The Benzyl Ester Group of Amino Acid Monomers Enhances Substrate Affinity and Broadens the Substrate Specificity of the Enzyme Catalyst in Chemoenzymatic Copolymerization

Molecular modification and biotechnological applications of microbial aspartic proteases

The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.

Mechanoenzymatic Reactions Involving Polymeric Substrates or Products

Mechanoenzymology is an emerging field in which mechanical mixing is used to sustain enzymatic reactions in low-solvent or solvent-free mixtures. Many enzymes have been reported that thrive under such conditions. Considering the central role of biopolymers and synthetic polymers in our society, this minireview highlights the use of mechanoenzymology for the synthesis or depolymerization of oligomeric or polymeric materials. In contrast to traditional in-solution reactions, solvent-free mechanoenzymology has the advantages of avoiding solubility issues, proceeding in a minimal volume, and reducing solvent waste while potentially improving the reaction efficiency and accessing new reactivity. It is expected that this strategy will continue to gain popularity and find more applications.

Chemoenzymatic Polymerization of l-Serine Ethyl Ester in Aqueous Media without Side-Group Protection

Poly(l-serine) (polySer) has tremendous potential as a polypeptide-based functional material due to the utility of the hydroxyl group on its side chain; however, tedious protection/deprotection of the hydroxyl groups is required for its synthesis. In this study, polySer was synthesized by the chemoenzymatic polymerization (CEP) of l-serine ethyl ester (Ser-OEt) or l-serine methyl ester (Ser-OMe) using papain as a catalyst in an aqueous medium. The CEP of Ser-OEt proceeded at basic pH ranging from 7.5 to 9.5 and resulted in the maximum precipitate yield of polySer at an optimized pH of 8.5. A series of peaks detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry revealed that the formed precipitate consisted of polySer with a degree of polymerization ranging from 5 to 22. Moreover, infrared spectroscopy, circular dichroism spectroscopy, and synchrotron wide-angle X-ray diffraction measurements indicated that the obtained polySer formed a β-sheet/strand structure. This is the first time the synthesis of polySer was realized by CEP in aqueous solution without protecting the hydroxyl group of the Ser monomer.

Amino acid derived biopolymers: Recent advances and biomedical applications

Over the past few years, amino acids (AA) have emerged as promising biomaterials for the synthesis of functional polymers. Owing to the diversity of functional groups in amino acids, various polymerization methods may be used to make a wide range of well-defined functional amino-acid/peptide-based optically active polymers with varying polymer lengths, compositions, and designs. When incorporated with chirality and self-assembly, they offer a wide range of applications and are particularly appealing in the field of drug delivery, tissue engineering, and biosensing. There are several classes of these polymers that include polyamides (PA), polyesters (PE), poly(ester-amide)s (PEA)s, polyurethanes (PU)s, poly(depsipeptide)s (PDP)s, etc. They offer the ability to control functionality, conjugation, crosslinking, stimuli responsiveness, and tuneable mechanical/thermal properties. In this review, we present the recent advancements in the synthesis strategies for obtaining these amino acid-derived bio-macromolecules, their self-assembly properties, and the wealth of prevalent applications.

Prospects of Using Biocatalysis for the Synthesis and Modification of Polymers

Trends in the dynamically developing application of biocatalysis for the synthesis and modification of polymers over the past 5 years are considered, with an emphasis on the production of biodegradable, biocompatible and functional polymeric materials oriented to medical applications. The possibilities of using enzymes not only as catalysts for polymerization but also for the preparation of monomers for polymerization or oligomers for block copolymerization are considered. Special attention is paid to the prospects and existing limitations of biocatalytic production of new synthetic biopolymers based on natural compounds and monomers from biomass, which can lead to a huge variety of functional biomaterials. The existing experience and perspectives for the integration of bio- and chemocatalysis in this area are discussed.

How to define and study structural proteins as biopolymer materials

Structural proteins, including silk fibroins, play an important role in shaping the skeletons and structures of cells, tissues, and organisms. The amino acid sequences of structural proteins often show characteristic features, such as a repeating tandem motif, that are notably different from those of functional proteins such as enzymes and antibodies. In recent years, materials composed of or containing structural proteins have been studied and developed as biomedical, apparel, and structural materials. This review outlines the definition of structural proteins, methods for characterizing structural proteins as polymeric materials, and potential applications.

Computational study on the polymerization reaction of d-aminopeptidase for the synthesis of d-peptides

Almost all natural proteins are composed exclusively of l-amino acids, and this chirality influences their properties, functions, and selectivity. Proteases can recognize proteins composed of l-amino acids but display lower selectivity for their stereoisomers, d-amino acids. Taking this as an advantage, d-amino acids can be used to develop polypeptides or biobased materials with higher biostability. Chemoenzymatic peptide synthesis is a technique that uses proteases as biocatalysts to synthesize polypeptides, and d-stereospecific proteases can be used to synthesize polypeptides incorporating d-amino acids. However, engineered proteases with modified catalytic activities are required to allow the incorporation of d-amino acids with increased efficiency. To understand the stereospecificity presented by proteases and their involvement in polymerization reactions, we studied d-aminopeptidase. This enzyme displays the ability to efficiently synthesize poly d-alanine-based peptides under mild conditions. To elucidate the mechanisms involved in the unique specificity of d-aminopeptidase, we performed quantum mechanics/molecular mechanics simulations of its polymerization reaction and determined the energy barriers presented by the chiral substrates. The enzyme faces higher activation barriers for the acylation and aminolysis reactions with the l-stereoisomer than with the d-substrate (10.7 and 17.7 kcal mol-1 higher, respectively). The simulation results suggest that changes in the interaction of the substrate with Asn155 influence the stereospecificity of the polymerization reaction.

Facile terminal functionalization of peptides by protease-catalyzed chemoenzymatic polymerization toward synthesis of polymeric architectures consisting of peptides

Terminal functionalized polypeptides were synthesized in one-pot chemoenzymatic polymerization using protease for constructing special polymeric architectures.

A covalently crosslinked silk fibroin hydrogel using enzymatic oxidation and chemoenzymatically synthesized copolypeptide crosslinkers consisting of a GPG tripeptide motif and tyrosine: control of gelation and resilience

A covalently crosslinked silk fibroin hydrogel was successfully formedviaan enzymatic crosslinking reaction using copolypeptides, which consist of a glycine–proline–glycine tripeptide motif and tyrosine, as linker molecules.

Insights into the Stereospecificity in Papain-Mediated Chemoenzymatic Polymerization from Quantum Mechanics/Molecular Mechanics Simulations

Chemoenzymatic peptide synthesis is an efficient and clean method to generate polypeptides for new applications in the fields of biomedical and functional materials. However, this enzyme-mediated synthesis is dependent on the reaction rate of the protease biocatalyst, which is essentially determined by the natural substrate specificity of the enzyme. Papain, one of the most studied cysteine proteases, is extensively used for the chemoenzymatic synthesis of new polypeptides. Similar to most proteases, papain displays high stereospecificity toward l-amino acids, with limited reactivity for the d-stereoisomer counterparts. However, the incorporation of d-amino acids into peptides is a promising approach to increase their biostability by conferring intrinsic resistance to proteolysis. Herein, we determined the stereospecific-limiting step of the papain-mediated polymerization reaction with the chiral substrates l/d-alanine ethyl ester (Ala-OEt). Afterward, we used Quantum Mechanics/Molecular Mechanics (QM/MM) simulations to study the catalytic mechanism at atomic level of detail and investigate the origin of its stereospecificity. The experimental and computational results show that papain is able to attack both l- and d-stereoisomers of Ala-OEt, forming an enzyme-substrate intermediate, and that the two reactions display a similar activation barrier. Moreover, we found that the reduced catalytic activity of papain in the polymerization of d-amino acids arises from the aminolysis step of the reaction, in which l-Ala-OEt displays a significantly lower free-energy barrier (12 kcal/mol) than d-Ala-OEt (30 kcal/mol). Further simulations suggest that the main factor affecting the polymerization of d-amino acids is the configuration of the d-acyl-intermediate enzyme, and in particular the orientation of its methyl group, which hinders the nucleophilic attack by other monomers and thus the formation of polypeptides.

Chemoenzymatic synthesis of polypeptides containing the unnatural amino acid 2-aminoisobutyric acid

Polypeptides containing 2-aminoisobutyric acid (Aib) units as an unnatural amino acid residue were synthesized by papain-catalyzed chemoenzymatic polymerization of a tripeptide ethyl ester l-Ala-Aib-l-Ala-OEt in an aqueous medium. The Aib-containing polypeptide adopted an α-helix conformation in both the solid and solution phases, which was induced by the periodic Aib residue.

Template-Assisted Enzymatic Synthesis of Oligopeptides from a Polylactide Chain

Peptides are often attached to polymer materials, as bioactive components, for the control of interactions between the material and its surrounding proteins and cells. However, synthesizing peptides and attaching them to polymers can be challenging and laborious. Herein, we describe the grafting of oligopeptides to an aliphatic polyester, using a one-step chemo-enzymatic synthesis with papain as the biocatalyst. To enable enzyme-mediated functionalization of the polyester, ethyl hept-6-enoylalaninate (grafter) was synthesized and attached to polylactide chains using thiol-ene click reactions. The oligopeptides were grafted onto the polylactide chains using two different synthetic routes: the grafting from strategy, in which the grafter was attached to the polyester prior to oligopeptide synthesis, or the grafting to strategy, in which oligopeptides were synthesized on the grafter first, then attached to the polymer chain. The final products were analyzed and their structures were confirmed using nuclear magnetic resonance (NMR). The peptide attachment was evaluated using size exclusion chromatography (SEC), contact angle measurement and energy-dispersive X-ray spectroscopy-scanning electron microscopy (EDS-SEM). Furthermore, the mechanistic aspects of the synthesis of the oligopeptides on the grafter were studied using molecular dynamics (MD) simulations. The simulation revealed that hydrogen bonding (between the P1 amide nitrogen of the grafter backbone and the carbonyl oxygen of D158 in the papain) maintain the grafter in a productive conformation to stabilize the transition state of nitrogen inversion, a key step of the biocatalytic mechanism. Apart from being biologically relevant, both experimental and computational results suggest that the designed grafter is a good template for initiating chemo-enzymatic synthesis. The results also showed that the grafting to strategy was more successful compared to the grafting from strategy. Overall, a successful synthesis of predefined peptide functionalized polylactide was prepared, where the oligopeptides were grafted in an easy, time efficient, and environmentally friendly way.

Chemoenzymatic Synthesis of Polypeptides for Use as Functional and Structural Materials

Polypeptides inspired by the natural functional and structural proteins present in living systems are promising materials for various fields in terms of their versatile functionality and physical properties. Designing and synthesizing mimetic sequences of specific peptide motifs in proteins are important for exploring the functionality of natural proteins. Chemoenzymatic polymerization, which utilizes aminolysis (i.e., the reverse reaction of hydrolysis catalyzed by proteases), is a useful technique for synthesizing artificial polypeptide materials and has several advantages, including facile synthesis protocols, environmental friendliness, scalability, and atom economy. In this review, recent progress in chemoenzymatic polypeptide synthesis for the production of functional and structural materials for various applications is summarized in conjunction with the current status of technical challenges in the field.

Chemical Synthesis of Multiblock Copolypeptides Inspired by Spider Dragline Silk Proteins

Novel multiblock polypeptides with a structure similar to the unique sequence observed in spider silk proteins (spidroins) were synthesized via a two-step chemical synthesis method, that is, chemoenzymatic polymerization, using papain followed by postpolycondensation. Two types of polypeptide fragments were prepared by chemoenzymatic polymerization: polyalanine as a hard block, which forms β-sheets in the spider silk fibers, and poly(glycine-random-leucine) as a soft block. These two fragments were ligated by postpolycondensation using polyphosphoric acid as a condensing agent. Wide-angle X-ray diffraction (WAXD) and IR measurements revealed that the resulting multiblock polypeptides formed an antiparallel β-sheet structure with a degree of crystallinity similar to that of spider silk, which resulted in a fibrous morphology. This work provides the first example of a synthetic multiblock polypeptide mimicking the secondary structures of spider silk.

Chemoenzymatic synthesis of a peptide containing nylon monomer units for thermally processable peptide material application

Chemoenzymatic polymerization by papain produced the copolymer of l-leucine and nylon monomers, which showed melting behavior at around 200 °C.

Relationships between physical properties and sequence in silkworm silks

Silk has attracted widespread attention due to its superlative material properties and promising applications. However, the determinants behind the variations in material properties among different types of silk are not well understood. We analysed the physical properties of silk samples from a variety of silkmoth cocoons, including domesticated Bombyx mori varieties and several species from Saturniidae. Tensile deformation tests, thermal analyses, and investigations on crystalline structure and orientation of the fibres were performed. The results showed that saturniid silks produce more highly-defined structural transitions compared to B. mori, as seen in the yielding and strain hardening events during tensile deformation and in the changes observed during thermal analyses. These observations were analysed in terms of the constituent fibroin sequences, which in B. mori are predicted to produce heterogeneous structures, whereas the strictly modular repeats of the saturniid sequences are hypothesized to produce structures that respond in a concerted manner. Within saturniid fibroins, thermal stability was found to correlate with the abundance of poly-alanine residues, whereas differences in fibre extensibility can be related to varying ratios of GGX motifs versus bulky hydrophobic residues in the amorphous phase.

Papain-Catalyzed Synthesis of Polyglutamate Containing a Nylon Monomer Unit

Peptides have the potential to serve as an alternative for petroleum-based polymers to support a sustainable society. However, they lack thermoplasticity, owing to their strong intermolecular interactions. In contrast, nylon is famous for its thermoplasticity and chemical resistance. Here, we synthesized peptides containing a nylon unit to modify their thermal properties by using papain-catalyzed chemoenzymatic polymerization. We used l-glutamic acid alkyl ester as the amino acid monomer and nylon 1, 3, 4, and 6 alkyl esters as the nylon unit. Papain catalyzed the copolymerization of glutamic acid with nylon 3, 4, and 6 alkyl esters, whereas the nylon 1 unit could not be copolymerized. Other proteases used in this study, namely, bromelain, proteinase K, and Candida antarctica lipase (CALB), were not able to copolymerize with any nylon units. The broad substrate specificity of papain enabled the copolymerization of l-glutamic acid with a nylon unit. The peptides with nylon units demonstrated different thermal profiles from that of oligo(l-glutamic acid). Therefore, the resultant peptides with various nylon units are expected to form fewer intermolecular hydrogen bonds, thus altering their thermal properties. This finding is expected to broaden the applications of peptide materials and chemoenzymatic polymerization.