Placement of Tyrosine Residues as a Design Element for Tuning the Phase Transition of Elastin-peptide-containing Conjugates: Experiments and Simulations

Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials

The unique biophysical and biochemical properties of intrinsically disordered proteins (IDPs) and their recombinant derivatives, intrinsically disordered protein polymers (IDPPs) offer opportunities for producing multistimuli-responsive materials; their sequence-encoded disorder and tendency for phase separation facilitate the development of multifunctional materials. This review highlights the strategies for enhancing the structural diversity of elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs), and their self-assembled structures via genetic fusion to ordered motifs such as helical or beta sheet domains. In particular, this review describes approaches that harness the synergistic interplay between order-promoting and thermoresponsive building blocks to design hybrid biomaterials, resulting in well-structured, stimuli-responsive supramolecular materials ordered on the nanoscale.

Controlled Release of Drugs from Extracellular Matrix-Derived Peptide-Based Nanovesicles through Tailored Noncovalent Interactions

Elastin-collagen nanovesicles (ECnV) have emerged as a promising platform for drug delivery due to their tunable physicochemical properties and biocompatibility. The potential of nine distinct ECnVs to serve as drug-delivery vehicles was investigated in this study, and it was demonstrated that various small-molecule cargo (e.g., dexamethasone, methotrexate, doxorubicin) can be encapsulated in and released from a set of ECnVs, with extents of loading and rates of release dictated by the composition of the elastin domain of the ECnV and the type of cargo. Elastin-like peptides (ELPs) and collagen-like peptides (CLPs) of various compositions were produced; the secondary structure of the corresponding peptides was determined using CD, and the morphology and average hydrodynamic diameter (∼100 nm) of the ECnVs were determined using TEM and DLS. It was observed that hydrophobic drugs exhibited slower release kinetics than hydrophilic drugs, but higher drug loading was achieved for the more hydrophilic Dox. The collagen-binding ability of the ECnVs was demonstrated through a 2D collagen-binding assay, suggesting the potential for longer retention times in collagen-enriched tissues or matrices. Sustained release of drugs for up to 7 days was observed and, taken together with the collagen-binding data, demonstrates the potential of this set of ECnVs as a versatile drug delivery vehicle for longer-term drug release of a variety of cargo. This study provides important insights into the drug delivery potential of ECnVs and offers useful information for future development of ECnV-based drug delivery systems for the treatment of various diseases.

A Library of Elastin-like Proteins with Tunable Matrix Ligands for In Vitro 3D Neural Cell Culture

Hydrogels with encapsulated cells have widespread biomedical applications, both as tissue-mimetic 3D cultures in vitro and as tissue-engineered therapies in vivo. Within these hydrogels, the presentation of cell-instructive extracellular matrix (ECM)-derived ligands and matrix stiffness are critical factors known to influence numerous cell behaviors. While individual ECM biopolymers can be blended together to alter the presentation of cell-instructive ligands, this typically results in hydrogels with a range of mechanical properties. Synthetic systems that allow for the facile incorporation and modulation of multiple ligands without modification of matrix mechanics are highly desirable. In the present work, we leverage protein engineering to design a family of xeno-free hydrogels (i.e., devoid of animal-derived components) consisting of recombinant hyaluronan and recombinant elastin-like proteins (ELPs), cross-linked together with dynamic covalent bonds. The ELP components incorporate cell-instructive peptide ligands derived from ECM proteins, including fibronectin (RGD), laminin (IKVAV and YIGSR), collagen (DGEA), and tenascin-C (PLAEIDGIELTY and VFDNFVL). By carefully designing the protein primary sequence, we form 3D hydrogels with defined and tunable concentrations of cell-instructive ligands that have similar matrix mechanics. Utilizing this system, we demonstrate that neurite outgrowth from encapsulated embryonic dorsal root ganglion (DRG) cultures is significantly modified by cell-instructive ligand content. Thus, this library of protein-engineered hydrogels is a cell-compatible system to systematically study cell responses to matrix-derived ligands.

Enhancement of Aggregate Formation Through Aromatic Compound Adsorption in Elastin-like Peptide (FPGVG)5 Analogs

Elastin-like peptides (ELPs) exhibit temperature-dependent reversible self-assembly. Repetitive sequences derived from elastin, such as Val-Pro-Gly-Val-Gly (VPGVG), are essential for the self-assembly of ELPs. Previously, we developed (FPGVG)5 (F5), in which the first valine residue in the VPGVG sequence was replaced with phenylalanine, which showed strong self-aggregation ability. This suggests that interactions through the aromatic amino acid residues of ELPs could play an important role in self-assembly. In this study, we investigated the thermoresponsive behavior of F5 analogs in the presence of aromatic compounds. Turbidimetry, spectroscopy, and fluorescence measurements demonstrated that aromatic compounds interacted with F5 analogs below the transition temperature and enhanced the self-assembly ability of ELPs by stabilizing amyloid-like structures. Furthermore, quantitative high-performance liquid chromatography analyses showed that the F5 analogs could adsorb and remove hydrophobic aromatic compounds from aqueous solutions during aggregate formation. These results suggested that the F5 analogs can be applicable as scavengers of aromatic compounds.

Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments

The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3-12 mm) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 mm of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.

Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments

In this paper, we present a synergistic, experimental, and computational study of the self-assembly of N,N'-disubstituted polysulfamides driven by hydrogen bonds (H-bonds) between the H-bonding donor and acceptor groups present in repeating sulfamides as a function of the structural design of the polysulfamide backbone. We developed a coarse-grained (CG) polysulfamide model that captures the directionality of H-bonds between the sulfamide groups and used this model in molecular dynamics (MD) simulations to study the self-assembly of these polymers in implicit solvent. The CGMD approach was validated by reproducing experimentally observed trends in the extent of crystallinity for three polysulfamides synthesized with aliphatic and/or aromatic repeating units. After validation of our CGMD approach, we computationally predicted the effect of repeat unit bulkiness, length, and uniformity of segment lengths in the polymers on the extent of orientational and positional order among the self-assembled polysulfamide chains, providing key design principles for tuning the extent of crystallinity in polysulfamides in experiments. Those computational predictions were then experimentally tested through the synthesis and characterization of polysulfamide architectures.

Rational design of elastin-like polypeptide fusion proteins to tune self-assembly and properties of protein vesicles

Protein vesicles made from bioactive proteins have potential value in drug delivery, biocatalysis, and as artificial cells. As the proteins are produced recombinantly, the ability to precisely tune the protein sequence provides control not possible with polymeric vesicles. The tunability and biocompatibility motivated this work to develop protein vesicles using rationally designed protein building blocks to investigate how protein sequence influences vesicle self-assembly and properties. We have reported an elastin-like polypeptide (ELP) fused to an arginine-rich leucine zipper (Z_R) and functional, globular proteins fused to a glutamate-rich leucine zipper (Z_E) that self-assemble into protein vesicles when warmed from 4 to 25 °C due to the hydrophobic transition of ELP. Previously, we demonstrated the ability to tune vesicle properties by changing protein and salt concentration, Z_E : Z_R ratio, and warming rate. However, there is a limit to the properties that can be achieved via assembly conditions. In order to access a wider range of vesicle diameter and stability profiles, this work investigated how modifiying the hydrophobicity and length of the ELP sequence influenced self-assembly and the final properties of protein vesicles using mCherry as a model globular protein. The results showed that both transition temperature and diameter of protein vesicles were inversely correlated to the ELP guest residue hydrophobicity and the number of ELP pentapeptide repeats. Additionally, sequence manipulation enabled assembly of vesicles with properties not accessible by changes to assembly conditions. For example, introduction of tyrosine at 5 guest residue positions in ELP enabled formation of nanoscale vesicles stable at physiological salt concentration. This work yields design guidelines for modifying the ELP sequence to manipulate protein vesicle transition temperature, size and stability to achieve desired properties for particular biofunctional applications.

Laccase-mediated formation of hydrogels based on silk-elastin-like protein polymers with ultra-high molecular weight

As artificial extracellular matrix-like materials, silk-elastin-like protein (SELP) hydrogels, with excellent mechanical properties, high tunability, favorable biocompatibility, and controlled degradability, have become an important candidate in biomedical materials. In this study, SELP is composed of silk-like (GAGAGS) and elastin-like (GXGVP) tandem repeats, in which X residues are set as tyrosine and lysine. Furthermore, SELP polymers are prepared via SpyTag/SpyCatcher. To explore a gentler and more efficient enzymatic crosslinking method, an innovative method was invented to apply laccase to catalyze the formation of SELP hydrogels. Gelation could be successfully achieved in 2-5 min . SELP hydrogels mediated by laccase had the characteristic of low swelling rate, which could maintain a relatively stable shape even when immersed in water, and hence had the potential to be further developed into injectable biomaterials. Additionally, SELP hydrogels cross-linked by laccase showed excellent biocompatibility verified by L929 and HEK 293 T cells with cell viability >93.8 %. SELP hydrogels also exhibit good properties in sustained drug release and cell encapsulation in vitro. This study demonstrates a novel method to construct SELP hydrogels with excellent biocompatibility and expands the possibility of SELP-based material applications in biomedical fields.

Controlled Delivery of Vancomycin from Collagen-tethered Peptide Vehicles for the Treatment of Wound Infections

Despite the great promise of antibiotic therapy in wound infections, antibiotic resistance stemming from frequent dosing diminishes drug efficacy and contributes to recurrent infection. To identify improvements in antibiotic therapies, new antibiotic delivery systems that maximize pharmacological activity and minimize side effects are needed. In this study, we developed elastin-like peptide and collagen-like peptide nanovesicles (ECnVs) tethered to collagen-containing matrices to control vancomycin delivery and provide extended antibacterial effects against methicillin-resistant Staphylococcus aureus (MRSA). We observed that ECnVs showed enhanced entrapment efficacy of vancomycin by 3-fold as compared to liposome formulations. Additionally, ECnVs enabled the controlled release of vancomycin at a constant rate with zero-order kinetics, whereas liposomes exhibited first-order release kinetics. Moreover, ECnVs could be retained on both collagen-fibrin (co-gel) matrices and collagen-only matrices, with differential retention on the two biomaterials resulting in different local concentrations of released vancomycin. Overall, the biphasic release profiles of vancomycin from ECnVs/co-gel and ECnVs/collagen more effectively inhibited the growth of MRSA for 18 and 24 h, respectively, even after repeated bacterial inoculation, as compared to matrices containing free vancomycin, which just delayed the growth of MRSA. Thus, this newly developed antibiotic delivery system exhibited distinct advantages for controlled vancomycin delivery and prolonged antibacterial activity relevant to the treatment of wound infections.

Structural and Dynamical Properties of Elastin-Like Peptides near Their Lower Critical Solution Temperature

Elastin-like peptides (ELPs) are artificially derived intrinsically disordered proteins (IDPs) mimicking the hydrophobic repeat unit in the protein elastin. ELPs are characterized by a lower critical solution temperature (LCST) in aqueous media. Here, we investigate the sequence GVG(VPGVG)₃ over a wide range of temperatures (below, around, and above the LCST) and peptide concentrations employing all-atom molecular dynamics simulations, where we focus on the role of intra- and interpeptide interactions. We begin by investigating the structural properties of a single peptide that demonstrates a hydrophobic collapse with temperature, albeit moderate, because the sequence length is short. We observe a change in the interaction between two peptides from repulsive to attractive with temperature by evaluating the potential of mean force, indicating an LCST-like behavior. Next, we explore dynamical and structural properties of peptides in multichain systems. We report the formation of dynamical aggregates with coil-like conformation, in which valine central residues play an important role. Moreover, the lifetime of contacts between chains strongly depends on the temperature and can be described by a power-law decay that is consistent with the LCST-like behavior. Finally, the peptide translational and internal motion are slowed by an increase in the peptide concentration and temperature.

Peptide-based coacervates in therapeutic applications

Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.

Peptide-based assembled nanostructures that can direct cellular responses

Natural originated materials have been well-studied over the past several decades owing to their higher biocompatibility compared to the traditional polymers. Peptides, consisting of amino acids, are among the most popular programable building blocks, which is becoming a growing interest in nanobiotechnology. Structures assembled using those biomimetic peptides allow the exploration of chemical sequences beyond those been routinely used in biology. In this Review, we discussed the most recent experimental discoveries on the peptide-based assembled nanostructures and their potential application at the cellular level such as drug delivery. In particular, we explored the fundamental principles of peptide self-assembly and the most recent development in improving their interactions with biological systems. We believe that as the fundamental knowledge of the peptide assemblies evolves, the more sophisticated and versatile nanostructures can be built, with promising biomedical applications.

Flexible customization of the self-assembling abilities of short elastin-like peptide Fn analogs by substituting N-terminal amino acids

Elastin-like peptides (ELPs) are thermoresponsive biopolymers inspired by the characteristic repetitive sequences of natural elastin. As ELPs exhibit temperature-dependent reversible self-assembly, they are expected to be biocompatible thermoresponsive materials for drug delivery carriers. One of the most widely studied ELPs in this field is the repetitive pentapeptide, (VPGXG)_n . We previously reported that phenylalanine-containing ELP (Fn) analogs, in which the former Val residue of the repetitive sequence (VPGVG)_n is replaced by Phe, show coacervation with a short chain length (n = 5). Owing to their short sequences, Fn analogs are easily modified in amino acid sequences via simple chemical synthesis, and are useful for investigating the relationship between peptide sequences and temperature responsiveness. In this study, we developed Fn analogs by replacing Phe residue(s) with other amino acids or introducing another amino acid at the N-terminus. The temperature responsiveness of the Fn analogs changed drastically with the substitution of a single Phe residue, suggesting that aromatic amino acids play an important role in their self-assembly. In addition, the self-assembling ability of Fn was enhanced by increasing the bulkiness of the N-terminal amino acids. Therefore, the N-terminal residue was considered to be important for hydrophobicity-induced intermolecular interactions between the peptides during coacervation.

Tuning the Properties of Protein-Based Polymers Using High-Performance Orthogonal Translation Systems for the Incorporation of Aromatic Non-Canonical Amino Acids

The incorporation of non-canonical amino acids (ncAAs) using engineered aminoacyl-tRNA synthetases (aaRSs) has emerged as a powerful methodology to expand the chemical repertoire of proteins. However, the low efficiencies of typical aaRS variants limit the incorporation of ncAAs to only one or a few sites within a protein chain, hindering the design of protein-based polymers (PBPs) in which multi-site ncAA incorporation can be used to impart new properties and functions. Here, we determined the substrate specificities of 11 recently developed high-performance aaRS variants and identified those that enable an efficient multi-site incorporation of 15 different aromatic ncAAs. We used these aaRS variants to produce libraries of two temperature-responsive PBPs-elastin- and resilin-like polypeptides (ELPs and RLPs, respectively)-that bear multiple instances of each ncAA. We show that incorporating such aromatic ncAAs into the protein structure of ELPs and RLPs can affect their temperature responsiveness, secondary structure, and self-assembly propensity, yielding new and diverse families of ELPs and RLPs, each from a single DNA template. Finally, using a molecular model, we demonstrate that the temperature-responsive behavior of RLPs is strongly affected by both the hydrophobicity and the size of the unnatural aromatic side-chain. The ability to efficiently incorporate multiple instances of diverse ncAAs alongside the 20 natural amino acids can help to elucidate the effect of ncAA incorporation on these and many other PBPs, with the aim of designing additional precise and chemically diverse polymers with new or improved properties.

Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: a coarse-grained molecular dynamics simulation study

Collagen-like peptides (CLP) are multifunctional materials garnering a lot of recent interest from the biomaterials community due to their hierarchical assembly and tunable physicochemical properties. In this work, we present a computational study that links the design of CLP heterotrimers to the thermal stability of the triple helix and their self-assembly into fibrillar aggregates and percolated networks. Unlike homotrimeric helices, the CLP heterotrimeric triple helices in this study are made of CLP strands of different chain lengths that result in 'sticky' ends with available hydrogen bonding groups. These 'sticky' ends at one end or both ends of the CLP heterotrimer then facilitate inter-helix hydrogen bonding leading to self-assembly into fibrils (clusters) and percolated networks. We consider the cases of three sticky end lengths - two, four, and six repeat units - present entirely on one end or split between two ends of the CLP heterotrimer. We observe in CLP heterotrimer melting curves generated using coarse grained Langevin dynamics simulations at low CLP concentration that increasing sticky end length results in lower melting temperatures for both one and two sticky ended CLP designs. At higher CLP concentrations, we observe non-monotonic trends in cluster sizes with increasing sticky end length with one sticky end but not for two sticky ends with the same number of available hydrogen bonding groups as the one sticky end; this nonmonotonicity stems from the formation of turn structures stabilized by hydrogen bonds at the single, sticky end for sticky end lengths greater than four repeat units. With increasing CLP concentration, heterotrimers also form percolated networks with increasing sticky end length with a minimum sticky end length of four repeat units required to observe percolation. Overall, this work informs the design of thermoresponsive, peptide-based biomaterials with desired morphologies using strand length and dispersity as a handle for tuning thermal stability and formation of supramolecular structures.

Adaptive Recombinant Nanoworms from Genetically Encodable Star Amphiphiles

Recombinant nanoworms are promising candidates for materials and biomedical applications ranging from the templated synthesis of nanomaterials to multivalent display of bioactive peptides and targeted delivery of theranostic agents. However, molecular design principles to synthesize these assemblies (which are thermodynamically favorable only in a narrow region of the phase diagram) remain unclear. To advance the identification of design principles for the programmable assembly of proteins into well-defined nanoworms and to broaden their stability regimes, we were inspired by the ability of topologically engineered synthetic macromolecules to acess rare mesophases. To test this design principle in biomacromolecular assemblies, we used post-translational modifications (PTMs) to generate lipidated proteins with precise topological and compositional asymmetry. Using an integrated experimental and computational approach, we show that the material properties (thermoresponse and nanoscale assembly) of these hybrid amphiphiles are modulated by their amphiphilic architecture. Importantly, we demonstrate that the judicious choice of amphiphilic architecture can be used to program the assembly of proteins into adaptive nanoworms, which undergo a morphological transition (sphere-to-nanoworms) in response to temperature stimuli.

Therapeutic nanocarriers comprising extracellular matrix-inspired peptides and polysaccharides

INTRODUCTION

The extracellular matrix (ECM) is vital for cell and tissue development. Given its importance, extensive work has been conducted to develop biomaterials and drug delivery vehicles that capture features of ECM structure and function.

AREAS COVERED

This review highlights recent developments of ECM-inspired nanocarriers and their exploration for drug and gene delivery applications. Nanocarriers that are inspired by or created from primary components of the ECM (e.g. elastin, collagen, hyaluronic acid (HA), or combinations of these) are explicitly covered. An update on current clinical trials employing elastin-like proteins is also included.

EXPERT OPINION

Novel ECM-inspired nanoscale structures and conjugates continue to be of great interest in the materials science and bioengineering communities. Hyaluronic acid nanocarrier systems in particular are widely employed due to the functional activity of HA in mediating a large number of disease states. In contrast, collagen-like peptide nanocarriers are an emerging drug delivery platform with potential relevance to a myriad of ECM-related diseases, making their continued study most pertinent. Elastin-like peptide nanocarriers have a well-established tolerability and efficacy track record in preclinical analyses that has motivated their recent advancement into the clinical arena.

Application of Thermoresponsive Intrinsically Disordered Protein Polymers in Nanostructured and Microstructured Materials

Modulation of inter- and intramolecular interactions between bioinspired designer molecules can be harnessed for developing functional structures that mimic the complex hierarchical organization of multicomponent assemblies observed in nature. Furthermore, such multistimuli-responsive molecules offer orthogonal tunability for generating versatile multifunctional platforms via independent biochemical and biophysical cues. In this review, the remarkable physicochemical and mechanical properties of genetically engineered protein polymers derived from intrinsically disordered proteins, specifically elastin and resilin, are discussed. This review highlights emerging technologies which use them as building blocks in the fabrication of highly programmable structured biomaterials for applications in delivery of biotherapeutic cargo and regenerative medicine.

Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers

We present a coarse-grained (CG) molecular dynamics (MD) simulation study of polymer nanocomposites (PNCs) containing nanorods with homogeneous and patchy surface chemistry/functionalization, modeled with isotropic and directional nanorod-nanorod attraction, respectively. We show how the PNC morphology is impacted by the nanorod design (i.e., aspect ratio, homogeneous or patchy surface chemistry/functionalization) for nanorods with a diameter equal to the Kuhn length of the polymer in the matrix. For PNCs with 10 vol % nanorods that have an aspect ratio ≤5, we observe percolated morphology with directional nanorod-nanorod attraction and phase-separated (i.e., nanorod aggregation) morphology with isotropic nanorod-nanorod attraction. In contrast, for nanorods with higher aspect ratios, both types of attractions result in aggregated nanorods morphology due to the dominance of entropic driving forces that cause long nanorods to form orientationally ordered aggregates. For most PNCs with isotropic or directional nanorod-nanorod attractions, the average matrix polymer conformation is not perturbed by the inclusion of up to 20 vol % nanorods. The polymer chains in contact with nanorods (i.e., interfacial chains) are on average extended and statistically different from the conformations the matrix chains adopt in the pure melt state (with no nanorods); in contrast, the polymer chains far from nanorods (i.e., bulk chains) adopt the same conformations as the matrix chains adopt in the pure melt state. We also study the effect of other parameters, such as attraction strength, nanorod volume fraction, and matrix chain length, for PNCs with isotropic or directional nanorod-nanorod attractions. Collectively, our results provide valuable design rules to achieve specific PNC morphologies (i.e., dispersed, aggregated, percolated, and orientationally aligned nanorods) for various potential applications.