Molecular level investigations of the inter- and intramolecular interactions of pH-responsive artificial triblock proteins

Intelligent materials that can undergo physical gelation in response to environmental stimuli have potential impacts in the bioengineering and biomedical fields where the entrapment of cellular or molecular species is desired. Here, we utilize atomic force microscopy (AFM) to perform molecular level investigations of designer artificial proteins that undergo physical gelation. These are engineered as triblock copolymers with independent interchain binding and solvent retention functions, namely, two terminal leucine zipper-like peptide sequences and a central alanylglycine rich sequence, respectively. AFM force measurements between probes and surfaces functionalized with molecules of this triblock protein revealed adhesive interactions that increased in average force and frequency as the pH was lowered from pH 11.2 to 7.4 to 4.5, reflecting an increase in the numbers of interacting molecular strands. In bulk solution, lowering the pH results in a viscous liquid to gel transition. The modular design of the triblock protein was also exploited for single molecule force spectroscopy investigations, which revealed altered intramolecular interactions in response to changes in pH. An increased understanding of the inter- and intramolecular forces involved in biomolecule driven gelation processes is not only of great fundamental interest in the study of the biomolecular systems involved but may also prove key in enabling the rational design of new generations of intelligent hydrogel systems.     

Sulfonamide-based pH- and temperature-sensitive biodegradable block copolymer hydrogels

Novel pH- and temperature-sensitive biodegradable poly(epsilon-caprolactone-co-lactide)-poly(ethylene glycol) (PCLA-PEG) block copolymers were synthesized with oligomeric sulfamethazine (OSM) end groups (OSM-PCLA-PEG-PCLA-OSM). Aqueous solutions of these block copolymers have shown sol-gel transition behavior upon both temperature and pH changes under physiological conditions (37 degrees C, pH 7.4). The sol-gel transition of these block copolymer solutions was fine-tuned by controlling the PEG length, the hydrophobic to hydrophilic block ratio (PCLA/PEG), and the molecular weight of the sulfamethazine oligomer. Since changes in temperature do not induce gel formation in this pH- and temperature-sensitive block copolymer solution, this hydrogel can be employed as an injectable carrier using a long guide catheter into the body. In addition, the pH of the block copolymer solution showed no change following PCLA degradation over 1 month, and no indication of gel collapse was observed on addition of buffer solution. As such, these properties make the OSM-PCLA-PEG-PCLA-OSM hydrogel an ideal candidate for use as an injectable carrier for certain protein-based drugs known to denature in low-pH environments.     

Reversible hydrogels from self-assembling genetically engineered protein block copolymers

A series of triblock protein copolymers composed of a central water-soluble polyelectrolyte segment flanked by two coiled-coil domains was synthesized by genetic engineering methods. The copolymers self-assembled into reversible hydrogels in response to changes in temperature, pH, and the presence or absence of denaturating agent (guanidine hydrochloride, GdnHCl). Hydrogel formation was concentration-dependent, and the concentration needed for hydrogel formation correlated with the oligomerization state of the coiled-coil domains in the protein copolymers. The morphology of the hydrogels, as determined by scanning electron microscopy (SEM), indicated the presence of porous interconnected networks. The thermal stabilities and self-assembling properties of the protein copolymers were successfully controlled by manipulating the amino acid sequences of the coiled-coil domains. The stimuli responsiveness and reversibility of the hydrogel self-assembly suggest that these protein copolymers may have potential in biomedical applications.     

Protein-based block copolymers

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers.     

Novel Pentablock Copolymer-Based Nanoparticulate Systems for Sustained Protein Delivery

The design, synthesis, and application of novel biodegradable and biocompatible pentablock (PB) copolymers, i.e., polyglycolic acid-polycaprolactone-polyethylene glycol-polycaprolactone-polyglycolic acid (PGA-PCL-PEG-PCL-PGA) and polylactic acid-polycaprolactone-polyethylene glycol-polycaprolactone-polylactic acid (PLA-PCL-PEG-PCL-PLA) for sustained protein delivery, are reported. The PB copolymers can be engineered to generate sustained delivery of protein therapeutics to the posterior segment of the eye. PB copolymers with different block arrangements and molecular weights were synthesized by ring-opening polymerization and characterized by proton nuclear magnetic resonance (¹H-NMR), gel permeation chromatography (GPC), and X-ray diffraction (XRD) spectroscopy. Immunoglobulin G (IgG) was selected as a model protein due to its structural similarity to bevacizumab. The influence of polymer molecular weight, composition, and isomerism on formulation parameters such as entrapment efficiency, drug loading, and in vitro release profile was delineated. Crystallinity and molecular weight of copolymers exhibited a substantial effect on formulation parameters. A secondary structure of released IgG was confirmed by circular dichroism (CD) spectroscopy. In vitro cytotoxicity, cell viability, and biocompatibility studies performed on human retinal pigment epithelial cells (ARPE-19) and/or macrophage cell line (RAW 264.7) demonstrated PB copolymers to be excellent biomaterials. Novel PB polymers may be the answer to the unmet need of a sustained release protein formulation.KEY WORDS: block copolymers, controlled drug delivery, IgG, intravitreal, nanoparticles, ocular delivery, pentablock copolymers, posterior segment, protein therapeutics, sustained drug delivery     

Exploring molecular and mechanical gradients in structural bioscaffolds

Most organisms consist of a functionally adaptive assemblage of hard and soft tissues. Despite the obvious advantages of reinforcing soft protoplasm with a hard scaffold, such composites can lead to tremendous mechanical stresses where the two meet. Although little is known about how nature relieves these stresses, it is generally agreed that fundamental insights about molecular adaptation at hard/soft interfaces could profoundly influence how we think about biomaterials. Based on two noncellular tissues, mussel byssus and polychaete jaws, recent studies suggest that one natural strategy to minimize interfacial stresses between adjoining stiff and soft tissue appears to be the creation of a "fuzzy" boundary, which avoids abrupt changes in mechanical properties. Instead there is a gradual mechanical change that accompanies the transcendence from stiff to soft and vice versa. In byssal threads, the biochemical medium for achieving such a gradual mechanical change involves the elegant use of collagen-based self-assembling block copolymers. There are three distinct diblock copolymer types in which one block is always collagenous, whereas the other can be either elastin-like (soft), amorphous polyglycine (intermediate), or silk-like (stiff). Gradients of these are made by an incrementally titrated expression of the three proteins in secretory cells the titration phenotype of which is linked to their location. Thus, reflecting exactly the composition of each thread, the distal cells secrete primarily the silk- and polyglycine-collagen diblocks, whereas the proximal cells secrete the elastin- and polyglycine-collagen diblocks. Those cells in between exhibit gradations of collagens with silk or elastin blocks. Spontaneous self-assembly appears to be by pH triggered metal binding by histidine (HIS)-rich sequences at both the amino and carboxy termini of the diblocks. In the polychaete jaws, HIS-rich sequences are expanded into a major block domain. Histidine predominates at over 20 mol % near the distal tip and diminishes to about 5 mol % near the proximal base. The abundance of histidine is directly correlated to transition metal content (Zn or Cu) as well as hardness determined by nanoindentation. EXAFS analyses of the jaws indicate that transition metals such as Zn are directly bound to histidine ligands and may serve as cross-linkers.     

Synthesis of an Intein-mediated Artificial Protein Hydrogel

We present the synthesis of a highly stable protein hydrogel mediated by a split-intein-catalyzed protein trans-splicing reaction. The building blocks of this hydrogel are two protein block-copolymers each containing a subunit of a trimeric protein that serves as a crosslinker and one half of a split intein. A highly hydrophilic random coil is inserted into one of the block-copolymers for water retention. Mixing of the two protein block copolymers triggers an intein trans-splicing reaction, yielding a polypeptide unit with crosslinkers at either end that rapidly self-assembles into a hydrogel. This hydrogel is very stable under both acidic and basic conditions, at temperatures up to 50 °C, and in organic solvents. The hydrogel rapidly reforms after shear-induced rupture. Incorporation of a "docking station peptide" into the hydrogel building block enables convenient incorporation of "docking protein"-tagged target proteins. The hydrogel is compatible with tissue culture growth media, supports the diffusion of 20 kDa molecules, and enables the immobilization of bioactive globular proteins. The application of the intein-mediated protein hydrogel as an organic-solvent-compatible biocatalyst was demonstrated by encapsulating the horseradish peroxidase enzyme and corroborating its activity.     

Poly(ethylene glycol) block copolymers

The ubiquitous use of poly(ethylene glycol) in the biomaterials field has also boosted the research activity in the chemical derivatization of this polymer. We focused our interest on the preparation of tailor-made poly(ethylene glycol)-based structures and on the study of structure-activity relationships for its functionalization, as preliminary steps for the preparation of smart functional materials. More specifically, amphiphilic and cationic block copolymers were prepared for prospective use in the preparation of self-assembled carriers, and Michael-type addition of thiols onto acrylates was studied as a model for end-group reaction leading to hydrogel formation.     

Protein interface remodeling in a chemically induced protein dimer

Although the development of chemically induced, self-assembled protein-based materials is rapidly expanding, methods for directing their assembly in solution are sparse, and problems of population heterogeneity remain. By exerting control over the assembly of advanced protein structures, new classes of ordered protein nanomaterials become feasible, affecting numerous applications ranging from therapeutics to nanostructural engineering. Focusing on a protein-based method for modulating the stability of a chemically induced dihydrofolate reductase (DHFR) dimer, we demonstrate the sensitivity of a methotrexate competition assay in determining the change in DHFR-DHFR binding cooperativity via interfacial mutations over a 1.3 kcal/mol range. This represents a change of more than 40% of the dimer complex binding energy conferred from protein-protein cooperativity (~3.1 kcal/mol). With the development of this investigative system and refinement of protein-based techniques for complex stability modulation, the directed assembly of protein nanomaterials into heterocomplexes and a concomitant decrease in population heterogeneity becomes a realizable goal.     

Engineered metal binding sites on green fluorescence protein

The ability to assay a variety of metals by noninvasive methods has applications in both biomedical and environmental research. Green fluorescent protein (GFP) is a protein isolated from coelenterates that exhibits spontaneous fluorescence. GFP does not require any exogenous cofactors for fluorescence, and can be easily appended to other proteins at the DNA level, producing a fluorescence-labeled target protein in vivo. Metals in close proximity to chromophores are known to quench fluorescence in a distance-dependent fashion. Potential metal binding sites on the surface of GFP have been identified and mutant proteins have been designed, created, and characterized. These metal-binding mutants of GFP exhibit fluorescence quenching at lower transition metal ion concentrations than those of the wild-type protein. These GFP mutants represent a new class of protein-based metal sensors.     

A Chimeric Fusion Protein Engineered with Disparate Functionalities—Enzymatic Activity and Self-assembly

The fusion of protein domains is an important mechanism in molecular evolution and a valuable strategy for protein engineering. We are interested in creating fusion proteins containing both globular and structural domains so that the final chimeric protein can be utilized to create novel bioactive biomaterials. Interactions between fused domains can be desirable in some fusion protein applications, but in this case the optimal configuration will enable the bioactivity to be unaffected by the structural cross-linking. To explore this concept, we have created a fusion consisting of a thermostable aldo-keto reductase, two α-helical leucine zipper domains, and a randomly coiled domain. The resulting protein is bifunctional in that (1) it can self-assemble into a hydrogel material as the terminal leucine zipper domains form interprotein coiled-coil cross-links, and (2) it expresses alcohol dehydrogenase and aldo-keto reductase activity native to AdhD from Pyrococcus furiosus. The kinetic parameters of the enzyme are minimally affected by the addition of the helical appendages, and rheological studies demonstrate that a supramolecular assembly of the bifunctional protein building blocks forms a hydrogel. An active hydrogel is produced at temperatures up to 60 °C, and we demonstrate the functionality of the biomaterial by monitoring the oxidation and reduction of the native substrates by the gel. The design of chimeric fusion proteins with both globular and structural domains is an important advancement for the creation of bioactive biomaterials for biotechnology applications such as tissue engineering, bioelectrocatalysis, and biosensing and for the study of native assembled enzyme structures and clustered enzyme systems such as metabolons.     

Complete recombinant silk-elastinlike protein-based tissue scaffold

Due to their improved biocompatibility and specificity over synthetic materials, protein-based biomaterials, either derived from natural sources or genetically engineered, have been widely fabricated into nanofibrous scaffolds for tissue engineering applications. However, their inferior mechanical properties often require the reinforcement of protein-based tissue scaffolds using synthetic polymers. In this study, we report the electrospinning of a completely recombinant silk-elastinlike protein-based tissue scaffold with excellent mechanical properties and biocompatibility. In particular, SELP-47K containing tandemly repeated polypeptide sequences derived from native silk and elastin was electrospun into nanofibrous scaffolds, and stabilized via chemical vapor treatment and mechanical preconditioning. When fully hydrated in 1× PBS at 37 °C, mechanically preconditioned SELP-47K scaffolds displayed elastic moduli of 3.4-13.2 MPa, ultimate tensile strengths of 5.7-13.5 MPa, deformabilities of 100-130% strain, and resilience of 80.6-86.9%, closely matching or exceeding those of protein-synthetic blend polymeric scaffolds. Additionally, SELP-47K nanofibrous scaffolds promoted cell attachment and growth, demonstrating their in vitro biocompatibility.     

Designer protein-based performance materials

Repeat sequence protein polymer (RSPP) technology provides a platform to design and make protein-based performance polymers and represents the best nature has to offer. We report here that the RSPP platform is a novel approach to produce functional protein polymers that have both biomechanical and biofunctional blocks built into one molecule by design, using peptide motifs. We have shown that protein-based designer biopolymers can be made using recombinant DNA technology and fermentation and offer the ability to screen for desired properties utilizing the tremendous potential diversity of amino acid combinations. The technology also allows for large-scale manufacturing with a favorable fermentative cost-structure to deliver commercially viable performance polymers. Using three diverse examples with antimicrobial, textile targeting, and UV-protective agent, we have introduced functional attributes into structural protein polymers and shown, for example, that the functionalized RSPPs have possible applications in biodefense, industrial biotechnology, and personal care areas. This new class of biobased materials will simulate natural biomaterials that can be modified for desired function and have many advantages over conventional petroleum-based polymers.     

Gel formation driven by tunable hydrophobic domain: design of acrylamide macromonomer with oligo hydrophobic segment

Nowadays, biomaterials with amphiphilic properties are undergoing remarkable development. Here, we present one such development, in which we prepared amphiphilic graft copolymers, with a main chain composed of hydroxyethyl acrylamide (HEAA), to introduce hydrophilicity, and a side chain composed of poly(trimethylene carbonate) (PTMC) to introduce tunable hydrophobicity. These macromonomers were created with a novel molecular design, which introduced a ring-opening polymerization by the hydroxyl end group of HEAA in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene, and were analyzed by (1)H NMR and gel permeation chromatography. The amphiphilic graft copolymers were shown to form a hydrogel, the swelling ratio of which was greatly influenced by the number of trimethylene carbonate units. These copolymers also exhibited the Tyndall phenomenon in aqueous solution; they aggregated spontaneously due to hydrogen bonding and hydrophobic interactions, and a sodium 8-anilino-1-naphthalenesulfonate (ANS) fluorescence probe was introduced into the hydrophobic domain. The solution property of ANS in the polymer solution was analyzed by fluorescence measurement and (1)H NMR. The maximum fluorescence wavelength of ANS shifted to shorter wavelengths as the degree of polymerization of the hydrophobic PTMC, the composition of the macromonomer, and the concentration of the copolymer increased. The resulting copolymer formed a polymer micelle structure due to the tunable hydrophobic domain formation in selected solvents. Therefore, these amphiphilic graft copolymers containing a PTMC segment are excellent candidates for use as hydrophobic drug delivery carriers.     

Fabrication of elastomeric silk fibers

Methods to generate fibers from hydrogels, with control over mechanical properties, fiber diameter, and crystallinity, while retaining cytocompatibility and degradability, would expand options for biomaterials. Here, we exploited features of silk fibroin protein for the formation of tunable silk hydrogel fibers. The biological, chemical, and morphological features inherent to silk were combined with elastomeric properties gained through enzymatic crosslinking of the protein. Postprocessing via methanol and autoclaving provided tunable control of fiber features. Mechanical, optical, and chemical analyses demonstrated control of fiber properties by exploiting the physical cross‐links, and generating double network hydrogels consisting of chemical and physical cross‐links. Structure and chemical analyses revealed crystallinity from 30 to 50%, modulus from 0.5 to 4 MPa, and ultimate strength 1–5 MPa depending on the processing method. Fabrication and postprocessing combined provided fibers with extensibility from 100 to 400% ultimate strain. Fibers strained to 100% exhibited fourth order birefringence, revealing macroscopic orientation driven by chain mobility. The physical cross‐links were influenced in part by the drying rate of fabricated materials, where bound water, packing density, and microstructural homogeneity influenced cross‐linking efficiency. The ability to generate robust and versatile hydrogel microfibers is desirable for bottom‐up assembly of biological tissues and for broader biomaterial applications.     

Purification of His-tagged proteins using Ni2+-poly(2-acetamidoacrylic acid) hydrogel

In this study, a new matrix for immobilized metal affinity chromatography (IMAC) using poly(2-acetamidoacrylic acid) (PAAA) hydrogels complexed with Ni(2+) was developed for the purification of the recombinant histidine-tagged green fluorescence protein (His6-GFP). The Ni(2+)-complexed PAAA hydrogel was prepared by polymerizing 2-acetamidoacrylic acid (AAA) and 2,2'-[(1,4-dioxo-1,4-butanediyl)diamino] bis(2-propenoic acid) (DBDBPA) with potassium persulfate in DMSO, followed by Ni(2+) complexation. Confocal laser scanning microscopy was used to determine the binding of His6-GFP to the Ni(2+)-PAAA hydrogel in three-dimensional space. Photoluminescence spectroscopy revealed an 81% binding efficiency of His6-GFP to the Ni(2+)-PAAA hydrogel yielded with a recovery of 59%. The specificity of His6-GFP binding to Ni(2+)-PAAA hydrogel was compared with that of the PAAA hydrogel without Ni(2+). His6-GFP was purified directly from the cell lysate with Ni(2+)-PAAA hydrogel matrix but the PAAA hydrogel without Ni(2+) had no effect. The major advantage of the Ni(2+)-PAAA hydrogel system over current methods, such as Ni-nitrilotriacetic acid (NTA) agarose beads, was the simple and low-cost procedure for preparing the matrix.     

Genome‐wide computational determination of the human metalloproteome

Accurate prediction of protein function in humans is important for understanding biological processes at the molecular level in biomedicine and drug design. Over a third of proteins are commonly held to bind metal, and ～10% of human proteins, to bind zinc. Therefore, an initial step in protein function prediction frequently involves predicting metal ion binding. In recent years, methods have been developed to predict a set of residues in 3D space forming the metal‐ion binding site, often with a high degree of accuracy. Here, using extensions of these methods, we provide an extensive list of human proteins and their putative metal ion binding site residues, using translated gene sequences derived from the complete, resolved human genome. Under conditions of ～90% selectivity, over 900 new human putative metal ion binding proteins are identified. A statistical analysis of resolved metal ion binding sites in the human metalloproteome is furnished and the importance of remote homology analysis is demonstrated. As an example, a novel metal‐ion binding site involving a complex of a botulinum substrate with its inhibitor is presented. On the basis of the location of the predicted site and the interactions of the contacting residues at the complex interface, we postulate that metal ion binding in this region could influence complex formation and, consequently, the functioning of the protein. Thus, this work provides testable hypotheses about novel functions of known proteins. Proteins 2015; 83:931–939. © 2015 Wiley Periodicals, Inc.     

Controlled thermoresponsive hydrogels by stereocomplexed PLA-PEG-PLA prepared via hybrid micelles of pre-mixed copolymers with different PEG lengths

The stereocomplexed hydrogels derived from the micelle mixture of two enantiomeric triblock copolymers, PLLA-PEG-PLLA and PDLA-PEG-PDLA, reported in 2001 exhibited sol-to-gel transition at approximately body temperature upon heating. However, the showed poor storage modulus (ca. 1000 Pa) determined their insufficiency as injectable implant biomaterials for many applications. In this study, the mechanical property of these hydrogels was significantly improved by the modifications of molecular weights and micelle structure. Co-micelles composed of block copolymers with two sizes of PEG block length were shown to possess unique and dissimilar properties from the micelles composed of single-sized block copolymers. The stereomixture of PLA-PEG-PLA comicelles showed a controllable sol-to-gel transition at a wide temperature range of 4 and 80 °C. The sol-gel phase diagram displays a linear relationship of temperature versus copolymer composition; hence, a transition at body temperature can be readily achieved by adjusting the mixed copolymer ratio. The resulting thermoresponsive hydrogels exhibit a storage modulus notably higher (ca. 6000 Pa) than that of previously reported hydrogels. As a physical network solely governed by self-reorganization of micelles, followed by stereocomplexation, this unique system offers practical, safe, and simple implantable biomaterials.     

FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure‐based approaches showing considerable promise. In this article, we present FINDSITE‐metal, a new threading‐based method designed specifically to detect metal‐binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE‐metal. Combining structure/evolutionary information with machine learning results in highly accurate metal‐binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the native structure is 8.9 Å, 59.5% (71.9%) of the best of top five predicted metal locations are within 4 Å (8 Å) from a bound metal in the crystal structure. For most of the targets, multiple metal‐binding sites are detected with the best predicted binding site at rank 1 and within the top two ranks in 65.6% and 83.1% of the cases, respectively. Furthermore, for iron, copper, zinc, calcium, and magnesium ions, the binding metal can be predicted with high, typically 70% to 90%, accuracy. FINDSITE‐metal also provides a set of confidence indexes that help assess the reliability of predictions. Finally, we describe the proteome‐wide application of FINDSITE‐metal that quantifies the metal‐binding complement of the human proteome. FINDSITE‐metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite‐metal/ . Proteins 2011. © 2010 Wiley‐Liss, Inc.     

Genetically encoded synthesis of protein-based polymers with precisely specified molecular weight and sequence by recursive directional ligation: examples from the elastin-like polypeptide system

We report a new strategy for the synthesis of genes encoding repetitive, protein-based polymers of specified sequence, chain length, and architecture. In this stepwise approach, which we term "recursive directional ligation" (RDL), short gene segments are seamlessly combined in tandem using recombinant DNA techniques. The resulting larger genes can then be recursively combined until a gene of a desired length is obtained. This approach is modular and can be used to combine genes encoding different polypeptide sequences. We used this method to synthesize three different libraries of elastin-like polypeptides (ELPs); each library encodes a unique ELP sequence with systematically varied molecular weights. We also combined two of these sequences to produce a block copolymer. Because the thermal properties of ELPs depend on their sequence and chain length, the synthesis of these polypeptides provides an example of the importance of precise control over these parameters that is afforded by RDL.