Optimizing anthocyanin Oral delivery: Effects of food biomacromolecule types on Nanocarrier performance for enhanced bioavailability.

Wall material types influence the efficacy of nanocarriers in oral delivery systems. We utilized three food biomacromolecules (whey protein isolate, oxidized starch, lipids) to prepare three types of nanocarriers. Our aim was to investigate their performance in digestion, cellular absorption, mucus penetration, intestinal retention, and bioavailability of the encapsulated anthocyanins (Ant). The release rate of protein nanocarriers (Pro-NCs) was twice that of starch nanocarriers (Sta-NCs) and four times that of lipid nanocarriers (Lip-NCs) in simulated gastrointestinal fluid. Additionally, Pro-NCs demonstrated superior transmembrane transport capacity and over three times cellular internalization efficiency than Sta-NCs and Lip-NCs. Sta-NCs exhibited the highest mucus-penetrating capacity, while Pro-NCs displayed the strongest mucoadhesion, resulting in extended gastrointestinal retention time for Pro-NCs. Sta-NCs significantly enhanced the in vivo bioavailability of Ant, nearly twice that of free Ant. Our results demonstrate the critical role of wall material types in optimizing nanocarriers for the specific delivery of bioactive compounds.

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.

The design of protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.

Simple and complex coacervation in systems involving plant proteins.

Plant-based foods are gaining popularity as alternatives to meat and dairy products due to sustainability and health concerns. As a consequence, there is a renewed interest in the phase behaviour of plant proteins and of mixtures of plant proteins and polysaccharides, in particular in the cases where coacervation is found to occur, i.e., liquid-liquid phase separation (LLPS) into two phases, one of which is rich in biopolymers and one of which is poor in biopolymer. Here we review recent research into both simple and complex coacervation in systems involving plant proteins, and their applications in food- as well as other technologies, such as microencapsulation, microgel production, adhesives, biopolymer films, and more.

pH-Responsive Elastin-Like Polypeptide Designer Condensates.

Biomolecular condensates are macromolecular complexes formed by liquid-liquid phase separation. They regulate key biological functions by reversibly compartmentalizing molecules in cells, in a stimulus-dependent manner. Designing stimuli-responsive synthetic condensates is crucial for engineering compartmentalized synthetic cells that are able to mimic spatiotemporal control over the biochemical reactions. Here, we design and test a family of condensate-forming, pH-responsive elastin-like polypeptides (ELPs) that form condensates above critical pH values ranging between 4 and 7, for temperatures between 20 and at 37 °C. We show that the condensation occurs rapidly, in sharp pH intervals (ΔpH < 0.3). For eventual applications in engineering synthetic cell compartments, we demonstrate that multiple types of pH-responsive ELPs can form mixed condensates inside micron-sized vesicles. When genetically fused with enzymes, receptors, and signaling molecules, these pH-responsive ELPs could be potentially used as pH-switchable functional condensates for spatially controlling biochemistry in engineered synthetic cells.

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.

The design of novel protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. A new generation of deep learning methods promises to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.

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, EZn = (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.

De novo designed ice-binding proteins from twist-constrained helices.

Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

Virus-Like Particle-Encapsulated Doxorubicin Enters and Kills Murine Tumor Cells Differently from Free Doxorubicin.

The use of nanoparticles as chemotherapeutic carriers has been suggested as a way to overcome a range of side effects associated with classical cancer treatment such as poor selectivity and tumor resurgence. Obtaining precise control of the size and shape of therapeutic nanoparticles is crucial to optimize the targeting of tumor sites. In this work, it is shown that a previously developed system of polypeptide encapsulating individual DNA molecules, that forms rod-shaped nanoparticles of precisely controlled aspect ratio, can be loaded with the DNA-intercalating chemotherapeutic drug doxorubicin (DOX). It is characterized the size and shape of the DOX loaded-Virus-Like DNA Particles (DOX-VLDP) and shown that in this system the DOX payload does not leak out. Through in vitro cell studies, it is shown that DOX-VLDP is internalized by melanoma tumor cells (B16F10 cells) in a delayed and endocytosis-dependent way culminating in increased cytotoxicity and selectivity to tumor cells in comparison with free DOX. In addition, it is found that DOX-VLDP trigger apoptosis and autophagy pathways in treated cells. Taken together, the data on the DOX-VLDP nanoparticles shows that they kill cancer cells differently from free DOX.

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.

Engineered Protein Copolymers for Heparin Neutralization and Detection.

Heparin is a widely applied anticoagulant agent. However, in clinical practice, it is of vital importance to reverse its anticoagulant effect to restore the blood-clotting cascade and circumvent side effects. Inspired by protein cages that can encapsulate and protect their cargo from surroundings, we utilize three designed protein copolymers to sequester heparin into inert nanoparticles. In our design, a silk-like sequence provides cooperativity between proteins, generating a multivalency effect that enhances the heparin-binding ability. Protein copolymers complex heparin into well-defined nanoparticles with diameters below 200 nm. We also develop a competitive fluorescent switch-on assay for heparin detection, with a detection limit of 0.01 IU mL-1 in plasma that is significantly below the therapeutic range (0.2-8 IU mL-1). Moreover, moderate cytocompatibility is demonstrated by in vitro cell studies. Therefore, such engineered protein copolymers present a promising alternative for neutralizing and sensing heparin, but further optimization is required for in vivo applications.

Active microrheology of protein condensates using colloidal probe-AFM.

Protein condensates resulting from liquid-liquid phase separation have long been studied as bio-adhesives and coating materials for various applications. More recently, they are also being scrutinized as models for membraneless organelles in cells. Quantifying their interfacial mechanics and rheology at micrometer scales is vital for better understanding the physics underlying membraneless organelles in cells and for developing and improving technological applications of protein condensates. This study demonstrates how colloidal probe atomic force microscopy with an oscillating tip can be used to simultaneously investigate the interfacial mechanics and dynamic rheological properties of micro-scale protein condensates, formed via carefully controlled capillary condensation. This new approach can access oscillation frequencies ranging from 1 to 104 rad/s. By analyzing the data using an equivalent mechanical model, three characteristic frequency domains for the mechanics of micro-scale protein condensates are found: an interfacial tension-dominated domain at low frequencies, a transition domain (viscous-to-elastic crossover) at intermediate frequencies, and an elasticity-dominated domain at high frequencies, covering a broad range of time scales relevant in biology and technological applications of protein condensates.

Design of Polypeptides Self-Assembling into Antifouling Coatings: Exploiting Multivalency.

We propose to exploit multivalent binding of solid-binding peptides (SBPs) for the physical attachment of antifouling polypeptide brushes on solid surfaces. Using a silica-binding peptide as a model SBP, we find that both tandem-repeated SBPs and SBPs repeated in branched architectures implemented via a multimerization domain work very well to improve the binding strength of polypeptide brushes, as compared to earlier designs with a single SBP. At the same time, for many of the designed sequences, either the solubility or the yield of recombinant production is low. For a single design, with the domain structure B-M-E, both solubility and yield of recombinant production were high. In this design, B is a silica-binding peptide, M is a highly thermostable, de novo-designed trimerization domain, and E is a hydrophilic elastin-like polypeptide. We show that the B-M-E triblock polypeptide rapidly assembles into highly stable polypeptide brushes on silica surfaces, with excellent antifouling properties against high concentrations of serum albumin. Given that SBPs attaching to a wide range of materials have been identified, the B-M-E triblock design provides a template for the development of polypeptides for coating many other materials such as metals or plastics.

Core-Shell Microcapsules from Unpurified Legume Flours.

Plant-based ingredients are key building blocks for future sustainable advanced materials. Functionality is typically higher for highly purified plant-based ingredients, but this is at the expense of their sustainability value. Here, a method is introduced for creating a soft functional material, with structural elements ranging from the nanometer to the millimeter scale, directly from legume flours. Globulins from soy and pea flours are extracted in their native state at acidic pH and mixed with gum arabic, resulting in liquid-liquid phase separation into a dilute phase and a viscoelastic complex coacervate. Interfacial tensions of the coacervates, determined via AFM-based probing of capillary condensation, are found to be very low (γ = 48.5 and 32.3 µN/m for, respectively, soy and pea), thus promoting the deposition of a shell of coacervate material around oil droplets. Despite the complex nature of the starting material, the dependence of interfacial tensions on salt concentrations follows a scaling law previously shown to hold for model complex coacervates. Curing of the coacervate material into a strong and purely elastic hydrogel is shown to be possible via simple heating, both in bulk and as a shell around oil droplets, thus providing proof of principle for the fabrication of precise core-shell microcapsules directly from legume flours.

Self-Assembly of Elastin-like Polypeptide Brushes on Silica Surfaces and Nanoparticles.

Control over the placement and activity of biomolecules on solid surfaces is a key challenge in bionanotechnology. While covalent approaches excel in performance, physical attachment approaches excel in ease of processing, which is equally important in many applications. We show how the precision of recombinant protein engineering can be harnessed to design and produce protein-based diblock polymers with a silica-binding and highly hydrophilic elastin-like domain that self-assembles on silica surfaces and nanoparticles to form stable polypeptide brushes that can be used as a scaffold for later biofunctionalization. From atomic force microscopy-based single-molecule force spectroscopy, we find that individual silica-binding peptides have high unbinding rates. Nevertheless, from quartz crystal microbalance measurements, we find that the self-assembled polypeptide brushes cannot easily be rinsed off. From atomic force microscopy imaging and bulk dynamic light scattering, we find that the binding to silica induces fibrillar self-assembly of the peptides. Hence, we conclude that the unexpected stability of these self-assembled polypeptide brushes is at least in part due to peptide-peptide interactions of the silica-binding blocks at the silica surface.

Supramolecular virus-like particles by co-assembly of triblock polypolypeptide and PAMAM dendrimers.

Virus-like particles are of special interest as functional delivery vehicles in a variety of fields ranging from nanomedicine to materials science. Controlled formation of virus-like particles relies on manipulating the assembly of the viral coat proteins. Herein, we report a new assembly system based on a triblock polypolypeptide C4-S10-BK12 and -COONa terminated PAMAM dendrimers. The polypolypeptide has a cationic BK12 block with 12 lysines; its binding with anionic PAMAM triggers the folding of the peptide's middle silk-like block and leads to formation of virus-like nanorods, stabilized against aggregation by the long hydrophilic "C" block of the polypeptide. Varying the dendrimer/polypeptide mixing ratio hardly influences the structure and size of the nanorod. However, increasing the dendrimer generation, that is, increasing the dendrimer size results in increased particle length and height, without affecting the width of the nanorod. The branched structure and well-defined size of the dendrimers allows delicate control of the particle size; it is impossible to achieve similar control over assembly of the polypeptide with linear polyelectrolyte as template. In conclusion, we report a novel protein assembling system with properties resembling a viral coat; the findings may therefore be helpful for designing functional virus-like particles like vaccines.

Rod-shaped polypeptide nanoparticles for siRNA delivery.

Rod-shaped nanoparticles have been reported to exhibit improved cellular uptake, intracellular processing and transport through tissues and organs, as compared to spherical nanoparticles. We use C-S-B triblock polypeptides composed of a collagen-like block (C), a silk-like block (S) and an oligolysine domain (B) for one-dimensional co-assembly with siRNA into rod-shaped nanoparticles. Here we investigate these siRNA encapsulating rod-shaped nanoparticles as a gene delivery system. Uptake experiments for C-S-B and C-S-B/siPlk1 particles indicate that these rod-shaped nanoparticles can efficiently deliver siPlk1 into HeLa cells. Moreover, C-S-B/siPlk1 complexes display significant mPlk1 gene knockdown in a dose-dependent manner, causing apoptosis as intended. The lower effectiveness of C-S-B/siPlk1 in inducing cell death as compared to cationic lipid-based formulations is explained by the high lysosome-C-S-B/siPlk1 co-localization ratio, which will need to be addressed in a future redesign of polypeptide sequence. Overall, the non-toxic and unique rod-shaped C-S-B nanoparticles deserve further optimization as a new siRNA delivery system for cancer therapy.

Physicochemical-guided design of cathelicidin-derived peptides generates membrane active variants with therapeutic potential.

The spread of multi-drug resistance and the slow pace at which antibiotics come onto the market are undermining our ability to treat human infections, leading to high mortality rates. Aiming to overcome this global crisis, antimicrobial peptides are considered promising alternatives to counter bacterial infections with multi-drug resistant bacteria. The cathelicidins comprise a well-studied class of AMPs whose members have been used as model molecules for sequence modifications, aiming at enhanced biological activities and stability, along with reduced toxic effects on mammalian cells. Here, we describe the antimicrobial activities, modes of action and structural characterization of two novel cathelicidin-like peptides, named BotrAMP14 and CrotAMP14, which were re-designed from snake batroxicidin and crotalicidin, respectively. BotrAMP14 and CrotAMP14 showed broad-spectrum antibacterial activity against susceptible microorganisms and clinical isolates with minimal inhibitory concentrations ranging from 2-35.1 µM. Moreover, both peptides had low cytotoxicity against Caco-2 cells in vitro. In addition, in vivo toxicity against Galleria mellonella moth larvae revealed that both peptides led to>76% larval survival after 144 h. Microscopy studies suggest that BotrAMP14 and CrotAMP14 destabilize E. coli membranes. Furthermore, circular dichroism and molecular dynamics simulations indicate that, in a membrane-like environment, both peptides adopt α-helical structures that interact with bilayer phospholipids through hydrogen bonds and electrostatic interaction. Thus, we concluded that BotrAMP14 and CrotAMP14 are helical membrane active peptides, with similar antibacterial properties but lower cytotoxicity than the larger parent peptides batroxicidin and crotalicidin, having advantages for drug development strategies.

Encapsulation Using Plant Proteins: Thermodynamics and Kinetics of Wetting for Simple Zein Coacervates.

Traditionally, complex coacervates of oppositely charged biopolymers have been used to form coatings around oil droplets for encapsulation of oil-soluble payloads. However, many proteins can form coacervates by themselves under certain conditions. Here, we revisit the well-known simple coacervates of prolamins such as zein in mixed solvents to explore whether they can be used for plant-based encapsulation systems. We show that, for zein in mixed water/propylene glycol (PG) solvents, we can encapsulate limonene droplets but only under specific conditions. We illustrate that this limitation is due to the very different physical properties of the simple zein coacervates as compared to those of the more extensively studied complex coacervates. Droplets of simple coacervates of zein can carry a significant net charge, whereas complex coacervates are usually close to being charge-balanced. In particular, we demonstrate that the spreading of zein coacervates at the interface of the droplets is thermodynamically favorable due to their extremely low interfacial tensions in both the dispersed (∼0.24 mN/m) and oil phases (∼0.68 mN/m), but the kinetics of coacervate droplet deposition and the interactions among coacervate droplets that oppose coacervate droplet coalescence are highly pH-dependent, leading to a sharp pH optimum (around pH 8) for capsule formation.

Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides.

Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different ß-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.