Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States

With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.

Self-assembly of protein-polymer conjugates for drug delivery

Protein-polymer conjugates are a class of molecules that combine the stability of polymers with the diversity, specificity, and functionality of biomolecules. These bioconjugates can result in hybrid materials that display properties not found in their individual components and can be particularly relevant for drug delivery applications. Engineering amphiphilicity into these bioconjugate materials can lead to phase separation and the assembly of high-order structures. The assembly, termed self-assembly, of these hierarchical structures entails multiple levels of organization: at each level, new properties emerge, which are, in turn, influenced by lower levels. Here, we provide a critical review of protein-polymer conjugate self-assembly and how these materials can be used for therapeutic applications and drug delivery. In addition, we discuss central bioconjugate design questions and propose future perspectives for the field of protein-polymer conjugate self-assembly.

SANS quantification of bound water in water-soluble polymers across multiple concentration regimes

Contrast-variation small-angle neutron scattering (CV-SANS) is a widely used technique for quantifying hydration water in soft matter systems, but it is predominantly applied in the dilute regime or for systems with a well-defined structure factor. Here, CV-SANS was used to quantify the number of hydration water molecules associating with three water-soluble polymers with different critical solution temperatures and types of water-solute interactions in dilute, semidilute, and concentrated solution through the exploration of novel methods of data fitting and analysis. Multiple SANS fitting workflows with varying levels of model assumptions were evaluated and compared to give insight into SANS model selection. These fitting pathways ranged from general, model-free algorithms to more standard form and structure factor fitting. In addition, Monte Carlo bootstrapping was evaluated as a method to estimate parameter uncertainty through simulation of technical replicates. The most robust fitting workflow for dilute solutions was found to be form factor fitting without CV-SANS (i.e. polymer in 100% D2O). For semidilute and concentrated solutions, while the model-free approach can be mathematically defined for CV-SANS data, the addition of a structure factor imposes physical constraints on the optimization problem, suggesting that the optimal fitting pathway should include appropriate form and structure factor models. The measured hydration numbers were consistent with the number of tightly bound water molecules associated with each monomer unit, and the concentration dependence of the hydration number was largely governed by the chemistry-specific interactions between water and polymer. Polymers with weaker water-polymer interactions (i.e. those with fewer hydration water molecules) were found to have more bound water at higher concentrations than those with stronger water-polymer interactions due to the increase in the number of forced water-polymer contacts in the concentrated system. This SANS-based method to count hydration water molecules can be applied to polymers in any concentration regime, which will lead to improved understanding of water-polymer interactions and their impact on materials design.

Secondary structure drives self-assembly in weakly segregated globular protein–rod block copolymers

Imparting secondary structure to the polymer block can drive self-assembly in globular protein–helix block copolymers, increasing the effective segregation strength between blocks with weak or no repulsion.

Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study

Peptide conjugation modulates the stability and biological acitivty of proteins via the allosteric effect.

SANS partial structure factor analysis for determining protein-polymer interactions in semidilute solution

The interaction between proteins and polymers in solution contributes to numerous important technological processes, including protein crystallization, biofouling, and the self-assembly of protein-polymer bioconjugates. To quantify these interactions, three different polymers-PNIPAM, POEGA, and PDMAPS-were each blended with a model protein mCherry and studied using contrast variation small angle neutron scattering (SANS). This technique allows for the decomposition of the SANS scattering intensity into partial structure factors corresponding to interactions between two polymer chains, interactions between two proteins, and interactions between a polymer chain and a protein, even for concentrations above the overlap concentration. Examining correlations between each component offers insight into the interactions within the system. In particular, mCherry-PNIPAM interactions are consistent with a depletion interaction, and mCherry-POEGA interactions suggest a considerable region of polymer enrichment close to the protein surface, indicative of attractive forces between the two. Interactions between mCherry and PDMAPS are more complex, with possible contributions from both depletion forces and electrostatic forces.

Predicting Protein-Polymer Block Copolymer Self-Assembly from Protein Properties

Protein–polymer bioconjugate self-assembly has attracted a great deal of attention as a method to fabricate protein nanomaterials in solution and the solid state. To identify protein properties that affect phase behavior in protein–polymer block copolymers, a library of 15 unique protein-b-poly(N-isopropylacrylamide) (PNIPAM) copolymers comprising 11 different proteins was compiled and analyzed. Many attributes of phase behavior are found to be similar among all studied bioconjugates regardless of protein properties, such as formation of micellar phases at high temperature and low concentration, lamellar ordering with increasing temperature, and disordering at high concentration, but several key protein-dependent trends are also observed. In particular, hexagonal phases are only observed for proteins within the molar mass range 20–36 kDa, where ordering quality is also significantly enhanced. While ordering is generally found to improve with increasing molecular weight outside of this range, most large bioconjugates exhibited weaker than predicted assembly, which is attributed to chain entanglement with increasing polymer molecular weight. Additionally, order–disorder transition boundaries are found to be largely uncorrelated to protein size and quality of ordering. However, the primary finding is that bioconjugate ordering can be accurately predicted using only protein molecular weight and percentage of residues contained within β sheets. This model provides a basis for designing protein–PNIPAM bioconjugates that exhibit well-defined self-assembly and a modeling framework that can generalize to other bioconjugate chemistries.

Synthesis of Zwitterionic Copolymers via Copper-Mediated Aqueous Living Radical Grafting Polymerization on Starch

[2-(Methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide (SBMA) is a well-studied sulfobetaine-methacrylate as its zwitterionic structure allows the synthesis of polymers with attractive properties like antifouling and anti-polyelectrolyte behavior. In the present work, we report the Cu⁰-mediated living radical polymerization (Cu⁰-mediated LRP) of SBMA in sodium nitrate aqueous solution instead of previously reported solvents like trifluoroethanol and sodium chloride aqueous/alcoholic solution. Based on this, starch-g-polySBMA (St-g-PSBMA) was also synthesized homogeneously by using a water-soluble waxy potato starch-based macroinitiator and CuBr/hexamethylated tris(2-aminoethyl)amine (Me₆TREN) as the catalyst. The structure of the macroinitiator was characterized by ¹H-NMR, 13C-NMR, gHSQC, and FT-IR, while samples of PSBMA and St-g-PSBMA were characterized by ¹H-NMR and FT-IR. Monomer conversion was monitored by ¹H-NMR, on the basis of which the reaction kinetics were determined. Both kinetic study and GPC results indicate reasonable controlled polymerization. Furthermore, a preliminary study of the thermal response behavior was also carried through rheological tests performed on aqueous solutions of the prepared materials. Results show that branched zwitterionic polymers are more thermal-sensitive than linear ones.

Topology effects on protein–polymer block copolymer self-assembly

Bioconjugates made of the model red fluorescent protein mCherry and synthetic polymer blocks show that topology, i.e. the BA, BA₂, ABA and ABC chain structure of the block copolymers, where B represents the protein and A and C represent polymers, has a significant effect on ordering transitions and the type and size of nanostructures formed during microphase separation.

Peptide-Dendron Hybrids that Adopt Sequence-Encoded β-Sheet Conformations

Rational design rules for programming hierarchical organization and function through mutations of monomers in sequence-defined polymers can accelerate the development of novel polymeric and supramolecular materials. Our strategy for designing peptide-dendron hybrids that adopt predictable secondary and quaternary structures in bulk is based on patterning the sites at which dendrons are conjugated to short peptides. To validate this approach, we have designed and characterized a series of β-sheet-forming peptide-dendron hybrids. Spectroscopic studies of the hybrids in films reveal that the peptide portion of the hybrids adopts the intended secondary structure.

Elastin-like Polypeptide (ELP) Charge Influences Self-Assembly of ELP-mCherry Fusion Proteins

Self-assembly of protein-polymer bioconjugates presents an elegant strategy for controlling nanostructure and orientation of globular proteins in functional materials. Recent work has shown that genetic fusion of globular protein mCherry to an elastin-like polypeptide (ELP) yields similar self-assembly behavior to these protein-polymer bioconjugates. In the context of studying protein-polymer bioconjugate self-assembly, the mutability of the ELP sequence allows several different properties of the ELP block to be tuned orthogonally while maintaining consistent polypeptide backbone chemistry. This work uses this ELP sequence tunability in combination with the precise control offered by genetic engineering of an amino acid sequence to generate a library of four novel ELP sequences that are used to study the combined effect of charge and hydrophobicity on ELP-mCherry fusion protein self-assembly. Concentrated solution self-assembly is studied by small-angle X-ray scattering (SAXS) and depolarized light scattering (DPLS). These experiments show that fusions containing a negatively charged ELP block do not assemble at all, and fusions with a charge balanced ELP block exhibit a weak propensity for assembly. By comparison, the fusion containing an uncharged ELP block starts to order at 40 wt % in solution and at all concentrations measured has sharper, more intense SAXS peaks than other fusion proteins. These experiments show that charge character of the ELP block is a stronger predictor of self-assembly behavior than the hydrophobicity of the ELP block. Dilute solution small-angle neutron scattering (SANS) on the ELPs alone suggests that all ELPs used in this study (including the uncharged ELP) adopt dilute solution conformations similar to those of traditional polymers, including polyampholytes and polyelectrolytes. Finally, dynamic light scattering studies on ELP-mCherry blends shows that there is no significant complexation between the charged ELPs and mCherry. Therefore, it is proposed that the superior self-assembly of fusion proteins containing uncharged ELP block is due to effective repulsions between charged and uncharged blocks due to local charge correlation effects and, in the case of anionic ELPs, repulsion between like charges within the ELP block.

Nano-thin walled micro-compartments from transmembrane protein-polymer conjugates

The high interfacial activity of protein-polymer conjugates has inspired their use as stabilizers for Pickering emulsions, resulting in many interesting applications such as synthesis of templated micro-compartments and protocells or vehicles for drug and gene delivery. In this study we report, for the first time, the stabilization of Pickering emulsions with conjugates of a genetically modified transmembrane protein, ferric hydroxamate uptake protein component A (FhuA). The lysine residues of FhuA with open pore (FhuA ΔCVF^tev) were modified to attach an initiator and consequently controlled radical polymerization (CRP) carried out via the grafting-from technique. The resulting conjugates of FhuA ΔCVF^tev with poly(N-isopropylacrylamide) (PNIPAAm) and poly((2-dimethylamino)ethyl methacrylate) (PDMAEMA), the so-called building blocks based on transmembrane proteins (BBTP), have been shown to engender larger structures. The properties such as pH-responsivity, temperature-responsivity and interfacial activity of the BBTP were analyzed using UV-Vis spectrophotometry and pendant drop tensiometry. The BBTP were then utilized for the synthesis of highly stable Pickering emulsions, which could remain non-coalesced for well over a month. A new UV-crosslinkable monomer was synthesized and copolymerized with NIPAAm from the protein. The emulsion droplets, upon crosslinking of polymer chains, yielded micro-compartments. Fluorescence microscopy proved that these compartments are of micrometer scale, while cryo-scanning electron microscopy and scanning force microscopy analysis yielded a thickness in the range of 11.1 ± 0.6 to 38.0 ± 18.2 nm for the stabilizing layer of the conjugates. Such micro-compartments would prove to be beneficial in drug delivery applications, owing to the possibility of using the channel of the transmembrane protein as a gate and the smart polymer chains as trigger switches to tune the behavior of the capsules.