Evolutionary screening of collagen-like peptides that nucleate hydroxyapatite crystals

Human collagen sequence polypeptides mediated biomineralization and its molecular mechanism

Biotechnology provides alternatives for regenerative medicine with more controllable functions. Herein, the polypeptides encoded with human collagen I amino-acid sequences were studied for the first time to modulate biomimetic hydroxyapatite (HAP). With a length of 50-100 nm and a width of 20-30 nm, the HAP crystal formed was plate-like. The interaction of the human collagen sequence polypeptide on the (001), (100), and (211) crystal faces of HAP crystal had been studied using Molecular Dynamics (MD) simulations, respectively. Based on MD simulations, van der Waals forces and hydrogen bonds are the main interactions between polypeptides and HAP through the -NH2, -CH2-, -OH, and -COOH, respectively. According to the calculated results, der Waals forces might be the main interaction. The human collagen sequence polypeptides exhibited the highest adsorption energy on the (001) plane of HAP, significantly higher than any of the adsorption energy on the (100) and (211) planes. Therefore, the growth of the (001) would be inhibited, which kept accurate with the result of images from the Transmission Electron Microscope (TEM). Study results provide a basis for rational designing of peptides with human collagen sequences to regenerate hard tissues.

Evolutionary Design of Self-Templated Supramolecular Fibrils Using M13 Bacteriophage for Tissue Engineering

Biomaterials in nature form hierarchical structures and functions across various length scales through binding and assembly processes. Inspired by nature, we developed hierarchically organized tissue engineering materials through evolutionary screening and self-templating assembly. Leveraging the M13 bacteriophage (phage), we employed an evolutionary selection process against hydroxyapatite (HA) to isolate HA-binding phage (HAPh). The newly discovered phage exhibits a bimodal length, comprising 950 nm and 240 nm, where the synergistic effect of these dual lengths promotes the formation of supramolecular fibrils with periodic banded structures. The assembled HAPh fibrils show the capability of HA mineralization and the directional growth of osteoblast cells. When applied to a dentin surface, it induces the regeneration of dentin-like tissue structures, showcasing its potential applications as a scaffold in tissue engineering. The integration of evolutionary screening and self-templating assembly holds promise for the future development of hierarchically organized tissue engineering materials.

Virus-Based Separation of Rare Earth Elements

The utilization of biomaterials for the separation of rare earth elements (REEs) has attracted considerable interest due to their inherent advantages, including diverse molecular structures for selective binding and the use of eco-friendly materials for sustainable systems. We present a pioneering methodology for developing a safe virus to selectively bind REEs and facilitate their release through pH modulation. We engineered the major coat protein of M13 bacteriophage (phage) to incorporate a lanthanide-binding peptide. The engineered lanthanide-binding phage (LBPh), presenting ∼3300 copies of the peptide, serves as an effective biological template for REE separation. Our findings demonstrate the LBPh's preferential binding for heavy REEs over light REEs. Moreover, the LBPh exhibits remarkable robustness with excellent recyclability and stability across multiple cycles of separations. This study underscores the potential of genetically integrating virus templates with selective binding motifs for REE separation, offering a promising avenue for environmentally friendly and energy-efficient separation processes.

Effects of chain lengths and backbone chirality on the bone-targeting ability of poly(glutamic acid)s

Anionic synthetic polypeptides are promising candidates as standalone bone-targeting drug carriers. Nevertheless, the structure-property relationship of the bone-targeting ability of polypeptides remains largely unexplored. Herein we report the optimization of the in vitro and in vivo bone-targeting ability of poly(glutamic acid)s (PGAs) by altering their chain lengths and backbone chirality. PGA 100-mers exhibited higher hydroxyapatite affinity in vitro, but their rapid macrophage clearance limited their targeting ability. Shorter PGA was therefore favored in terms of in vivo bone targeting. Meanwhile, the backbone chirality showed less significant impact on the in vitro and in vivo targeting behavior. This study highlights the modulation of structural parameters on the bone-targeting performance of anionic polypeptides, shedding light on the future design of polypeptide-based carriers.

Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification

Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.

Regulation of recombinant humanized collagen on HAP growth and its molecule simulation

Hydroxyapatite (HAP) in natural bone is formed under the regulation of natural collagen I. Here, we report how recombinant humanized collagen I (rhCol I) regulates the growth of HAP nanocrystals in a long belt shape 100-150 nm in width and 200-300 nm in length. MD simulation results showed that the interactions between rhCol I and the (001), (100), and (211) planes of HAP mainly contributed to the electrostatic force and van der Waals forces via COO⋯Ca, -NH⋯Ca, CH⋯OPO3, and NH⋯OPO3 bonds, respectively. On the (001) plane, the interaction between -COO- and Ca was stronger than on the (100) and (211) planes, resulting in a large electrostatic force, which inhibited the growth of the (001) plane. The lowest energy of adsorption to the (211) plane resulted in the preferential growth of the (211) plane due to the weakest interaction with rhCol I. The detailed correlation between HAP and rhCol I could explain HAP growth under regulation by rhCol I. This study provides a reference for the bio-application of recombinant collagen.

Modular Design for Proteins Assembling into Antifouling Coatings: Case of Gold Surfaces

We analyze modularity for a B-M-E triblock protein designed to self-assemble into antifouling coatings. Previously, we have shown that the design performs well on silica surfaces when B is taken to be a silica-binding peptide, M is a thermostable trimer domain, and E is the uncharged elastin-like polypeptide (ELP), E = (GSGVP)₄₀. Here, we demonstrate that we can modulate the nature of the substrate on which the coatings form by choosing different solid-binding peptides as binding domain B and that we can modulate antifouling properties by choosing a different hydrophilic block E. Specifically, to arrive at antifouling coatings for gold surfaces, as binding block B we use the gold-binding peptide GBP1 (with the sequence MHGKTQATSGTIQS), while we replace the antifouling blocks E by zwitterionic ELPs of different lengths, E^Z_n = (GDGVP-GKGVP)_n/2, with n = 20, 40, or 80. We find that even the B-M-E proteins with the shortest E blocks make coatings on gold surfaces with excellent antifouling against 1% human serum (HS) and reasonable antifouling against 10% HS. This suggests that the B-M-E triblock protein can be easily adapted to form antifouling coatings on any substrate for which solid-binding peptide sequences are available.

Engineered M13 phage as a novel therapeutic bionanomaterial for clinical applications: From tissue regeneration to cancer therapy

Bacteriophages (phages) are nanostructured viruses with highly selective antibacterial properties that have gained attention beyond eliminating bacteria. Specifically, M13 phages are filamentous phages that have recently been studied in various aspects of nanomedicine due to their biological advantages and more compliant engineering capabilities over other phages. Having nanofiber-like morphology, M13 phages can reach varied target sites and self-assemble into multidimensional scaffolds in a relatively safe and stable way. In addition, genetic modification of the coat proteins enables specific display of peptides and antibodies on the phages, allowing for precise and individualized medicine. M13 phages have also been subjected to novel engineering approaches, including phage-based bionanomaterial engineering and phage-directed nanomaterial combinations that enhance the bionanomaterial properties of M13 phages. In view of these features, researchers have been able to utilize M13 phages for therapeutic applications such as drug delivery, biodetection, tissue regeneration, and targeted cancer therapy. In particular, M13 phages have been utilized as a novel bionanomaterial for precisely mimicking natural tissue environment in order to overcome the shortage in tissue and organ donors. Hence, in this review, we address the recent studies and advances of using M13 phages in the field of nanomedicine as therapeutic agents based upon their characteristics as novel bionanomaterial with biomolecules displayed. This paper also emphasizes the novel engineering approach that enhances M13 phage's bionanomaterial capabilities. Current limitations and future approaches are also discussed to provide insight in further progress for M13 phage-based clinical applications.

Synthetic extracellular matrices with function-encoding peptides

The communication of cells with their surroundings is mostly encoded in the epitopes of structural and signalling proteins present in the extracellular matrix (ECM). These peptide epitopes can be incorporated in biomaterials to serve as function-encoding molecules to modulate cell-cell and cell-ECM interactions. In this Review, we discuss natural and synthetic peptide epitopes as molecular tools to bioengineer bioactive hydrogel materials. We present a library of functional peptide sequences that selectively communicate with cells and the ECM to coordinate biological processes, including epitopes that directly signal to cells, that bind ECM components that subsequently signal to cells, and that regulate ECM turnover. We highlight how these epitopes can be incorporated in different biomaterials as individual or multiple signals, working synergistically or additively. This molecular toolbox can be applied in the design of biomaterials aimed at regulating or controlling cellular and tissue function, repair and regeneration.

Phage for regenerative medicine and cosmetics

Phage or bacteriophage is a specific virus with the ability to defeat bacteria. Because of the rising prevalence of antimicrobial-resistant bacteria, the bacteriophage is now receiving interest again, with it application in skin infection or acne treatment. Moreover, bacteriophages also express their efficacy in wound healing or skin regeneration. Thanks to the development of bioengineering technology, phage display, which is a technique using bacteriophage as a tool, has recently been applied in many biotechnological and medical fields, especially in regenerative medicines. Bacteriophages can be used as nanomaterials, delivery vectors, growth factor alternatives, or in several bacteriophage display-derived therapeutics and stem cell technology. Although bacteriophage is no doubt to be a potential and effective alternative in modern medicine, there are still controversial evidence about the antibacterial efficacy as well as the affinity to expected targets of bacteriophage. Future mission is to optimize the specificity, stability, affinity and biodistribution of phage-derived substances. In this chapter, we focused on introducing several mechanisms and applications of bacteriophage and analyzing its future potential in regenerative medicines as well as cosmetics via previous research's results.

Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO3 Biological Crystallization

A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO₃ crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. This foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.

A novel peptide isolated from Catla skin collagen acts as a self-assembling scaffold promoting nucleation of calcium-deficient hydroxyapatite nanocrystals

Catla collagen hydrolysate (CH) was fractionated by chromatography and each fraction was subjected to HA nucleation, with the resultant HA-fraction composites being scored based on the structural and functional group of the HA formed. The process was repeated till a single peptide with augmented HA nucleation capacity was obtained. The peptide (4.6 kDa), exhibited high solubility, existed in polyproline-II conformation and displayed a dynamic yet stable hierarchical self-assembling property. The 3D modelling of the peptide revealed multiple calcium and phosphate binding sites and a high propensity to self-assemble. Structural analysis of the peptide-HA crystals revealed characteristic diffraction planes of HA with mineralization following the (002) plane, retention of the self-assembled hierarchy of the peptide and intense ionic interactions between carboxyl groups and calcium. The peptide-HA composite crystals were mostly of 25-40 nm dimensions and displayed 79% mineralization, 92% crystallinity, 39.25% porosity, 12GPa Young's modulus and enhanced stability in physiological pH. Cells grown on peptide-HA depicted faster proliferation rates and higher levels of osteogenic markers. It was concluded that the prerequisite for HA nucleation by a peptide included: a conserved sequence with a unique charge topology allowing calcium chelation and its ability to form a dynamic self-assembled hierarchy for crystal propagation.

Biomimetic mineralization based on self-assembling peptides

Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.

Biomedical applications of solid-binding peptides and proteins

Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.

Chemically Crosslinked Amphiphilic Degradable Shape Memory Polymer Nanocomposites with Readily Tuned Physical, Mechanical, and Biological Properties

Facile surgical delivery and stable fixation of synthetic scaffolds play roles just as critically as degradability and bioactivity in ensuring successful scaffold-guided tissue regeneration. Properly engineered shape memory polymers (SMPs) may meet these challenges. Polyhedral oligomeric silsesquioxanes (POSSs) can be covalently integrated with urethane-crosslinked polylactide (PLA) to give high-strength, degradable SMPs around physiological temperatures. To explore their potential for guided bone regeneration, here we tune their hydrophilicity, degradability, cytocompatibility, and osteoconductivity/osteoinductivity by crosslinking star-branched POSS-PLA with hydrophilic polyethylene glycol diisocyanates of different lengths and up to 60 wt % hydroxyapatite (HA). The composites exhibit high compliance, toughness, up to gigapascal storage moduli, and excellent shape recovery (>95%) at safe triggering temperatures. Water swelling ratios and hydrolytic degradation rates positively correlated with the hydrophilic crosslinker lengths, while the negative impact of degradation on the proliferation and osteogenesis of bone marrow stromal cells was mitigated with HA incorporation. Macroporous composites tailored for a rat femoral segmental defect were fabricated, and their ability to stably retain and sustainedly release recombinant osteogenic bone morphogenetic protein-2 and support cell attachment and osteogenesis was demonstrated. These properties combined make these amphiphilic osteoconductive degradable SMPs promising candidates as next-generation synthetic bone grafts.

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.

Supramolecular Peptide Nanofiber Hydrogels for Bone Tissue Engineering: From Multihierarchical Fabrications to Comprehensive Applications

Bone tissue engineering is becoming an ideal strategy to replace autologous bone grafts for surgical bone repair, but the multihierarchical complexity of natural bone is still difficult to emulate due to the lack of suitable biomaterials. Supramolecular peptide nanofiber hydrogels (SPNHs) are emerging biomaterials because of their inherent biocompatibility, satisfied biodegradability, high purity, facile functionalization, and tunable mechanical properties. This review initially focuses on the multihierarchical fabrications by SPNHs to emulate natural bony extracellular matrix. Structurally, supramolecular peptides based on distinctive building blocks can assemble into nanofiber hydrogels, which can be used as nanomorphology-mimetic scaffolds for tissue engineering. Biochemically, bioactive motifs and bioactive factors can be covalently tethered or physically absorbed to SPNHs to endow various functions depending on physiological and pharmacological requirements. Mechanically, four strategies are summarized to optimize the biophysical microenvironment of SPNHs for bone regeneration. Furthermore, comprehensive applications about SPNHs for bone tissue engineering are reviewed. The biomaterials can be directly used in the form of injectable hydrogels or composite nanoscaffolds, or they can be used to construct engineered bone grafts by bioprinting or bioreactors. Finally, continuing challenges and outlook are discussed.

Understanding the Adhesion Mechanism of Hydroxyapatite-Binding Peptide

Understanding the interactions between the protein collagen and hydroxyapatite is of high importance for understanding biomineralization and bone formation. Here, we undertook a reductionist approach and studied the interactions between a short peptide and hydroxyapatite. The peptide was selected from a phage-display library for its high affinity to hydroxyapatite. To study its interactions with hydroxyapatite, we performed an alanine scan to determine the contribution of each residue. The interactions of the different peptide derivatives were studied using a quartz crystal microbalance with dissipation monitoring and with single-molecule force spectroscopy by atomic force microscopy. Our results suggest that the peptide binds via electrostatic interactions between cationic moieties of the peptide and the negatively charged groups on the crystal surface. Furthermore, our findings show that cationic residues have a crucial role in binding. Using molecular dynamics simulations, we show that the peptide structure is a contributing factor to the adhesion mechanism. These results suggest that even small conformational changes can have a significant effect on peptide adhesion. We suggest that a bent structure of the peptide allows it to strongly bind hydroxyapatite. The results presented in this study improve our understanding of peptide adhesion to hydroxyapatite. On top of physical interactions between the peptide and the surface, peptide structure contributes to adhesion. Unveiling these processes contributes to our understanding of more complex biological systems. Furthermore, it may help in the design of de novo peptides to be used as functional groups for modifying the surface of hydroxyapatite.

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ∼ 10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. The findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration

Abstract

The development of natural biomaterials applied for hard tissue repair and regeneration is of great importance, especially in societies with a large elderly population. Self-assembled peptide hydrogels are a new generation of biomaterials that provide excellent biocompatibility, tunable mechanical stability, injectability, trigger capability, lack of immunogenic reactions, and the ability to load cells and active pharmaceutical agents for tissue regeneration. Peptide-based hydrogels are ideal templates for the deposition of hydroxyapatite crystals, which can mimic the extracellular matrix. Thus, peptide-based hydrogels enhance hard tissue repair and regeneration compared to conventional methods. This review presents three major self-assembled peptide hydrogels with potential application for bone and dental tissue regeneration, including ionic self-complementary peptides, amphiphilic (surfactant-like) peptides, and triple-helix (collagen-like) peptides. Special attention is given to the main bioactive peptides, the role and importance of self-assembled peptide hydrogels, and a brief overview on molecular simulation of self-assembled peptide hydrogels applied for bone and dental tissue engineering and regeneration.

Graphic abstract

Curli-Mediated Self-Assembly of a Fibrous Protein Scaffold for Hydroxyapatite Mineralization

Nanostructures formed by self-assembled peptides have been increasingly exploited as functional materials for a wide variety of applications, from biotechnology to energy. However, it is sometimes challenging to assemble free short peptides into functional supramolecular structures, since not all peptides have the ability to self-assemble. Here, we report a self-assembly mechanism for short functional peptides that we derived from a class of fiber-forming amyloid proteins called curli. CsgA, the major subunit of curli fibers, is a self-assembling β-helical subunit composed of five pseudorepeats (R1-R5). We first deleted the internal repeats (R2, R3, R4), known to be less essential for the aggregation of CsgA monomers into fibers, forming a truncated CsgA variant (R1/R5). As a proof-of-concept to introduce functionality in the fibers, we then genetically substituted the internal repeats by a hydroxyapatite (HAP)-binding peptide, resulting in a R1/HAP/R5 construct. Our method thus utilizes the R1/R5-driven self-assembly mechanism to assemble the HAP-binding peptide and form hydrogel-like materials in macroscopic quantities suitable for biomineralization. We confirmed the expression and fibrillar morphology of the truncated and HAP-containing curli-like amyloid fibers. X-ray diffraction and TEM showed the functionality of the HAP-binding peptide for mineralization and formation of nanocrystalline HAP. Overall, we show that fusion to the R1 and R5 repeats of CsgA enables the self-assembly of functional peptides into micron long fibers. Further, the mineral-templating ability that the R1/HAP/R5 fibers possesses opens up broader applications for curli proteins in the tissue engineering and biomaterials fields.

Spider Silk Fusion Proteins for Controlled Collagen Binding and Biomineralization

The development of biomaterials for the interface between tendon and bone is important for realizing functional tendon replacements. Toward the development of new materials for such applications, engineered recombinant spider silk proteins were modified with peptide tag sequences derived from noncollagenous proteins in bone, so-called SIBLING proteins, such as osteopontin and sialoprotein, which are known to interact with collagen and to initiate mineralization. Materials made of these spider silk-SIBLING hybrids were analyzed concerning mineralization and interaction with cells. They showed enhanced calcium phosphate formation upon incubation in mineralization agents. In gradient films, MC3T3-E1 mouse preosteoblasts adhered preferentially along the gradient toward the variant with a collagen binding motif.

Mechanics of Mineralized Collagen Fibrils upon Transient Loads

Collagen is a key structural protein in the human body, which undergoes mineralization during the formation of hard tissues. Earlier studies have described the mechanical behavior of bone at different scales, highlighting material features across hierarchical structures. Here we present a study that aims to understand the mechanical properties of mineralized collagen fibrils upon tensile/compressive transient loads, investigating how the kinetic energy propagates and it is dissipated at the molecular scale, thus filling a gap of knowledge in this area. These specific features are the mechanisms that nature has developed to passively dissipate stress and prevent structural failures. In addition to the mechanical properties of the mineralized fibrils, we observe distinct nanomechanical behaviors for the two regions (i.e., overlap and gap) of the D-period to highlight the effect of the mineralization. We notice decreasing trends for both wave speeds and Young's moduli over input velocity with a marked strengthening effect in the gap region due to the accumulation of the hydroxyapatite. In contrast, the dissipative behavior is not affected by either loading conditions or the mineral percentage, showing a stronger damping effect upon faster inputs compatible to the bone behavior at the macroscale. Our results offer insights into the dissipative behavior of mineralized collagen composites to design and characterize bioinspired composites for replacement devices (e.g., prostheses for sound transmission or conduction) or optimized structures able to bear transient loads, for example, impact, fatigue, in structural applications.

Peptides as surface coatings of nanoparticles that penetrate human cystic fibrosis sputum and uniformly distribute in vivo following pulmonary delivery

Therapeutic delivery of drug and gene delivery systems have to traverse multiple biological barriers to achieve efficacy. Mucosal administration, such as pulmonary delivery in cystic fibrosis (CF) disease, remains a significant challenge due to concentrated viscoelastic mucus, which prevents drugs and particles from penetrating the mucus barrier. To address this problem, we used combinatorial peptide-presenting phage libraries and next-generation sequencing (NGS) to identify hydrophilic, net-neutral charged peptide coatings that enable penetration through human CF mucus ex vivo with ~600-fold better penetration than control, improve uptake into lung epithelial cells compared to uncoated or PEGylated-nanoparticles, and exhibit enhanced uniform distribution and retention in the mouse lung airways. These peptide coatings address multiple delivery barriers and effectively serve as excellent alternatives to standard PEG surface chemistries to achieve mucus penetration and address some of the challenges encountered using these chemistries. This biomolecule-based strategy can address multiple delivery barriers and hold promise to advance efficacy of therapeutics for diseases like CF.

Enhanced Biosorption of Nickel Ions on Immobilized Surface-Engineered Yeast Using Nickel-Binding Peptides

Three nickel-binding peptides were screened from a phage peptide library and displayed separately or in combination with surface-engineered Saccharomyces cerevisiae EBY100. The sorption of nickel ions on the surface of yeast cells increased with the increasing number of nickel Ni(II)-binding peptides displayed. The combined expression of the three peptides by EBY100/pYD1-N123 demonstrated the highest sorption of Ni(II) (2.603 ± 0.004 g g^-1, dry weight) and an enhanced sorption capacity of 60.15%, compared to S. cerevisiae EBY100. An orthogonal test for yeast immobilization was designed. A maximum sorption capability of 68.62% was observed for a treatment at 25°C with 2.0% calcium chloride and 3.0% sodium alginate.

Bacteriophage-based biomaterials for tissue regeneration

Bacteriophage, also called phage, is a human-safe bacteria-specific virus. It is a monodisperse biological nanostructure made of proteins (forming the outside surface) and nucleic acids (encased in the protein capsid). Among different types of phages, filamentous phages have received great attention in tissue regeneration research due to their unique nanofiber-like morphology. They can be produced in an error-free format, self-assemble into ordered scaffolds, display multiple signaling peptides site-specifically, and serve as a platform for identifying novel signaling or homing peptides. They can direct stem cell differentiation into specific cell types when they are organized into proper patterns or display suitable peptides. These unusual features have allowed scientists to employ them to regenerate a variety of tissues, including bone, nerves, cartilage, skin, and heart. This review will summarize the progress in the field of phage-based tissue regeneration and the future directions in this field.

Building two-dimensional materials one row at a time: Avoiding the nucleation barrier

Assembly of two-dimensional (2D) molecular arrays on surfaces produces a wide range of architectural motifs exhibiting unique properties, but little attention has been given to the mechanism by which they nucleate. Using peptides selected for their binding affinity to molybdenum disulfide, we investigated nucleation of 2D arrays by molecularly resolved in situ atomic force microscopy and compared our results to molecular dynamics simulations. The arrays assembled one row at a time, and the nuclei were ordered from the earliest stages and formed without a free energy barrier or a critical size. The results verify long-standing but unproven predictions of classical nucleation theory in one dimension while revealing key interactions underlying 2D assembly.

Mucus-penetrating phage-displayed peptides for improved transport across a mucus-like model

The objective of this work is to use phage display libraries as a screening tool to identify peptides that facilitate transport across the mucus barrier. Mucus is a complex selective barrier to particles and molecules, limiting penetration to the epithelial surface of mucosal tissues. In mucus-associated diseases such as cystic fibrosis (CF), mucus has increased viscoelasticity and a higher concentration of covalent and non-covalent physical entanglements compared to healthy tissues, which greatly hinders permeability and transport of drugs and particles across the mucosae for therapeutic delivery. Treatment of CF lung diseases and associated infections must overcome this abnormal mucosal barrier. Critical bottlenecks hindering effective drug penetration remain and while recent studies have shown hydrophilic, net-neutral charge polymers can improve the transport of nanoparticles and minimize interactions with mucus, there is a dearth of alternative carriers available. We hypothesized that the screening of a phage peptide library against a CF mucus model would lead to the identification of phage-displayed peptide sequences able to improve transport in mucus. These combinatorial libraries possess a large diversity of peptide-based formulations (10⁸-10⁹) to achieve unprecedented screening for potential mucus-penetrating peptides. Here, phage clones displaying discovered peptides were shown to have up to 2.6-fold enhanced diffusivity in the CF mucus model. In addition, we demonstrate reduced binding affinities to mucin compared to wild-type control. These findings suggest that phage display libraries can be used as a strategy to improve transmucosal delivery.

Engineering of M13 Bacteriophage for Development of Tissue Engineering Materials

M13 bacteriophages have several qualities that make them attractive candidates as building blocks for tissue regenerating scaffold materials. Through genetic engineering, a high density of functional peptides and proteins can be simultaneously displayed on the M13 bacteriophage's outer coat proteins. The resulting phage can self-assemble into nanofibrous network structures and can guide the tissue morphogenesis through proliferation, differentiation and apoptosis. In this manuscript, we will describe methods to develop major coat-engineered M13 phages as a basic building block and aligned tissue-like matrices to develop regenerative nanomaterials.

Virus-Derived Peptides for Clinical Applications

Novel affinity agents with high specificity are needed to make progress in disease diagnosis and therapy. Over the last several years, peptides have been considered to have fundamental benefits over other affinity agents, such as antibodies, due to their fast blood clearance, low immunogenicity, rapid tissue penetration, and reproducible chemical synthesis. These features make peptides ideal affinity agents for applications in disease diagnostics and therapeutics for a wide variety of afflictions. Virus-derived peptide techniques provide a rapid, robust, and high-throughput way to identify organism-targeting peptides with high affinity and selectivity. Here, we will review viral peptide display techniques, how these techniques have been utilized to select new organism-targeting peptides, and their numerous biomedical applications with an emphasis on targeted imaging, diagnosis, and therapeutic techniques. In the future, these virus-derived peptides may be used as common diagnosis and therapeutics tools in local clinics.

Solid-Binding Peptides in Biomedicine

Some peptides are able to bind to inorganic materials such as silica and gold. Over the past decade, Solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to a diverse range of inorganic surfaces e.g. metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers and minerals. They can be used in applications such as protein purification and synthesis, assembly and the functionalization of nanomaterials. They offer simple and versatile bioconjugation methods that can increase biocompatibility and also direct the immobilization and orientation of nanoscale entities onto solid supports without impeding their functionality. SBPs have been employed in numerous nanobiotechnological applications such as the controlled synthesis of nanomaterials and nanostructures, formation of hybrid biomaterials, immobilization of functional proteins and improved nanomaterial biocompatibility. With advances in nanotechnology, a multitude of novel nanomaterials have been designed and synthesized for diagnostic and therapeutic applications. New approaches have been developed recently to exert a greater control over bioconjugation and eventually, over the optimal and functional display of biomolecules on the surfaces of many types of solid materials. In this chapter we describe SBPs and highlight some selected examples of their potential applications in biomedicine.

Phage Display Technology in Biomaterials Engineering: Progress and Opportunities for Applications in Regenerative Medicine

The field of regenerative medicine has been gaining momentum steadily over the past few years. The emphasis in regenerative medicine is to use various in vitro and in vivo approaches that leverage the intrinsic healing mechanisms of the body to treat patients with disabling injuries and chronic diseases such as diabetes, osteoarthritis, and degenerative disorders of the cardiovascular and central nervous system. Phage display has been successfully employed to identify peptide ligands for a wide variety of targets, ranging from relatively small molecules (enzymes, cell receptors) to inorganic, organic, and biological (tissues) materials. Over the past two decades, phage display technology has advanced tremendously and has become a powerful tool in the most varied fields of research, including biotechnology, materials science, cell biology, pharmacology, and diagnostics. The growing interest in and success of phage display libraries is largely due to its incredible versatility and practical use. This review discusses the potential of phage display technology in biomaterials engineering for applications in regenerative medicine.

Nanoparticle Assembly and Gelatin Binding Mediated by Triple Helical Collagen Mimetic Peptide

Peptide-conjugated nanoparticles (NPs) have promising potential for applications in biosensing, diagnosis, and therapeutics because of their appropriate size, unique self-assembly, and specific substrate-binding properties. However, controlled assembly and selective target binding are difficult to achieve with simple peptides on NP surfaces because high surface energy makes NPs prone to self-aggregate and adhere nonspecifically. Here, we report the self-assembly and gelatin binding properties of collagen mimetic peptide (CMP) conjugated gold NPs (CMP-NPs). We show that the orientation of CMPs displayed on the NP surface can control NP assembly either by promoting or hindering triple helical folding between CMPs of neighboring NPs. We also show that CMP-NPs can specifically bind to denatured collagen by forming triple-helical hybrids between denatured collagen strands and CMPs, demonstrating their potential use for detection and selective removal of gelatin from protein mixtures. CMP conjugated NPs offer a simple and effective method for NP assembly and for targeting denatured collagens with high specificity. Therefore, they may lead to new types of functional nanomaterials for detection and study of denatured collagen associated with diseases characterized by high levels of collagen degradation.

Accelerated Nucleation of Hydroxyapatite Using an Engineered Hydrophobin Fusion Protein

Calcium phosphate mineralization is of particular interest in dental repair. A biomimetic approach using proteins or peptides is a highly promising way to reconstruct eroded teeth. In this study, the screening of several proteins is described for their binding and nucleating activities toward hydroxyapatite. Out of 27 tested candidates, only two hydrophobin fusion proteins showed binding abilities to hydroxyapatite in a mouthwash formulation and an increased nucleation in artificial saliva. Using a semirational approach, one of the two candidates (DEWA_5), a fusion protein consisting of a truncated section of the Bacillus subtilis synthase YaaD, the Aspergillus nidulans hydrophobin DEWA, and the rationally designed peptide P11-4 described in the literature, could be further engineered toward a faster mineral formation. The variants DEWA_5a (40aaYaaD-SDSDSD-DEWA) and DEWA_5b (40aaYaaD-RDRDRD-DEWA) were able to enhance the nucleation activity without losing the ability to form hydroxyapatite. In the case of variant DEWA_5b, an additional increase in the binding toward hydroxyapatite could be achieved. Especially with the variant DEWA_5a, the protein engineering of the rationally designed peptide sequence resulted in a resemblance of an amino acid motif that is found in nature. The engineered peptide resembles the amino acid motif in dentin phosphoprotein, one of the major proteins involved in dentinogenesis.

Biomimetic Self-Templated Hierarchical Structures of Collagen-Like Peptide Amphiphiles

Developing hierarchically structured biomaterials with tunable chemical and physical properties like those found in nature is critically important to regenerative medicine and studies on tissue morphogenesis. Despite advances in materials synthesis and assembly processes, our ability to control hierarchical assembly using fibrillar biomolecules remains limited. Here, we developed a bioinspired approach to create collagen-like materials through directed evolutionary screening and directed self-assembly. We first synthesized peptide amphiphiles by coupling phage display-identified collagen-like peptides to long-chain fatty acids. We then assembled the amphiphiles into diverse, hierarchically organized, nanofibrous structures using directed self-assembly based on liquid crystal flow and its controlled deposition. The resulting structures sustained and directed the growth of bone cells and hydroxyapatite biominerals. We believe these self-assembling collagen-like amphiphiles could prove useful in the structural design of tissue regenerating materials.

Experimental and numerical measurements of adhesion energies between PHEMA and PGLYMA with hydroxyapatite crystal

Synthetic orthopaedic materials consisting of a single bioinert polymeric material do not meet the complex biological and physical requirements of scaffold-guided bone tissue repair and regeneration. Of particular interest is the design of biocompatible hydrogel-hydroxyapatite composite bone substitutes with outstanding interfacial adhesion that would warranty the ability for the composite to withstand functional loadings without exhibiting brittle fractures during the dynamic guided tissue regeneration. For this purpose, the hydroxylated side chain of chemically cross-linked poly (2-hydroxyethyl methacrylate) (pHEMA) is substitute with a carboxylated side chain to make poly (glycerol methacrylate) (pGLYMA). Here, we carry out atomistic simulations and atomic force microscopy to predict and experimentally determine the interfacial adhesion energies of pHEMA and pGLYMA with the surface of single-crystalline hydroxyapatite (HA) whiskers. Both experimental and numerical results showed that pGLYMA has stronger adhesion forces with HA and may be used for preparing a high-affinity polymer-HA composite. The high adhesive interactions between pGLYMA and HA were found to be due to strong electrostatic energies.

Solid-binding peptides: smart tools for nanobiotechnology

Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.

Bioinspired structural materials

Natural structural materials are built at ambient temperature from a fairly limited selection of components. They usually comprise hard and soft phases arranged in complex hierarchical architectures, with characteristic dimensions spanning from the nanoscale to the macroscale. The resulting materials are lightweight and often display unique combinations of strength and toughness, but have proven difficult to mimic synthetically. Here, we review the common design motifs of a range of natural structural materials, and discuss the difficulties associated with the design and fabrication of synthetic structures that mimic the structural and mechanical characteristics of their natural counterparts.

Designing ECM-mimetic materials using protein engineering

The natural extracellular matrix (ECM), with its multitude of evolved cell-instructive and cell-responsive properties, provides inspiration and guidelines for the design of engineered biomaterials. One strategy to create ECM-mimetic materials is the modular design of protein-based engineered ECM (eECM) scaffolds. This modular design strategy involves combining multiple protein domains with different functionalities into a single, modular polymer sequence, resulting in a multifunctional matrix with independent tunability of the individual domain functions. These eECMs often enable decoupled control over multiple material properties for fundamental studies of cell-matrix interactions. In addition, since the eECMs are frequently composed entirely of bioresorbable amino acids, these matrices have immense clinical potential for a variety of regenerative medicine applications. This brief review demonstrates how fundamental knowledge gained from structure-function studies of native proteins can be exploited in the design of novel protein-engineered biomaterials. While the field of protein-engineered biomaterials has existed for over 20years, the community is only now beginning to fully explore the diversity of functional peptide modules that can be incorporated into these materials. We have chosen to highlight recent examples that either (i) demonstrate exemplary use as matrices with cell-instructive and cell-responsive properties or (ii) demonstrate outstanding creativity in terms of novel molecular-level design and macro-level functionality.

Reconciling disparate views of template-directed nucleation through measurement of calcite nucleation kinetics and binding energies

The physical basis for how macromolecules regulate the onset of mineral formation in calcifying tissues is not well established. A popular conceptual model assumes the organic matrix provides a stereochemical match during cooperative organization of solute ions. In contrast, another uses simple binding assays to identify good promoters of nucleation. Here, we reconcile these two views and provide a mechanistic explanation for template-directed nucleation by correlating heterogeneous nucleation barriers with crystal-substrate-binding free energies. We first measure the kinetics of calcite nucleation onto model substrates that present different functional group chemistries (carboxyl, thiol, phosphate, and hydroxyl) and conformations (C11 and C16 chain lengths). We find rates are substrate-specific and obey predictions of classical nucleation theory at supersaturations that extend above the solubility of amorphous calcium carbonate. Analysis of the kinetic data shows the thermodynamic barrier to nucleation is reduced by minimizing the interfacial free energy of the system, γ. We then use dynamic force spectroscopy to independently measure calcite-substrate-binding free energies, ΔGb. Moreover, we show that within the classical theory of nucleation, γ and ΔGb should be linearly related. The results bear out this prediction and demonstrate that low-energy barriers to nucleation correlate with strong crystal-substrate binding. This relationship is general to all functional group chemistries and conformations. These findings provide a physical model that reconciles the long-standing concept of templated nucleation through stereochemical matching with the conventional wisdom that good binders are good nucleators. The alternative perspectives become internally consistent when viewed through the lens of crystal-substrate binding.