. In this context, a thorough overview of application-oriented metallogels is provided. Considering that many well-established metallogels start from serendipitous discoveries, insights into the structure-gelation relationship will offer a profound impact on the development of metallogels. Initially, design strategies for discovering new metallogels are discussed, then the advanced applications of metallogels are summarized. Finally, perspectives regarding the design of metallogels, the potential applications of metallogels and their derivative materials are briefly proposed.

Programmable Mechanical Properties from a Worm Jaw-Derived Biopolymer through Hierarchical Ion Exposure

Mechanisms of biomaterial sclerotization in natural systems promise new insights into how the mechanical properties of engineered materials may be dynamically modulated. One such example involves the proteinaceous jaw of the marine sandworm, Nereis virens. Previously, the mechanical properties of the N. virens jaw were shown to be modulated by Zn binding, a property that was proposed to be enabled by the presence of the histidine-rich jaw protein, Nvjp-1. Here we demonstrate the creation of Nvjp-1-based hydrogels and show that progressive sclerotization of these hydrogels can be accomplished with hierarchical exposure to metal cations and anions. Divalent Zn cations are capable of reversibly sclerotizing the hydrogels through the formation of coordinate cross-links, an effect that is shown to be remarkably specific for Zn. Additionally, the degree of Zn-induced sclerotization is strongly influenced by the identity of the anion present in the hydrogel. Thus, the viscoelastic properties of Nvjp-1 hydrogels can be modulated through programmed, hierarchical exposure to specific cations and anions present in the sclerotizing salts. These observations have resulted in new hydrogel capabilities, such as the creation of anion-controlled shape-memory polymers, and will add to the number of control parameters that can be used to tune the properties of functional hydrogels in a dynamic manner.

Melanin and Melanin-Related Polymers as Materials with Biomedical and Biotechnological Applications-Cuttlefish Ink and Mussel Foot Proteins as Inspired Biomolecules

The huge development of bioengineering during the last years has boosted the search for new bioinspired materials, with tunable chemical, mechanical, and optoelectronic properties for the design of semiconductors, batteries, biosensors, imaging and therapy probes, adhesive hydrogels, tissue restoration, photoprotectors, etc. These new materials should complement or replace metallic or organic polymers that cause cytotoxicity and some adverse health effects. One of the most interesting biomaterials is melanin and synthetic melanin-related molecules. Melanin has a controversial molecular structure, dependent on the conditions of polymerization, and therefore tunable. It is found in animal hair and skin, although one of the common sources is cuttlefish (Sepia officinalis) ink. On the other hand, mussels synthesize adhesive proteins to anchor these marine animals to wet surfaces. Both melanin and mussel foot proteins contain a high number of catecholic residues, and their properties are related to these groups. Dopamine (DA) can easily polymerize to get polydopamine melanin (PDAM), that somehow shares properties with melanin and mussel proteins. Furthermore, PDAM can easily be conjugated with other components. This review accounts for the main aspects of melanin, as well as DA-based melanin-like materials, related to their biomedical and biotechnological applications.

Materials Nanoarchitecturing via Cation-Mediated Protein Assembly: Making Limpet Teeth without Mineral

Teeth are designed to deliver high forces while withstanding the generated stresses. Aside from isolated mineral-free exception (e.g., marine polychaetes and squids), minerals are thought to be indispensable for tooth-hardening and durability. Here, the unmineralized teeth of the giant keyhole limpet (Megathura crenulata) are shown to attain a stiffness, which is twofold higher than any known organic biogenic structures. In these teeth, protein and chitin fibers establish a stiff compact outer shell enclosing a less compact core. The stiffness and its gradients emerge from a concerted interaction across multiple length-scales: packing of hydrophobic proteins and folding into secondary structures mediated by Ca²⁺ and Mg²⁺ together with a strong spatial control in the local fiber orientation. These results integrating nanoindentation, acoustic microscopy, and finite-element modeling for probing the tooth's mechanical properties, spatially resolved small- and wide-angle X-ray scattering for probing the material ordering on the micrometer scale, and energy-dispersive X-ray scattering combined with confocal Raman microscopy to study structural features on the molecular scale, reveal a nanocomposite structure hierarchically assembled to form a versatile damage-tolerant protein-based tooth, with a stiffness similar to mineralized mammalian bone, but without any mineral.