Probing the structure-activity relationship of a novel artificial cellobiose hydrolase

A comparative study of two α-L-rhamnosidases with high sequence identity

The GH78 α-L-rhamnosidase from Aspergillus tubingensis (AT-Rha) was proved to be a new clade of Aspergillus α-L-rhamnosidases in the previous study. A putative α-L-rhamnosidase from A. kawachii IFO 4308 (AK-Rha) has 92 % identity in amino acid sequence with AT-Rha. In this study, AK-Rha was expressed in P. pastoris and characterized. Similar to AT-rRha, the recombinant AK-Rha (AK-rRha) showed a narrow substrate specificity to naringin. Interestingly, the enzyme activity of AK-rRha was 0.816 U/mg toward naringin, significantly lower than 125.142 U/mg of AT-rRha. Their large differences in catalytic efficiency was mainly due to their differences in kcat values between AK-rRha (0.67 s-1) and AT-rRha (4.89 × 104 s-1). The molecular dynamics simulation exhibited that the overall conformation of AK-Rha was rigid and that of AT-Rha was flexible; the Loop Y-L located above the catalytic domain formed different steric hindrances to naringin, and interacted with the flavonoid matrices at different strengths. The polar solvation energy analysis implied that the glycosidic bond was more easily hydrolysed in AT-Rha. The comparative study verified that the main feature of AK-Rha and AT-Rha represented Aspergillus α-L-rhamnosidase was the narrow substrate specificity toward naringin, and provided an insight of the relationships between their catalytic abilities and structures.

A study on the catalytic activity of polypeptides toward the hydrolysis of glucoside compounds gastrodin, polydatin and esculin

The self-assembly of a series of catalytically active polypeptides toward hydrolysis of glucoside compounds, namely, gastrodin, polydatin and esculin was investigated. These active peptides are composed of two functional fragments: one is the hydrophobic sequence LHLHLRL, which forms assembling segments in the presence of Zn ions (Zn²⁺); another functional sequence of active peptides are catalytic sites such as Glu (E), Asp (D) and His (H), where carboxylic acids (-COOH) or imidazole groups act like scissors to cleave glucoside bonds of the compounds (according to the acid-base coupling mechanism). The effects of the amino acid sequence of the peptide, Zn²⁺ concentration, pH and the size or steric hindrance of glucoside compounds on the hydrolytic activity were studied. It was found that the crystalline structure of assembled peptides was crucial to provide the peptide with catalytic hydrolytic activity. Noncovalent interaction index was used to analyse the noncovalent interaction of PEs with glucoside compounds, including hydrogen bonds, van der Waals, and steric effect in the complexes. The binding energy of complexes, the direction and site of nucleophilic attack during deglycosylation processes were also investigated by molecular docking and the electron density Laplace function. This revealed that the differences in the hydrolytic activity of peptides toward glucoside compounds with different sizes originated from different hydrogen bond interactions between the peptides and substrates. These active peptides may find application in the preparation of drugs by de-glycosylation of natural compounds.

Small Peptides in the Detection of Mycotoxins and Their Potential Applications in Mycotoxin Removal

Mycotoxins pose significant risks to humans and livestock. In addition, contaminated food- and feedstuffs can only be discarded, leading to increased economic losses and potential ecological pollution. Mycotoxin removal and real-time toxin level monitoring are effective approaches to solve this problem. As a hot research hotspot, small peptides derived from phage display peptide libraries, combinatorial peptide libraries, and rational design approaches can act as coating antigens, competitive antigens, and anti-immune complexes in immunoassays for the detection of mycotoxins. Furthermore, as a potential approach to mycotoxin degradation, small peptides can mimic the natural enzyme catalytic site to construct artificial enzymes containing oxidoreductases, hydrolase, and lyase activities. In summary, with the advantages of mature synthesis protocols, diverse structures, and excellent biocompatibility, also sharing their chemical structure with natural proteins, small peptides are widely used for mycotoxin detection and artificial enzyme construction, which have promising applications in mycotoxin degradation. This paper mainly reviews the advances of small peptides in the detection of mycotoxins, the construction of peptide-based artificial enzymes, and their potential applications in mycotoxin control.

Construction of Zn-heptapeptide bionanozymes with intrinsic hydrolase-like activity for degradation of di(2-ethylhexyl) phthalate

Nanozyme with intrinsic enzyme-like activity has emerged as favorite artificial catalyst during recent years. However, current nanozymes are mainly limited to inorganic-derived nanomaterials, while biomolecule-sourced nanozyme (bionanozyme) are rarely reported. Herein, inspired by the basic structure of natural hydrolase family, we constructed 3 oligopeptide-based bionanozymes with intrinsic hydrolase-like activity by implementing zinc induced self-assembly of histidine-rich heptapeptides. Under mild condition, divalent zinc (Zn²⁺) impelled the spontaneous assembly of short peptides (i.e. Ac-IHIHIQI-CONH₂, Ac-IHIHIYI-CONH₂, and Ac-IHVHLQI-CONH₂), forming hydrolase-mimicking bionanozymes with β-sheet secondary conformation and nanofibrous architecture. As expected, the resultant bionanozymes were able to hydrolyze a serious of p-nitrophenyl esters, including not only the simple substrate with short side-chain (p-NPA), but also more complicated ones (p-NPB, p-NPH, p-NPO, and p-NPS). Moreover, the self-assembled Zn-heptapeptide bionanozymes were also proven to be capable of degrading di(2-ethylhexyl) phthalate (DEHP), a typical plasticizer, showing great potential for environmental remediation. Based on this study, we aim to provide theoretical references and exemplify a specific case for directing the construction and application of bionanozyme.

Design of metalloenzyme mimics based on self-assembled peptides for organophosphorus pesticides detection

Organophosphorus pesticides (OPs) detection has attracted considerable attention because of the extensive application of OPs. In this research, non-toxic and high-performance metalloenzyme mimics of Zn²⁺-bonding peptides were developed by obtaining inspiration from phosphotriesterase (PTE) and nanofiber formation. Furthermore, based on the electrochemical activity of p-nitrophenol (PNP), the electrochemical sensor of metalloenzyme mimics was developed. By examining the effect of the active sites of peptides and fibril formation on the degradation of OPs, the optimal metalloenzyme mimic was selected. Furthermore, optimal metalloenzyme mimics were combined with NiCo₂O₄ to develop an electrochemical sensor of OPs. By monitoring square wave voltammetry (SWV) signals of PNP degraded from OPs, the amounts of OPs in actual samples could be determined in 15 min. We discovered that both the active sites of α metal and β metal were required for metalloenzyme mimics; Zn²⁺ promoted peptide fibrosis and especially acted as a cofactor for degrading OPs. Compared to traditional methods, the electrochemical sensor of metalloenzyme mimics was sensitive, reliable, and non-toxic; furthermore, the detection limit of methyl paraoxon was as low as 0.08 µM. The metalloenzyme mimics will be a promising material for detecting OPs in the food industry and environment fields.

Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.

Enzyme mimics based membrane reactor for di(2-ethylhexyl) phthalate degradation

Di(2-ethylhexyl) phthalate (DEHP), the most abundantly used plasticizer, was considered to be a hazardous chemical that was difficult to be degraded naturally. In this study, inspired by the "catalytic triad'' in serine proteases, an enzyme mimic material was developed by combining the proteases's active sites of serine, histidine and aspartate (S-H-D) with the self-assembling sequence of LKLKLKL and the aromatic group of fluorenylmethyloxycarbonyl (Fmoc). By mixing the monomer of peptides containing separate S, H and D residues with a ratio of 2:1:1, the enzyme mimics were found to co- assemble into nanofibers (Co-HSD) and showed the highest activity towards DEHP degradation because of the synergistic effects of active sites, orderly secondary structure and stable molecular conformation. To further improve ability and applicability, the high active mimetic enzyme was immobilized onto regenerated cellulose (RC) membranes for DEHP degradation in a continuous recycling mode. The RC membranes were first functionalized by the NaIO₄ oxidation method to form aldehyde groups and then conjugated with the enzyme mimics via Schiff-base reaction. As a biocatalytic membrane, this membrane could not only effectively degrade DEHP, but also showed good stability, thus establishing a promising biomaterial for large scale biodegradation of DEHP in water decontamination and liquid food depollution.

Electrochemical detection of organophosphorus pesticides based on amino acids-conjugated P3TAA-modified electrodes

In this work, amino acids (AAs) including serine (S), histidine (H) and glutamic acid (E)-conjugated poly(3-thiophene acetate acid) (P3TAA) were synthesized to promote the catalytic hydrolysis and in situ electrochemical detection of organophosphorus pesticides (OPs). The hydrolysis of OPs followed the mechanism of proton transfer relay composed of AAs of S, H, E, called the "catalytic triad", found in biomimetic hydrolases. P3TAA was used as a carrier to attach S, H, E, and these AA sites have the hydrolysis activity of Ops; the polymer P3TAA-AAs behaved like biomimetic enzymes. After the hydrolysis of OPs (e.g., methyl paraoxon, ethyl paraoxon and methyl parathion), p-nitrophenol (PNP) was generated, which can be detected electrochemically. Herein, an electrochemical method using P3TAA-conjugated S, H, E-modified electrodes for the determination of OPs was developed. OPs can be quantified by the electrochemical responses of PNP. This technique was selective toward OPs with the p-nitrophenol group. The detection limit of OPs (methyl paraoxon, methyl parathion and ethyl paraoxon) reached 0.5 μM. This detection technique was successfully applied to the detection of OPs in real samples with high detection accuracy.

Fluorescent peptide probes for organophosphorus pesticides detection

Extensive use of organophosphorus pesticides (OPs) in crop protection has aroused worldwidely great concern about safety and the detection of OPs is of great significance to food safety and human health. In this work, peptides attached with tetraphenylethylene (TPE) molecule were synthesized to from an aggregation-induced emission fluorescent probe (TPE-Peptide) for the determination of OPs. The working mechanism was as follows: in presence of OPs, OPs would react with active site serine in the peptide sequence via covalent bond and adducts were formed between OPs and the peptides; once formed, the adducts accelerated the aggregation of peptides, thus inducing strong emission of TPE-Peptide probe. So the adducts formation and the enhanced emission of the TPE-Peptide probe were the key factors for the OPs' sensing. Herein, the adducts formed between OPs and TPE-Peptide probe, the aggregated peptide fibrils were characterized by fluorescence, mass spectrometry, transmission electron microscopy, dynamic light scattering, atomic force microscopy, circular dichroism spectra and confocal fluorescence microscopy etc. This TPE-Peptide probe displayed highly sensitive fluorescence response where OPs' concentrations ranged from 1 to 100 μM with the limit of detection 0.6 μM and also showed selectivity.

Enzyme mimics based on self-assembled peptides for di(2-ethylhexyl)phthalate degradation

Enzyme mimics inspired by serine proteases are developed through self-assembled peptides to degrade di(2-ethylhexyl)phthalate (DEHP).

Amino acid-functionalized carbon nanotube framework as a biomimetic catalyst for cleavage of glycosidic bonds

In this work, carbon nanotubes (CNTs) functionalized by acidic amino acids were used as a framework, which aims to form a mimetic structure of an active site of the glycoside hydrolases. It was demonstrated that the glycosidic bonds of the disaccharides were cleaved by the fabricated biofunctionalized CNTs. It was implied that the number of carboxyl groups and their individual pKa values in the amino acids, and the distance between the NH₂ and the side chain carboxyl groups of the amino acid are predominant factors for determining the reaction efficiency and the optimum pH. It was suggested that glutamic acid functionalized CNTs framework showed the highest efficiency in the cleavage of glycosidic bond of cellobiose than other acidic biomolecules. It was also suggested that the glutamic acid functionalized CNT framework showed preference to the types of glycosidic bonds in the following order: β-1,2-glycoside  >  β-1,4-glycoside  >  α-1,4-glycoside [Formula: see text] α-1,1-glycoside bond.

Constructing peptide-based artificial hydrolases with customized selectivity

The substrate selectivity of peptide-based artificial enzymes can be customized by combining molecularly imprinted polymers as binding sites with peptide nanofibers as catalytic moieties.

Catalytic peptide assemblies

Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.

Homogenous graphene oxide-peptide nanofiber hybrid hydrogel as biomimetic polysaccharide hydrolase

Cellulose, an impressive potential sustainable fuel, is difficult to hydrolyze because of the protection of β-1,4-glycosidic bonds through the tight hydrogen bonding network. In this study, homogenous graphene oxide (GO)-peptide nanofiber hybrid hydrogels (GO-PNFs) were designed as a β-glycosyl hydrolase mimetic to achieve efficient degradation of cellobiose and cellopentaose. For comparison, free peptides, graphene oxide mixed with free peptides (GO-peptdies) and self-assembled peptide nanofibers (PNFs) were also studied for their activity as a hydrolase mimetics for degradation of cellobiose. Among these materials, GO-PNFs showed the highest hydrolysis activity. Transmission electron microscopy, atomic force microscopy, fluorescence analysis, circular dichroism spectroscopies, X-ray diffraction, Raman spectra and computational modeling were used to interpret the difference in activity mechanism in these artificially designed enzymes. These investigations suggested that high catalytic performance of GO-PNFs toward cellobiose and cellopentaose hydrolysis could be attributed to the formation of nanofiber structures of peptides, optimal molecular conformation and less steric hindrance to access the substrate. More importantly, GO not only served as a platform for attaching PNFs, but also created a hydrophobic microenvironment and facilitated proton transfer, an essential step in catalytic hydrolysis, thus enhancing catalytic activity. All these provided insights into the potential use of peptides and GO hybrid composite nanoenzymes in efficient cellulose hydrolysis.