Amphiphilic Peptide−Polymer Conjugates Based on the Coiled-Coil Helix Bundle

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure-function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc 1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density-voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium-indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

Tuning of Cationic Polymer Functionality in Complex Coacervate Artificial Cells for Optimized Enzyme Activity

Complex coacervates are a versatile platform to mimic the structure of living cells. In both living systems and artificial cells, a macromolecularly crowded condensate phase has been shown to be able to modulate enzyme activity. Yet, how enzyme activity is affected by interactions (particularly with cationic charges) inside coacervates is not well studied. Here, we synthesized a series of amino-functional polymers to investigate the effect of the type of amine and charge density on coacervate formation, stability, protein partitioning, and enzyme function. The polymers were prepared by RAFT polymerization using as monomers aminoethyl methacrylate (AEAM), 2-(dimethylamino)ethyl methacrylate (DMAEMA), imidazolepropyl methacrylamide (IPMAm), and [2-(methacryloyloxy)ethyl] trimethylammonium chloride (TMAEMA). Membranized complex coacervate artificial cells were formed with these polycations and an anionic amylose derivative. Results show that polycations with reduced charge density result in higher protein mobility in the condensates and also higher enzyme activity. Insights described here could help guide the use of coacervate artificial cells in applications such as sensing, catalysis, and therapeutic formulations.

Thermoresponsive Coiled-Coil Peptide-Polymer Grafts

Alkyl halide side groups are selectively incorporated into monodispersed, computationally designed coiled-coil-forming peptide nanoparticles. Poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA) is polymerized from the coiled-coil periphery using photoinitiated atom transfer radical polymerization (photoATRP) to synthesize well-defined, thermoresponsive star copolymer architectures. This facile synthetic route is readily extended to other monomers for a range of new complex star-polymer macromolecules.

Population-based heteropolymer design to mimic protein mixtures

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2-4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.

Enzyme-Responsive Amphiphilic Peptide Nanoparticles for Biocompatible and Efficient Drug Delivery

Self-assembled peptide nanostructures recently have gained much attention as drug delivery systems. As biomolecules, peptides have enhanced biocompatibility and biodegradability compared to polymer-based carriers. We introduce a peptide nanoparticle system containing arginine, histidine, and an enzyme-responsive core of repeating GLFG oligopeptides. GLFG oligopeptides exhibit specific sensitivity towards the enzyme cathepsin B that helps effective controlled release of cargo molecules in the cytoplasm. Arginine can induce cell penetration, and histidine facilitates lysosomal escape by its buffering capacity. Herein, we propose an enzyme-responsive amphiphilic peptide delivery system (Arg-His-(Gly-Phe-Lue-Gly)₃, RH-(GFLG)₃). The self-assembled RH-(GFLG)₃ globular nanoparticle structure exhibited a positive charge and formulation stability for 35 days. Nile Red-tagged RH-(GFLG)₃ nanoparticles showed good cellular uptake compared to the non-enzyme-responsive control groups with d-form peptides (LD (^LRH-^D(GFLG)₃), DL (^DRH-L(GFLG)₃), and DD (^DRH-^D(GFLG)₃). The RH-(GFLG)₃ nanoparticles showed negligible cytotoxicity in HeLa cells and human RBCs. To determine the drug delivery efficacy, we introduced the anticancer drug doxorubicin (Dox) in the RH-(GFLG)₃ nanoparticle system. LL-Dox exhibited formulation stability, maintaining the physical properties of the nanostructure, as well as a robust anticancer effect in HeLa cells compared to DD-Dox. These results indicate that the enzyme-sensitive RH-(GFLG)₃ peptide nanoparticles are promising candidates as drug delivery carriers for biomedical applications.

Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications

Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.

Molecular Modeling and Simulations of Peptide–Polymer Conjugates

Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.

Synthesis and Characterization of Bio-Active GFP-P4VP Core–Shell Nanoparticles

Bioactive core–shell nanoparticles (CSNPs) offer the unique ability for protein/enzyme functionality in non-native environments. For many decades, researchers have sought to develop synthetic materials which mimic the efficiency and catalytic power of bioactive macromolecules such as enzymes and proteins. This research studies a self-assembly method in which functionalized, polymer-core/protein-shell nanoparticles are prepared in mild conditions. Transmission electron microscopy (TEM) and dynamic light scattering (DLS) techniques were utilized to analyze the size and distribution of the CSNPs. The methods outlined in this research demonstrate a mild, green chemistry synthesis route for CSNPs which are highly tunable and allow for enzyme/protein functionality in non-native conditions.

Synthesis and Assembly of Laccase-Polymer Giant Amphiphiles by Self-Catalyzed CuAAC Click Chemistry

Covalent coupling of hydrophobic polymers to the exterior of hydrophilic proteins would mediate unique macroscopic assembly of bioconjugates to generate amphiphilic superstructures as novel nanoreactors or biocompatible drug delivery systems. The main objective of this study was to develop a novel strategy for the synthesis of protein-polymer giant amphiphiles by the combination of copper-mediated living radical polymerization and azide-alkyne cycloaddition reaction (CuAAC). Azide-functionalized succinimidyl ester was first synthesized for the facile introduction of azide groups to proteins such as albumin from bovine serum (BSA) and laccase from Trametes versicolor. Alkyne-terminal polymers with varied hydrophobicity were synthesized by using commercial copper wire as the activators from a trimethylsilyl protected alkyne-functionalized initiator in DMSO under ambient temperature. The conjugation of alkyne-functionalized polymers to the azide-functionalized laccase could be conducted even without additional copper catalyst, which indicated a successful self-catalyzed CuAAC reaction. The synthesized amphiphiles were found to aggregate into spherical nanoparticles in water and showed strong relevance to the hydrophobicity of coupled polymers. The giant amphiphiles showed decreased enzyme activity yet better stability during storage after chemical modification and self-assembly. These findings will deepen our understanding on protein folding, macroscopic self-assembly, and support potential applications in bionanoreactor, enzyme immobilization, and water purification.

Responsive Hybrid (Poly)peptide-Polymer Conjugates

(Poly)peptide-polymer conjugates continue to garner significant interest in the production of functional materials given their composition of natural and synthetic building blocks that confer select and synergistic properties. Owing to opportunities to design predefined architectures and structures with different morphologies, these hybrid conjugates enable new approaches for producing micro- or nanomaterials. Their modular design enables the incorporation of multiple responsive properties into a single conjugate. This review presents recent advances in (poly)peptide-polymer conjugates for drug-delivery applications, with a specific focus on the utility of the (poly)peptide component in the assembly of particles and nanogels, as well as the role of the peptide in triggered drug release.

Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes

Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.

Top-down mass spectrometry of hybrid materials with hydrophobic peptide and hydrophilic or hydrophobic polymer blocks

A multidimensional mass spectrometry (MS) methodology is introduced for the molecular level characterization of polymer-peptide (or polymer-protein) copolymers that cannot be crystallized or chromatographically purified. It encompasses electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) coupled with mass analysis, tandem mass spectrometry (MS(2)) and gas-phase separation by ion mobility mass spectrometry (IM-MS). The entire analysis is performed in the mass spectrometer ("top-down" approach) within milliseconds and with high sensitivity, as demonstrated for hybrid materials composed of hydrophobic poly(tert-butyl acrylate) (PtBA) or hydrophilic poly(acrylic acid) (PAA) blocks tethered to the hydrophobic decapeptide VPGVGVPGVG (VG2) via triazole linkages. The composition of the major products can be rapidly surveyed by MALDI-MS and MS(2). For a more comprehensive characterization, the ESI-IM-MS (and MS(2)) combination is more suitable, as it separates the hybrid materials based on their unique charges and shapes from unconjugated polymer and partially hydrolyzed products. Such separation is essential for reducing spectral congestion, deconvoluting overlapping compositions and enabling straightforward structural assignments, both for the hybrid copolymers as well as the polymer and peptide reactants. The IM dimension also permits the measurement of collision cross-sections (CCSs), which reveal molecular architecture. The MS and MS(2) spectra of the mobility separated ions conclusively showed that [PtBA-VG2]m and [PAA-VG2]m chains with the expected compositions and sequences were formed. Single and double copolymer blocks (m = 1-2) could be detected. Further, the CCSs of the hybrids, which were prepared via azide/alkyne cycloadditions, confirmed the formation of macrocyclic structures. The top-down methodology described would be particularly useful for the detection and identification of peptide/protein-polymer conjugates which are increasingly used in biomedical and pharmaceutical applications.

Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations

Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of β-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.

Molecular dynamics studies of PEGylated α-helical coiled coils and their self-assembled micelles

We performed coarse-grained (CG) molecular dynamics simulations of trimeric α-helical coiled coils grafted with poly(ethylene glycol) (PEG) of different sizes and conjugate positions and the self-assembled micelle of amphiphilic trimers. The CG model for the trimeric coiled coil is verified by comparing the α-helical structure and interhelical distance with those calculated from all-atom simulations. In CG simulations of PEGylated trimers, the end-to-end distances and radii of gyration of PEGs grafted to the sides of peptides become shorter than those of free PEGs in water, which agrees with experiments. This shorter size of the grafted PEGs is also confirmed by calculating the thickness of the PEG layer, which is less than the size of the mushroom. These indicate the adsorption of PEG chains onto coiled coils since hydrophobic residues in the exterior sites of coiled coils tend to be less exposed to water and thus interact with PEGs, leading to the compact conformation of adsorbed PEGs. Simulations of the self-assembly of amphiphilic trimers show that the randomly distributed trimers self-assemble to micelles. The outer radius and hydrodynamic radius of the micelle, which were calculated respectively from radial densities and diffusion coefficients, are ∼7 nm, in agreement with the experimental value of ∼7.5 nm, while the aggregation number of amphiphilic molecules per micelle is lower than the experimentally proposed value. These simulations predict the experimentally measured size of PEGs grafted to the trimeric coiled coils and their self-assembled amphiphilic micelles and suggest that the aggregation number of the micelle may be lower, which needs to be confirmed by experiments.

Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations

Using a novel coarse-grained model, large-scale molecular dynamics simulations were performed to examine self-assembly of 800 peptide amphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readily assemble into nanofibers leading to hydrogel construction as observed in experiments. Our simulations capture this spontaneous self-assembly process, including formation of secondary structure, to identify morphological transitions of distinctive nanostructures. As the hydrophobic interaction is increased, progression from open networks of secondary structures toward closed cylindrical nanostructures containing either β-sheets or random coils are observed. Moreover, temperature effects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. These understandings of the molecular interactions involved and the role of environmental factors on hydrogel formation provide useful insight for development of innovative smart biomaterials for biomedical applications.

Fluorescent amphiphilic PEG-peptide-PEG triblock conjugate micelles for cell imaging

A fluorescent amphiphilic poly(ethylene glycol)-peptide-fluorophore-peptide-poly(ethylene glycol) (PEG-Pep-F-Pep-PEG) triblock conjugate with a hydrophobic fluorophore moiety at the centre of the chain is synthesized by "grafting to" technique based on Schiff-base coupling chemistry. The conjugate is characterized by nuclear magnetic resonance (NMR), circular dichroism (CD), and fluorescence spectroscopy techniques. The aqueous solution of the triblock conjugate emits blue light and exhibits a fluorescence emission band at 430 nm. The amphiphilic conjugate molecules undergo self-assembly into micelles (D ≈ 15-20 nm) in aqueous solution as confirmed from transmission electron microscopy (TEM) and dynamic light scattering (DLS). The critical aggregation concentration is determined by pyrene fluorescence assay and is found to be 0.051 mg mL(-1) . The highly stable and low toxic fluorescent PEG-Pep-F-Pep-PEG conjugate micelles are used for imaging of HeLa cells.

Long-circulating 15 nm micelles based on amphiphilic 3-helix peptide-PEG conjugates

Generating stable, multifunctional organic nanocarriers will have a significant impact on drug formulation. However, it remains a significant challenge to generate organic nanocarriers with a long circulation half-life, effective tumor penetration, and efficient clearance of metabolites. We have advanced this goal by designing a new family of amphiphiles based on coiled-coil 3-helix bundle forming peptide-poly(ethylene glycol) conjugates. The amphiphiles self-assemble into monodisperse micellar nanoparticles, 15 nm in diameter. Using the 3-helix micelles, a drug loading of ∼8 wt % was obtained using doxorubicin and the micelles showed minimal cargo leakage after 12 h of incubation with serum proteins at 37 °C. In vivo pharmacokinetics studies using positron emission tomography showed a circulation half-life of 29.5 h and minimal accumulation in the liver and spleen. The demonstrated strategy, by incorporating unique protein tertiary structure in the headgroup of an amphiphile, opens new avenues to generate organic nanoparticles with tunable stability, ligand clustering, and controlled disassembly to meet current demands in nanomedicine.

Fabrication of ellagic acid incorporated self-assembled peptide microtubes and their applications

Ellagic acid (EA), a plant polyphenol known for its wide-range of health benefits was encapsulated within self-assembled threonine based peptide microtubes. The microtubes were assembled using the synthesized precursor bolaamphiphile bis(N-α-amido threonine)-1,5-pentane dicarboxylate. The self-assembly of the microstructures was probed at varying pH. In general, tubular formations were observed at a pH range of 4-6. The formed microtubes were then utilized for fabrication with EA. We probed the ability of the microtubes as drug release vehicles for EA as well as for antibacterial applications. It was found that the release of EA was both pH and concentration dependent. The biocompatibility as well as cytotoxicity of the EA-fabricated microtubes was examined in the presence of mammalian normal rat kidney (NRK) cells. Finally the antibacterial effects of the EA incorporated peptide microtubes was examined against Escherichia coli and Staphylococcus aureus.

Helix stabilization of poly(ethylene glycol)-peptide conjugates

Hybrid polymer-peptide conjugates offer the potential for incorporating biological function into synthetic materials. The secondary structure of short helical peptides, however, frequently becomes less stable when expressed independent of longer protein sequences or covalently linked with a conformationally disordered synthetic polymer. Recently, new amphipathic peptide-poly(ethylene glycol) conjugates were introduced (Shu, J., et al. Biomacromolecules 2008, 9, 2011), which displayed enhanced peptide helicity upon polymer functionalization while retaining tertiary coiled-coil associations. We report here a molecular simulation study of peptide helix stabilization by conjugation with poly(ethylene glycol). The polymer oxygens are shown to favorably interact with the cationic lysine side chains, providing an alternate binding site that protects against disruption of the peptide hydrogen-bonds that stabilize the helical conformation. When the peptide lysine charges are neutralized or poly(ethylene glycol) is conjugated with polyalanine, the polymer exhibits a negligible effect on the secondary structure. We also observe the interactions of poly(ethylene glycol) with the amphipathic peptide lysines tends to segregate the polymer away from the nonpolar face of the helix, suggesting no disruption of the interactions that drive tertiary contacts between helicies.

Stimulus-responsive hydrogels made from biosynthetic fibrinogen conjugates for tissue engineering: structural characterization

Nanostructured hydrogels based on "smart" polymer conjugates of poloxamers and protein molecules were developed in order to form stimulus-responsive materials with bioactive properties for 3-D cell culture. Functionalized Pluronic F127 was covalently attached to a fibrinopeptide backbone and cross-linked into a structurally versatile and mechanically stable polymer network endowed with bioactivity and temperature-responsive structural features. Small angle X-ray scattering and transmission electron microscopy combined with rheology were used to characterize the structural and mechanical features of this biosynthetic conjugate, both in solution and in hydrogel form. The temperature at which the chemical cross-linking of F127-fibrinopeptide conjugates was initiated had a profound influence on the mechanical properties of the thermo-responsive hydrogel. The analysis of the scattering data revealed modification in the structure of the protein backbone resulting from increases in ambient temperature, whereas the structure of the polymer was not affected by ambient temperature. The hydrogel cross-linking temperature also had a major influence on the modulus of the hydrogel, which was rationally correlated to the molecular structure of the polymer network. The hydrogel structure exhibited a small mesh size when cross-linked at low temperatures and a larger mesh size when cross-linked at higher temperatures. The mesh size was nicely correlated to the mechanical properties of the hydrogels at the respective cross-linking temperatures. The schematic charts that model this material's behavior help to illustrate the relationship that exists between the molecular structure, the cross-linking temperature, and the temperature-responsive features for this class of protein-polymer conjugates. The precise control over structural and mechanical properties that can be achieved with this bioactive hydrogel material is essential in designing a tissue-engineering scaffold for clinical applications.

Aggregation behaviour of peptide-polymer conjugates containing linear peptide backbones and multiple polymer side chains prepared by nitroxide-mediated radical polymerization

A series of peptides with an alternating sequence of alkoxyamine conjugated lysine and glycine residues were synthesized by classical solution phase peptide coupling. The resulting peptides containing up to eight alkoxyamine moieties were used as initiators in nitroxide-mediated polymerization (NMP) to obtain peptide-polymer conjugates with well defined linear peptide backbones and a defined number of polymeric side chains. Polymerization of styrene and N-isopropylacrylamide (NIPAM) occurred in a highly controlled fashion. Molecular weight and polydispersity index (PDI) were determined by gel permeation chromatography (GPC). Aggregation behaviour of these hybrid materials was investigated by dynamic light scattering (DLS) and atomic force microscopy (AFM). Depending on composition, number and length of the polymer side chains, the conjugates aggregate to different topologies. Whereas peptide-polystyrene conjugates may aggregate to so called honeycomb structures, peptide-poly-N-isopropylacrylamide conjugates show differentiated aggregation behaviour.