Chymosin and aspartic proteinases

Plant-derived rennet: research progress, novel strategies for their isolation, identification, mechanism, bioactive peptide generation, and application in cheese manufacturing

Rennet, an aspartate protease found in the stomach of unweaned calves, effectively cuts the peptide bond between Phe105-Met106 in κ-casein, hydrolyzing the casein micelles to coagulate the milk and is a crucial additive in cheese production. Rennet is one of the most used enzymes of animal origin in cheese making. However, using rennet al.one is insufficient to meet the increasing demand for cheese production worldwide. Numerous studies have shown that plant rennet can be an alternative to bovine rennet and exhibit a good renneting effect. Therefore, it is crucial and urgent to find a reliable plant rennet. Based on our team's research on rennet enzymes of plant origin, such as from Dregea sinensis Hemsl. and Moringa oleifer Lam., for more than ten years, this paper reviews the relevant literature on rennet sources, isolation, identification, rennet mechanism, functional active peptide screening, and application in cheese production. In addition, it proposes the various techniques for targeted isolation and identification of rennet and efficient screening of functionally active peptides, which show excellent prospects for development.

Oxidation of Cathepsin D by Hydroxy Radical: Its Effect on Enzyme Structure and Activity against Myofibrillar Proteins Extracted from Coregonus peled

In this study, cathepsin D was oxidized in vitro with different concentrations of H₂O₂, and the activity, structure, and extent of myofibrillar protein degradation by oxidized cathepsin D were evaluated. The sulfhydryl content of cathepsin D decreased to 9.20% after oxidation, while the carbonyl content increased to 100.06%. The β-sheet in the secondary structure altered due to oxidation as well. The changes in the intrinsic fluorescence and UV absorption spectra indicated that oxidation could cause swelling and aggregation of cathepsin D molecules. The structure of cathepsin D could change its activity, and the activity was highest under 1 mM H₂O₂. Cathepsin D could degrade myofibrillar proteins in different treatment groups, and the degree of degradation is various. Therefore, this study could provide a scientific basis for the mechanism of interaction among hydroxyl radical oxidation, cathepsin D, and MP degradation.

Characterization of a Novel Milk-Clotting Aspartic Protease from Penicillium sp. and Structural Explanation for its High Milk-Clotting Index

A novel milk-clotting enzyme isolated from Penicillium sp. ACCC 39790 (PsMCE) was prepared by heterologous expression. The recombinant PsMCE had an apparent molecular mass of 45 kDa and exhibited maximum casein hydrolysis activity at pH 4.0 and 50 °C. The PsMCE activity was enhanced by calcium ions and strongly inhibited by pepstatin A. Through hydrolysis pattern and cleavage site analyses, the milk-clotting activity of PsMCE was related to its specific hydrolysis between Phe₁₀₅ and Met₁₀₆ in the κ-casein proteins. The structural basis of PsMCE was characterized using homology modeling, molecular docking, and interactional analysis. The P1' region of PsMCE is critical for its selective binding to the hydrolytic site in κ-casein, and the hydrophobic forces play a decisive role in the specific cleavage of Phe₁₀₅ and Met₁₀₆. These interactional analyses between PsMCE and the ligand peptide clarified the fundamentals of its high milk-clotting index (MCI). PsMCE could be applied in cheese making due to its thermolability and high MCI value as a potential milk-clotting enzyme.

A novel milk-clotting enzyme from Aspergillus oryzae and A. luchuensis is an aspartic endopeptidase PepE presumed to be a vacuolar enzyme

Aspergillus oryzae RIB40 has 11 aspartic endopeptidase genes. We searched for milk-clotting enzymes based on the homology of the deduced amino acid sequence with chymosins. As a result, we identified a milk-clotting enzyme in A. oryzae. We expected other Aspergillus species to have a homologous enzyme with milk-clotting activity, and we found the most homologous aspartic endopeptidase from A. luchuensis had milk-clotting activity. Surprisingly, 2 enzymes were considered as vacuole enzymes according to a study on A. niger proteases. The 2 enzymes from A. oryzae and A. luchuensis cleaved a peptide between the 105Phe-106Met bond in κ-casein, similar to chymosin. Although both enzymes showed proteolytic activity using casein as a substrate, the optimum pH values for milk-clotting and proteolytic activities were different. Furthermore, the substrate specificities were highly restricted. Therefore, we expected that the Japanese traditional fermentation agent, koji, could be used as an enzyme source for cheese production.

Biophysical evaluation of milk-clotting enzymes processed by high pressure

High pressure processing (HPP) is able to promote changes in enzymes structure. This study evaluated the effect of HP on the structural changes in milk-clotting enzymes processed under activation conditions for recombinant camel chymosin (212MPa/5min/10°C), calf rennet (280MPa/20min/25°C), bovine rennet (222MPa/5min/23°C), and porcine pepsin (50MPa/5min/20°C) and under inactivation conditions for all enzymes (600MPa/10min/25°C) including the protease from Rhizomucor miehei. In general, it was found that the HPP at activation conditions was able to increase the intrinsic fluorescence of samples with high pepsin concentration (porcine pepsin and bovine rennet), increase significantly the surface hydrophobicity and induce changes in secondary structure of all enzymes. Under inactivation conditions, increases in surface hydrophobicity and a reduction of intrinsic fluorescence were observed, suggesting a higher exposure of hydrophobic sites followed by water quenching of Trp residues. Moreover, changes in secondary structure were observed (with minor changes seen in Rhizomucor miehei protease). In conclusion, HPP was able to unfold milk-clotting enzymes even under activation conditions, and the porcine pepsin and bovine rennet were more sensitive to HPP.

Allosteric-Activation Mechanism of Bovine Chymosin Revealed by Bias-Exchange Metadynamics and Molecular Dynamics Simulations

The aspartic protease, bovine chymosin, catalyzes the proteolysis of κ-casein proteins in milk. The bovine chymosin-κ-casein complex is of industrial interest as the enzyme is used extensively in the manufacturing of processed dairy products. The apo form of the enzyme adopts a self-inhibited conformation in which the side chain of Tyr77 occludes the binding site. On the basis of kinetic, mutagenesis, and crystallographic data, it has been widely reported that a HPHPH sequence in the P8-P4 residues of the natural substrate κ-casein acts as the allosteric activator, but the mechanism by which this occurs has not previously been elucidated due to the challenges associated with studying this process by experimental methods. Here we have employed two computational techniques, molecular dynamics and bias-exchange metadynamics simulations, to study the mechanism of allosteric activation and to compute the free energy surface for the process. The simulations reveal that allosteric activation is initiated by interactions between the HPHPH sequence of κ-casein and a small α-helical region of chymosin (residues 112-116). A small conformational change in the α-helix causes the side chain of Phe114 to vacate a pocket that may then be occupied by the side chain of Tyr77. The free energy surface for the self-inhibited to open transition is significantly altered by the presence of the HPHPH sequence of κ-casein.

Isolation and Partial Characterisation of Milk-clotting Aspartic Protease from Streblus asper

A rennin-like milk-clotting protease from the twigs of Streblus asper was purified by a factor of 65 times with 36% recovery using ethanol precipitation, ion-exchange and size-exclusion chromatographic techniques. The enzyme was found to be monomeric in nature having a molecular mass of 55kDa. The enzyme acts optimally at 55°C and was stable in the temperature range of 30–40°C. Easy enzyme inactivation by moderate heating, makes this protease extract potentially useful for cheese production. The purified enzyme is an acid protease with an optimum pH of 5.5 and it retained 96% of its residual activity between pH 5.0 and 6.0. Pepstatin A inhibited the proteinase activity, whereas iodoacetamide, phenylmethyl sulphonyl fluoride, β-mercaptoethanol and ethylenediaminetetraacetic acid had no significant inhibitory effect suggesting the presence of aspartic acid residue at the active site. The milkclotting aspartic protease showed predominant α-helical conformation in phosphate buffer as evidenced from circular dichroic spectroscopy.

Production and characterization of a milk-clotting protease produced in submerged fermentation by the thermophilic fungus Thermomucor indicae-seudaticae N31

Proteases are some of the most important industrial enzymes, and one of their main applications is for the production of cheese in the dairy industry. Due to a shortage of animal rennet, microbial coagulant proteases are being sought. In this work, the production of microbial rennet from Thermomucor indicae-seudaticae N31 was studied in submerged fermentation. The best enzyme production was obtained in a fermentation medium containing 4 % wheat bran as the substrate in 0.3 % saline solution, incubated for 72 h at 45 °C and 150 rpm. The value of the milk clotting activity (MCA) was 60.5 U/mL, and the ratio to proteolytic activity (MCA/PA) was 510. The crude enzyme showed optimum pH at 5.5 and two peaks of optimum temperature (MCA at 65 °C and PA at 60 °C). The MCA was stable in the pH range 4.0-4.5 for 24 h and up to 55 °C for 1 h. It was stable during storage at different temperatures (-20 to 25 °C) for 10 weeks. Based on these results, we conclude that microbial rennet from T. indicae-seudaticae N31 produced by submerged fermentation showed good prospects of replacing traditional rennet.

Hot-spot mapping of the interactions between chymosin and bovine κ-casein

Chymosin is a commercially important enzyme in the manufacturing of cheese. Chymosin cleaves the milk protein κ-casein, which initiates the clotting process. Recently, it has been shown that camel chymosin has superior enzymatic properties toward cow's milk, compared to bovine chymosin. The two enzymes possess a high degree of homology. There are only minor differences in the binding cleft; hence, these must be important for binding the substrate. Models for the binding of a 16 amino acid fragment, consisting of the chymosin-sensitive region of bovine κ-casein (97-112), to both enzymes have previously been presented. Computational alanine scanning for mutating 39 residues in the substrate and the bovine enzyme are presented herein, and warm- (ΔΔG > 1 kcal/mol) and hot-spot (ΔΔG > 2 kcal/mol) residues in the bovine enzyme are identified. These residues are relevant for site-directed mutagenesis, with the aim of modifying the binding affinity and in turn affecting the catalytic efficacy of the enzyme.

Interactions between tea catechins and casein micelles and their impact on renneting functionality

Many studies have shown that tea catechins bind to milk proteins. This research focused on the association of tea polyphenols with casein micelles, and the consequences of the interactions on the renneting behaviour of skim milk. It was hypothesized that epigallocatechin-gallate (EGCG), the main catechin present in green tea, forms complexes with the casein micelles and that the association modifies the processing functionality of casein micelles. The binding of EGCG to casein micelles was quantified using HPLC. The formation of catechin-casein micelles complexes affected the rennet induced gelation of milk, and the effect was concentration dependent. Both the primary as well as the secondary stage of gelation were affected. These experiments clearly identify the need for a better understanding of the effect of tea polyphenols on the processing functionality of casein micelles, before milk products can be used as an appropriate platform for delivery of bioactive compounds.

PsoP1, a milk-clotting aspartic peptidase from the basidiomycete fungus Piptoporus soloniensis

The first enzyme of the basidiomycete Piptoporus soloniensis, a peptidase (PsoP1), was characterized after isolation from submerged cultures, purification by fractional precipitation, and preparative native-polyarylamide gel electrophoresis (PAGE). The native molecular mass of PsoP1 was 38 kDa with an isoelectric point of 3.9. Similar to chymosin from milk calves, PsoP1 showed a maximum milk-clotting activity (MCA) at 35-40 °C and was most stable at pH 6 and below 40 °C. The complete inhibition by pepstatin A identified this enzyme as an aspartic peptidase. Electrospray ionization-tandem MS showed an amino acid partial sequence that was more homologous to mammalian milk clotting peptidases than to the chymosin substitute from a fungal species, such as the Zygomycete Mucor miehei. According to sodium dodecyl sulfate-PAGE patterns, the peptidase cleaved κ-casein in a way similar to chymosin and hydrolyzed β-casein slowly, as it would be expected from an efficient chymosin substitute.

Initial stage of cheese production: a molecular modeling study of bovine and camel chymosin complexed with peptides from the chymosin-sensitive region of κ-casein

Bovine chymosin has long been the preferred enzyme used to coagulate cow's milk, in the initial stage of cheese production, during which it cleaves a specific bond in the milk protein κ-casein. Recently, camel chymosin has been shown to have a 70% higher clotting activity toward cow's milk and, moreover, to cleave κ-casein more selectively. Bovine chymosin, on the other hand, is a poor clotting agent toward camel's milk. This paper reports a molecular modeling study aimed at understanding this disparity, based on homology modeling and molecular dynamics simulations using peptide fragments of κ-casein from cow and camel in both bovine and camel chymosin. The results show that the complex between bovine chymosin and the fragment of camel κ-casein is indeed less stable in the binding pocket. The results also indicate that this in part may be due to charge repulsion between a lysine residue in bovine chymosin and an arginine residue in the P4 position of camel κ-casein.

Bovine chymosin: a computational study of recognition and binding of bovine kappa-casein

Bovine chymosin is an aspartic protease that selectively cleaves the milk protein kappa-casein. The enzyme is widely used to promote milk clotting in cheese manufacturing. We have developed models of residues 97-112 of bovine kappa-casein complexed with bovine chymosin, using ligand docking, conformational search algorithms, and molecular dynamics simulations. In agreement with limited experimental evidence, the model suggests that the substrate binds in an extended conformation with charged residues on either side of the scissile bond playing an important role in stabilizing the binding pose. Lys111 and Lys112 are observed to bind to the N-terminal domain of chymosin displacing a conserved water molecule. A cluster of histidine and proline residues (His98-Pro99-His100-Pro101-His102) in kappa-casein binds to the C-terminal domain of the protein, where a neighboring conserved arginine residue (Arg97) is found to be important for stabilizing the binding pose. The catalytic site (including the catalytic water molecule) is stable in the starting conformation of the previously proposed general acid/base catalytic mechanism for 18 ns of molecular dynamics simulations.

Multifunctional aspartic peptidase prosegments

The structure-function relationships of aspartic peptidases (APs) (EC 3.4.23.X) have been extensively investigated, yet much remains to be elucidated regarding the various molecular mechanisms of these enzymes. Over the past years, APs have received considerable interest for food applications (e.g. cheese, fermented foods) and as potential targets for pharmaceutical intervention in human diseases including hypertension, cancer, Alzheimer's disease, AIDS (acquired immune deficiency syndrome), and malaria. A deeper understanding of the structure and function of APs, therefore, will have a direct impact on the design of peptidase inhibitors developed to treat such diseases. Most APs are synthesized as zymogens which contain an N-terminal prosegment (PS) domain that is removed at acidic pH by proteolytic cleavage resulting in the active enzyme. While the nature of the AP PS function is not entirely understood, the PS can be important in processes such as the initiation of correct folding, protein stability, blockage of the active site, pH-dependence of activation, and intracellular sorting of the zymogen. This review summarizes the current knowledge of AP PS function (especially within the A1 family), with particular emphasis on protein folding, cellular sorting, and inhibition.

Dependence of chymosin and pepsin partition coefficient with phase volume and polymer pausidispersity in polyethyleneglycol–phosphate aqueous two-phase system

The influence of the phase volume ratio and polymer pausidispersity on chymosin and pepsin partition in polyethylenglycol-phosphate aqueous two-phase systems was studied. Both proteins showed a high affinity for the polyethylenglycol rich phase with a partition coefficient from 20 to 100 for chymosin and from 20 to 180 for pepsin, when the polyethyleneglycol molecular mass in the system varied between 1450 and 8000. The partition coefficient of chymosin was not affected by the volume phase ratio, while the pepsin coefficient showed a significant decrease in its partition coefficient with the increase in the top/bottom phase volume ratio.

Features of the acid protease partition in aqueous two-phase systems of polyethylene glycol–phosphate: Chymosin and pepsin

The partitioning of chymosin (from Aspergilus niger) and pepsin (from bovine stomach) was carried out in aqueous-two phase systems formed by polyethyleneglycol-potassium phosphate. The effects of polymer concentration, molecular mass and temperature were analysed. The partition was assayed at pH 7.0 in systems of polyethyleneglycol of molecular mass: 1450, 3350, 6000 and 8000. Both proteins showed high affinity for the polyethyleneglycol rich phase. The increase of polyethyleneglycol concentration favoured the protein transfer to the top phase, suggesting an important protein-polymer interaction. Polyethyleneglycol proved to have a stabilizing effect on the chymosin and pepsin, increasing its protein secondary structure. This finding agreed with the enhancement of the milk clotting activity by the polyethyleneglycol. The method appears to be suitable as a first step for the purification of these proteins from their natural sources.