De novo rational design of a freestanding, supercharged polypeptide, proton-conducting membrane

Tuning the Dimensionality of Protein-Peptide Coassemblies to Build 2D Conductive Nanomaterials

The natural self-assembly tendency of proteins to build complex structural architectures has kindled inspiration in developing supramolecular structures through the rational design of biomacromolecules. While there has been significant progress in achieving precise control over the morphology of self-assembled structures, combining different molecules within assemblies enables the design of materials with increased complexity, sophisticated structures, and a broad spectrum of functionalities. Here, the development of 1D and 2D peptide-protein coassembled systems based on the design of amphiphilic peptides and engineered proteins is described. The peptide was optimized to form stable self-assembled fibers by evaluating, computationally and experimentally, the assembling tendencies and the supramolecular features of peptides with different lengths and negative charges. A superhelical repeat protein was engineered by fusing one or two amphiphilic peptides into one or both termini. This modification drove the coassembly between the self-assembled fibers and the protein with one or two peptides, resulting in 1D or 2D coassembled systems. The protein films and the 2D coassembled system exhibited high ionic conductivity for a biomolecular system, attributed to their high content of charged residues, positioning these materials as promising candidates for developing bioelectronic devices. Thus, this work provides a versatile framework for developing coassembled materials with tunable dimensionality by using biocompatible building blocks without any additional chemical moieties, highlighting the potential for their use in biocompatible electronics.

A Novel Gene Synthesis Platform for Designing Functional Protein Polymers

Recombinant protein polymers with repeat sequences of specific amino acids can be regarded as sustainable functional materials that can be designed using genetic engineering. However, synthesizing genes encoding these proteins is significantly time-consuming and labor-intensive owing to the difficulty of using common gene synthesis tools, such as restriction enzymes and PCR primers. To overcome these obstacles, a novel method is proposed herein: seamless cloning of rolling-circle amplicons (SCRCA). This method involves one-pot preparation of repetitive-sequence genes with overlapping ends for cloning, facilitating the easy construction of the desired recombinants. SCRCA is used to synthesize 10 genes encoding hydrophilic resilin-like and hydrophobic elastin-like repeat units that induce liquid-liquid phase separation. SCRCA shows higher transformation efficiency and better workability than conventional methods, and the time and budget required for SCRCA are comparable to those required for non-repetitive-sequence gene synthesis. Additionally, SCRCA facilitates the construction of a repeat unit library at a low cost. The library shows considerably higher diversity than that of the current state-of-the-art method. By combining this library construction with the directed evolution concept, an elastin-like protein polymer with the desired functions can be rapidly developed. SCRCA can greatly accelerate research on protein polymers.

Spontaneous Self-Organized Order Emerging From Intrinsically Disordered Protein Polymers

Intrinsically disordered proteins (IDPs) are proteins that, despite lacking a defined 3D structure, are capable of adopting dynamic conformations. This structural adaptability allows them to play not only essential roles in crucial cellular processes, such as subcellular organization or transcriptional control, but also in coordinating the assembly of macromolecules during different stages of development. Thus, in order to artificially replicate the complex processes of morphogenesis and their dynamics, it is crucial to have materials that recapitulate the structural plasticity of IDPs. In this regard, intrinsically disordered protein polymers (IDPPs) emerge as promising materials for engineering synthetic condensates and creating hierarchically self-assembled materials. IDPPs exhibit remarkable properties for their use in biofabrication, such as functional versatility, tunable sequence order-disorder, and the ability to undergo liquid-liquid phase separation (LLPS). Recent research has focused on harnessing the intrinsic disorder of IDPPs to design complex protein architectures with tailored properties. Taking advantage of their stimuli-responsiveness and degree of disorder, researchers have developed innovative strategies to control the self-assembly of IDPPs, resulting in the creation of hierarchically organized structures and intricate morphologies. In this review, we aim to provide an overview of the latest advances in the design and application of IDPP-based materials, shedding light on the fundamental principles that control their supramolecular assembly, and discussing their application in the biomedical and nanobiotechnological fields.

Long-Range Proton Channels Constructed via Hierarchical Peptide Self-Assembly

The quest to understand and mimic proton translocation mechanisms in natural channels has driven the development of peptide-based artificial channels facilitating efficient proton transport across nanometric membranes. It is demonstrated here that hierarchical peptide self-assembly can form micrometers-long proton nanochannels. The fourfold symmetrical peptide design leverages intermolecular aromatic interactions to align self-assembled cyclic peptide nanotubes, creating hydrophilic nanochannels between them. Titratable amino acid sidechains are positioned adjacent to each other within the channels, enabling the formation of hydrogen-bonded chains upon hydration, and facilitating efficient proton transport. Moreover, these chains are enriched with protons and water molecules by interacting with immobile counter ions introduced into the channels, increasing proton flow density and rate. This system maintains proton transfer rates closely resembling those in natural protein channels over micrometer distances. The functional behavior of these inherently recyclable and biocompatible systems opens the door for their exploitation in diverse applications in energy storage and conversion, biomedicine, and bioelectronics.

Engineered Protein Fibers with Reinforced Mechanical Properties Via β-Sheet High-Order Assembly

Protein fibers are ideal alternatives to synthetic polymers due to their unique mechanical properties, biocompatibility, and sustainability. However, engineering biomimetic protein fibers with high mechanical properties remains challenging, particularly in mimicking the high molecular weight of natural proteins and regulating their complex hierarchical structures. Here, a modular design and multi-scale assembly strategy is developed to manufacture robust protein fibers using low- or medium-molecular-weight proteins. The distinct functional and structural properties of flexible, rigid, and cross-linked domains in modular proteins are skillfully harnessed. By regulating the ratio of rigid to flexible domains, the formation of high-order β-sheet crystals aligned along the fiber axis is promoted, enhancing both strength and toughness. Furthermore, the dynamic imine cross-linking network, formed by the aldehyde-amine condensation reaction of the cross-linked domains, further reinforces the protein fibers. Remarkably, fibers spun from modular proteins significantly smaller than natural spidroin exhibit outstanding mechanical properties, surpassing those of protein fibers with same or even higher molecular weights. This strategy offers a promising pathway for fabricating protein fibers suitable for diverse applications.

Proton conductivity of the protein-based velvet worm slime

The properties of complex bodily fluids are linked to their biological functions through natural selection. Velvet worms capture their prey by ensnaring them with a proteinaceous fluid (slime). We examined the electrical conductivity of slime and found that dry slime is an insulator. However, its conductivity can increase by up to 106 times in its hydrated state, which can be further increased by an order in magnitude under acidic hydration (pH ≈ 2.3). The transient current measured using ion-blocking electrodes showed a continuous decay for up to 7 h, revealing slime's nature as a proton conducting material. Slime undergoes a spontaneous fibrilization process producing high aspect ratio ≈ 105 fibers that exhibit an average conductivity ≈2.4 ± 1.1 mS cm-1. These findings enhance our understanding of slime as a natural biopolymer and provide molecular-level guidelines to rationally design biomaterials that may be employed as hygroscopic conductors.

Emerging Landscape of Supercharged Proteins and Peptides for Drug Delivery

Although groundbreaking biotechnological techniques such as gene editing have significantly progressed, the effective and targeted transport of therapeutic agents into host cells remains a major obstacle to the development of biotherapeutics. Confronting the unique challenge posed by large macromolecules such as proteins, peptides, and nucleic acids adds complexity to this issue. Recent findings reveal that the supercharging of proteins and peptides not only enables control over critical properties, such as temperature resistance and catalytic activity, but also holds promise as a viable strategy for their use in drug delivery. This review provides a concise summary of the attributes of supercharged proteins and peptides, encompassing both their natural occurrence and engineered variants. Furthermore, it sheds light on the present status and future possibilities of supercharged proteins and peptides as carriers for significant biomolecules in the realms of medical research and therapeutic applications.

Solid-State Molecular Protonics Devices of Solid-Supported Biological Membranes Reveal the Mechanism of Long-Range Lateral Proton Transport

Lateral proton transport (PT) on the surface of biological membranes is a fundamental biochemical process in the bioenergetics of living cells, but a lack of available experimental techniques has resulted in a limited understanding of its mechanism. Here, we present a molecular protonics experimental approach to investigate lateral PT across membranes by measuring long-range (70 μm) lateral proton conduction via a few layers of lipid bilayers in a solid-state-like environment, i.e., without having bulk water surrounding the membrane. This configuration enables us to focus on lateral proton conduction across the surface of the membrane while decoupling it from bulk water. Hence, by controlling the relative humidity of the environment, we can directly explore the role of water in the lateral PT process. We show that proton conduction is dependent on the number of water molecules and their structure and on membrane composition, where we explore the role of the headgroup, the tail saturation, the membrane phase, and membrane fluidity. The measured PT as a function of temperature shows an inverse temperature dependency, which we explain by the desorption and adsorption of water molecules into the solid membrane platform. We explain our findings by discussing the role of percolating hydrogen bonding within the membrane structure in a Grotthuss-like mechanism.

Proton Transport Across Collagen Fibrils and Scaffolds: The Role of Hydroxyproline

Collagen is one of the most studied proteins due to its fundamental role in creating fibrillar structures and supporting tissues in our bodies. Accordingly, collagen is also one of the most used proteins for making tissue-engineered scaffolds for various types of tissues. To date, the high abundance of hydroxyproline (Hyp) within collagen is commonly ascribed to the structure and stability of collagen. Here, we hypothesize a new role for the presence of Hyp within collagen, which is to support proton transport (PT) across collagen fibrils. For this purpose, we explore here three different collagen-based hydrogels: the first is prepared by the self-assembly of natural collagen fibrils, and the second and third are based on covalently linking between collagen via either a self-coupling method or with an additional cross-linker. Following the formation of the hydrogel, we introduce here a two-step reaction, involving (1) attaching methanesulfonyl to the -OH group of Hyp, followed by (2) removing the methanesulfonyl, thus reverting Hyp to proline (Pro). We explore the PT efficiency at each step of the reaction using electrical measurements and show that adding the methanesulfonyl group vastly enhances PT, while reverting Hyp to Pro significantly reduces PT efficiency (compared with the initial point) with different efficiencies for the various collagen-based hydrogels. The role of Hyp in supporting the PT can assist in our understanding of the physiological roles of collagen. Furthermore, the capacity to modulate conductivity across collagen is very important to the use of collagen in regenerative medicine.

Near-Temperature-Independent Electron Transport Well beyond Expected Quantum Tunneling Range via Bacteriorhodopsin Multilayers

A key conundrum of biomolecular electronics is efficient electron transport (ETp) through solid-state junctions up to 10 nm, often without temperature activation. Such behavior challenges known charge transport mechanisms, especially via nonconjugated molecules such as proteins. Single-step, coherent quantum-mechanical tunneling proposed for ETp across small protein, 2-3 nm wide junctions, but it is problematic for larger proteins. Here we exploit the ability of bacteriorhodopsin (bR), a well-studied, 4-5 nm long membrane protein, to assemble into well-defined single and multiple bilayers, from ∼9 to 60 nm thick, to investigate ETp limits as a function of junction width. To ensure sufficient signal/noise, we use large area (∼10-3 cm2) Au-protein-Si junctions. Photoemission spectra indicate a wide energy separation between electrode Fermi and the nearest protein-energy levels, as expected for a polymer of mostly saturated components. Junction currents decreased exponentially with increasing junction width, with uniquely low length-decay constants (0.05-0.5 nm-1). Remarkably, even for the widest junctions, currents are nearly temperature-independent, completely so below 160 K. While, among other things, the lack of temperature-dependence excludes, hopping as a plausible mechanism, coherent quantum-mechanical tunneling over 60 nm is physically implausible. The results may be understood if ETp is limited by injection into one of the contacts, followed by more efficient charge propagation across the protein. Still, the electrostatics of the protein films further limit the number of charge carriers injected into the protein film. How electron transport across dozens of nanometers of protein layers is more efficient than injection defines a riddle, requiring further study.

Renewable Energy from Livestock Waste Valorization: Amyloid-Based Feather Keratin Fuel Cells

Increasing carbon emissions have accelerated climate change, resulting in devastating effects that are now tangible on an everyday basis. This is mirrored by a projected increase in global energy demand of approximately 50% within a single generation, urging a shift from fossil-fuel-derived materials toward greener materials and more sustainable manufacturing processes. Biobased industrial byproducts, such as side streams from the food industry, are attractive alternatives with strong potential for valorization due to their large volume, low cost, renewability, biodegradability, and intrinsic material properties. Here, we demonstrate the reutilization of industrial chicken feather waste into proton-conductive membranes for fuel cells, protonic transistors, and water-splitting devices. Keratin was isolated from chicken feathers via a fast and economical process, converted into amyloid fibrils through heat treatment, and further processed into membranes with an imparted proton conductivity of 6.3 mS cm-1 using a simple oxidative method. The functionality of the membranes is demonstrated by assembling them into a hydrogen fuel cell capable of generating 25 mW cm-2 of power density to operate various types of devices using hydrogen and air as fuel. Additionally, these membranes were used to generate hydrogen through water splitting and in protonic field-effect transistors as thin-film modulators of protonic conductivity via the electrostatic gating effect. We believe that by converting industrial waste into renewable energy materials at low cost and high scalability, our green manufacturing process can contribute to a fully circular economy with a neutral carbon footprint.

Biomimetic Structural Proteins: Modular Assembly and High Mechanical Performance

Protein-based biomaterials attract growing interests due to their encoded and programmable robust mechanical properties, superelasticity, plasticity, shape adaptability, excellent interfacial behavior, etc., derived from sequence-guided backbone structures, particularly compared to chemically synthetic counterparts in materials science and biomedical engineering. For example, protein materials have been successfully fabricated as (1) artificial implants (man-made tendons, cartilages, or dental tissues), due to programmable chemistry and biocompatibility; (2) smart biodevices with temperature/light-response and self-healing effects; and (3) impact resistance materials having great mechanical performance due to biomimetics. However, the existing method of regenerating protein materials from natural sources has two critical issues, low yield and structural damage, making it unable to meet demands. Therefore, it is crucial to develop an alternative strategy for fabricating protein materials. Heterologous expression of natural proteins with a modular assembly approach is an effective strategy for material preparation. Standardized, easy-to-assemble protein modules with specific structures and functions are developed through experimental and computational tools based on natural functional protein sequences. Through recombination and heterologous expression, these artificial protein modules become keys to material fabrication. Undergoing an assembly process similar to supramolecular self-assembly of proteins in cells, biomimetic modules can be fabricated for formation of macroscopic materials such as fibers and adhesives. This strategy inspired by synthetic biology and supramolecular chemistry is important for improving target protein yields and assembly integrity. It also preserves and optimizes the mechanical functions of structural proteins, accelerating the design and fabrication of artificial protein materials.In this Account, we overview recent studies on fabricating biomimetic protein materials to elucidate the concept of modular assembly. We discuss the design of biomimetic structural proteins at the molecular level, providing a wealth of details determining the bulk properties of materials. Additinally, we describe the modular self-assembly and assembly driven by inducing molecules, and mechanical properties and applications of resulting fibers. We used these strategies to develop fiber materials with high tensile strength, high toughness, and properties such as anti-icing and high-temperature resistance. We also extended this approach to design protein-based adhesives with ultra-strong adhesion, biocompatibility, and biodegradability for surgical applications such as wound sealing and healing. Other protein materials, including films and hydrogels, have been developed through chemical assembly routes. Finally, we describe exploiting synthetic biology and chemistry to overcome bottlenecks in structural protein modular design, biosynthesis, and material assembly and our perspectives for future development in structural biomaterials.

Proton Conducting Membranes with Molecular Self Assemblies and Ionic Channels for Efficient Proton Conduction

Supramolecular assemblies are vital for biological systems. This phenomenon in artificial materials is directly related to their numerous properties and their performance. Here, a simple approach to supramolecular assemblies is employed to fabricate highly efficient proton conducting molecular wires for fuel cell applications. Small molecule-based molecular assembly leading to a discotic columnar architecture is achieved, simultaneously with proton conduction that can take place efficiently in the absence of water, which otherwise is very difficult to obtain in interconnected ionic channels. High boiling point proton facilitators are incorporated into these columns possessing central ionic channels, thereby increasing the conduction multifold. Larger and asymmetrical proton facilitators disintegrated the self-assembly, resulting in low proton conduction efficiency. The highest conductivity was found to be approaching 10^-2 S/cm for the molecular wires in an anhydrous state, which is ascribed to the continuous network of hydrogen bonds in which protons can hop between with a lower energy barrier. The molecular wires with ionic channels presented here have potential as an alternative to proton conductors operating under anhydrous conditions at both low and high temperatures.

Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds

The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.

Light-Modulated Cationic and Anionic Transport across Protein Biopolymers*

Light is a convenient source of energy and the heart of light-harvesting natural systems and devices. Here, we show light-modulation of both the chemical nature and ionic charge carrier concentration within a protein-based biopolymer that was covalently functionalized with photoacids or photobases. We explore the capability of the biopolymer-tethered photoacids and photobases to undergo excited-state proton transfer and capture, respectively. Electrical measurements show that both the photoacid- and photobase-functionalized biopolymers exhibit an impressive light-modulated increase in ionic conductivity. Whereas cationic protons are the charge carriers for the photoacid-functionalized biopolymer, water-derived anionic hydroxides are the suggested charge carriers for the photobase-functionalized biopolymer. Our work introduces a versatile toolbox to photomodulate both protons and hydroxides as charge carriers in polymers, which can be of interest for a variety of applications.

A Protein-Based Free-Standing Proton-Conducting Transparent Elastomer for Large-Scale Sensing Applications

A most important endeavor in modern materials' research is the current shift toward green environmental and sustainable materials. Natural resources are one of the attractive building blocks for making environmentally friendly materials. In most cases, however, the performance of nature-derived materials is inferior to the performance of carefully designed synthetic materials. This is especially true for conductive polymers, which is the topic here. Inspired by the natural role of proteins in mediating protons, their utilization in the creation of a free-standing transparent polymer with a highly elastic nature and proton conductivity comparable to that of synthetic polymers, is demonstrated. Importantly, the polymerization process relies on natural protein crosslinkers and is spontaneous and energy-efficient. The protein used, bovine serum albumin, is one of the most affordable proteins, resulting in the ability to create large-scale materials at a low cost. Due to the inherent biodegradability and biocompatibility of the elastomer, it is promising for biomedical applications. Here, its immediate utilization as a solid-state interface for sensing of electrophysiological signals, is shown.

Attractive Pickering Emulsion Gels

Properties of emulsions highly depend on the interdroplet interactions and, thus, engineering interdroplet interactions at molecular scale are essential to achieve desired emulsion systems. Here, attractive Pickering emulsion gels (APEGs) are designed and prepared by bridging neighboring particle-stabilized droplets via telechelic polymers. In the APEGs, each telechelic molecule with two amino end groups can simultaneously bind to two carboxyl functionalized nanoparticles in two neighboring droplets, forming a bridged network. The APEG systems show typical shear-thinning behaviors and their viscoelastic properties are tunable by temperature, pH, and molecular weight of the telechelic polymers, making them ideal for direct 3D printing. The APEGs can be photopolymerized to prepare APEG-templated porous materials and their microstructures can be tailored to optimize their performances, making the APEG systems promising for a wide range of applications.

Natural biopolymers as proton conductors in bioelectronics

Bioelectronic devices sense or deliver information at the interface between living systems and electronics by converting biological signals into electronic signals and vice-versa. Biological signals are typically carried by ions and small molecules. As such, ion conducting materials are ideal candidates in bioelectronics for an optimal interface. Among these materials, ion conducting polymers that are able to uptake water are particularly interesting because, in addition to ionic conductivity, their mechanical properties can closely match the ones of living tissue. In this review, we focus on a specific subset of ion-conducting polymers: proton (H⁺ ) conductors that are naturally derived. We first provide a brief introduction of the proton conduction mechanism, and then outline the chemical structure and properties of representative proton-conducting natural biopolymers: polysaccharides (chitosan and glycosaminoglycans), peptides and proteins, and melanin. We then highlight examples of using these biopolymers in bioelectronic devices. We conclude with current challenges and future prospects for broader use of natural biopolymers as proton conductors in bioelectronics and potential translational applications.

Improving Bioavailability of Hydrophobic Prodrugs through Supramolecular Nanocarriers Based on Recombinant Proteins for Osteosarcoma Treatment

Supramolecular nanodrug assembly driven by supramolecular chemistry is becoming a powerful strategy for medication. The potential of engineered proteins as building blocks for nanoformulations is rarely investigated. Here, we developed a new generation of recombinant protein-based nanodrug carriers, which is very efficient for loading and delivering the hydrophobic prodrug aldoxorubicin. Significantly enhanced anti-tumor effects in osteosarcoma (OS) models were observed. The half-life of the nanodrug reached almost two days and the corresponding bioavailability increased by 17-fold. This is significantly superior to other drug counterparts, empowering long-acting OS treatment scenarios. Importantly, off-target side effects of the prodrug, including cardiotoxicity and lung-metastasis, were greatly mitigated with our medication. Thus, our assembly strategy enables the customized design of advanced nanodelivery systems employing broader biomaterial building blocks for cancer therapy.

Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions

De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.