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

Mammary fat globules as a source of mRNA to model alterations in the expression of some milk component genes during lactation in bovines

BACKGROUND

The milk's nutritional value is determined by its constituents, including fat, protein, carbohydrates, and minerals. The mammary gland's ability to produce milk is controlled by a complex network of genes. Thereby, the fat, protein, and lactose synthesis must be boost in milk to increase milk production efficiency. This can be accomplished by fusing genetic advancements with proper management practices. Therefore, this study aimed to investigate the association between the Lipoprotein lipase (LPL), kappa casein CSN3, and Glucose transporter 1 (GLUT1) genes expression levels and such milk components as fat, protein, and lactose in different dairy breeds during different stages of lactation.

METHODS

To achieve such a purpose, 94 milk samples were collected (72 samples from 36 multiparous black-white and red-white Holstein-Friesian (HF) cows and 22 milk samples from 11 Egyptian buffaloes) during the early and peak lactation stages. The milk samples were utilized for milk analysis and genes expressions analyses using non- invasive approach in obtaining milk fat globules (MFGs) as a source of Ribonucleic acid (RNA).

RESULTS

LPL and CSN3 genes expressions levels were found to be significantly higher in Egyptian buffalo than Holstein-Friesian (HF) cows as well as fat and protein percentages. On the other hand, GLUT1 gene expression level was shown to be significantly higher during peak lactation than early lactation. Moreover, lactose % showed a significant difference in peak lactation phase compared to early lactation phase. Also, fat and protein percentages were significantly higher in early lactation period than peak lactation period but lactose% showed the opposite pattern of Egyptian buffalo.

CONCLUSION

Total RNA can be successfully obtained from MFGs. The results suggest that these genes play a role in glucose absorption and lactose synthesis in bovine mammary epithelial cells during lactation. Also, these results provide light on the differential expression of these genes among distinct Holstein-Friesian cow breeds and Egyptian buffalo subspecies throughout various lactation phases.

Camel milk products: innovations, limitations and opportunities

Camel milk is the mainstay for millions of people in arid and semi-arid environments. In these areas, it is mainly consumed raw or after it spontaneously turns sour. Although some attempts have been made to produce dairy products from camel milk, processing of camel milk is generally considered to be difficult and the quality of the final products made from camel milk do not correspond to their bovine milk counterparts. This paper reports a comprehensive analysis of the literature on camel milk products and presents synthesis of the latest developments, limitations pertaining processing and opportunities for development of new and improved camel milk products. The protein composition and colloidal structure of camel milk differs from cow milk. It is characterized by absence of β-lactoglobulin, low κ-casein content, high proportion of β-casein, larger casein micelles and smaller fat globules. These differences lead to the difficulty of making dairy products from camel milk using the same technologies as for bovine milk. Some of the challenges of camel milk processing include poor stability of the milk during UHT treatment, impaired rennetability, formation of weak and fragile curd during coagulation, longer fermentation time, and low thermal stability of the milk during drying. Despite these difficulties, it has now become possible to produce a range of commercial and traditional dairy products from camel milk. Some of the strategies that could be applied to improve the quality and characteristics of camel milk products are discussed.

Graphical Abstract

Can Recombinant Tree Shrew (Tupaia belangeri chinensis) Chymosin Coagulate Cow (Bos taurus) Milk?

Abstract

Genetically engineered chymosin from the tree shrew (Tupaia belangeri chinensis) has been obtained and partially characterized for the first time. The target enzyme was produced in Escherichia coli, strain BL21(DE3). It was shown that tree shrew recombinant chymosin coagulates cow milk (Bos taurus). The total and specific milk-clotting activity of the obtained enzyme was 0.7–5.3 IMCU/mL and 8.8–16.6 IMCU/mg. The nonspecific proteolytic activity of tree shrew recombinant chymosin in relation to total bovine casein was 30 and 117% higher than that of recombinant chymosin of cow and of single-humped camel respectively. It was found that in comparison with most of the known genetically engineered chymosins, the tree shrew enzyme showed exceptionally low thermal stability. After heating at 45°C, the coagulation ability of tree shrew recombinant chymosin decreased by more than 40%, and at 50°C the enzyme lost more than 90% of the initial milk-clotting activity. The Michaelis constant (Km), enzyme turnover number (kcat), and catalytic efficiency (kcat/Km) for genetically engineered chymosin from the tree shrew were 6.3 ± 0.1 µM, 11 927 ± 3169 s–1 and 1968 ± 620 µM–1 s–1, respectively. Comparative analysis showed that the primary structure of the chymosin-sensitive site of cow kappa-casein and the supposed similar sequence of tree shrew kappa-casein differed by 75%. The ability of tree shrew recombinant chymosin to coagulate cow’s milk, along with a low thermal stability and high catalytic efficiency with respect to the substrate, imitating the chymosin-sensitive site of cow kappa-casein, suggests that this enzyme is of potential interest for cheese making.

Composition and aptitude for cheese-making of milk from cows, buffaloes, goats, sheep, dromedary camels, and donkeys

Bovines account for about 83% of the milk and dairy products consumed by humans worldwide, the rest represented by bubaline, caprine, ovine, camelid, and equine species, which are particularly important in areas of extensive pastoralism. Although milk is increasingly used for cheese production, the cheese-making efficiency of milk from the different species is not well known. This study compares the cheese-making ability of milk sampled from lactating females of the 6 dairy species in terms of milk composition, coagulation properties (using lactodynamography), curd-firming modeling, nutrients recovered in the curd, and cheese yield (through laboratory model-cheese production). Equine (donkey) milk had the lowest fat and protein content and did not coagulate after rennet addition. Buffalo and ewe milk yielded more fresh cheese (25.5 and 22.9%, respectively) than cow, goat, and dromedary milk (15.4, 11.9, and 13.8%, respectively). This was due to the greater fat and protein contents of the former species with respect to the latter, but also to the greater recovery of fat in the curd of bubaline (88.2%) than in the curd of camelid milk (55.0%) and consequent differences in the recoveries of milk total solids and energy in the curd; protein recovery, however, was much more similar across species (from 74.7% in dromedaries to 83.7% in bovine milk). Compared with bovine milk, the milk from the other Artiodactyla species coagulated more rapidly, reached curd firmness more quickly (especially ovine milk), had a more pronounced syneresis (especially caprine milk), had a greater potential asymptotical curd firmness (except dromedary and goat milk), and reached earlier maximum curd firmness (especially caprine and ovine milk). The maximum measured curd firmness was greater for bubaline and ovine milk, intermediate for bovine and caprine milk, and lower for camelid milk. The milk of all ruminant species can be used to make cheese, but, to improve efficiency, cheese-making procedures need to be optimized to take into account the large differences in their coagulation, curd-firming, and syneresis properties.

Structure rearrangement during rennet coagulation of milk modifies curd density

Milk curds are a semisolid structure resulting from the enzymatic coagulation of milk, consisting mainly of paracasein micelles, fat globules, and whey. This gel undergoes a series of changes in its composition and structure during setting and curing, affecting curd density. The present study investigated the composition and density of inoculated and noninoculated milk curds during a 60-min curing period conducted at 30, 35, and 40°C. The purpose of the study was to determine the density changes occurring in the protein phase of curds during curing under different conditions of temperature and pH to understand the nature of the structural changes happening in the paracasein matrix. Noninoculated curd density values oscillated between 1.0247 and 1.0294 g/cm³ after 60 min of curing, whereas inoculated treatments showed values between 1.0222 and 1.0321 g/cm³. This small difference in density between the studied samples was surprising because the whey content of samples differed greatly. Density of the protein phase reached values of 1.8002 and 1.4388 g/cm³ for noninoculated and inoculated curds, respectively, after 60 min of curing. Two independent mechanisms involved in the development of the protein-based structure of curds were identified upon comparison of the development of protein phase density in inoculated and noninoculated curds. Although the larger increase in protein phase density observed in noninoculated curds was probably due to the concurrent action of calcium-mediated electrostatic bonds and temperature-dependent hydrophobic bonds, inoculated curds showed a lower protein phase density caused by calcium solubilization and by a decrease in the net charge of paracasein micelles induced by pH reduction.

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.

Molecular docking to flexible targets

It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual screening protocols used for drug discovery remains a significant challenge. Here, stepwise methodologies are described to generate and select relevant protein conformations for virtual screening in the context of the relaxed complex scheme (RCS), to design small molecule libraries for docking, and to perform statistical analyses on the virtual screening results. Methods include equidistant spacing, RMSD-based clustering, and QR factorization protocols for ensemble generation and ROC analysis for ensemble selection.

Comparison of the milk-clotting properties of three plant extracts

Several proteases from plant sources have been proposed as milk coagulants, however, limited research has been done on their milk-clotting properties. The effect of temperature on the milk-clotting activity of kiwi fruit, melon and ginger extracts was evaluated, as well as the effects of the different extracts on curd properties. Melon extracts showed high milk-clotting activity over a broad temperature range (45-75 °C) while kiwi fruit and ginger extracts showed high activity over a narrower temperature range, with a maximum at 40 and 63 °C, respectively. Curds produced using kiwi extracts had textural properties comparable with those obtained using commercial rennet, while melon extracts produced a fragile gel and low curd yield. The milk-clotting behavior of the three plant extracts was related to the protease specificity present in these extracts. The kiwi proteases displayed chymosin-like properties and thus hold the best potential for use as a milk coagulant in cheese production.

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.

Camel and bovine chymosin: the relationship between their structures and cheese-making properties

Bovine and camel chymosin are aspartic peptidases that are used industrially in cheese production. They cleave the Phe105-Met106 bond of the milk protein κ-casein, releasing its predominantly negatively charged C-terminus, which leads to the separation of the milk into curds and whey. Despite having 85% sequence identity, camel chymosin shows a 70% higher milk-clotting activity than bovine chymosin towards bovine milk. The activities, structures, thermal stabilities and glycosylation patterns of bovine and camel chymosin obtained by fermentation in Aspergillus niger have been examined. Different variants of the enzymes were isolated by hydrophobic interaction chromatography and showed variations in their glycosylation, N-terminal sequences and activities. Glycosylation at Asn291 and the loss of the first three residues of camel chymosin significantly decreased its activity. Thermal differential scanning calorimetry revealed a slightly higher thermal stability of camel chymosin compared with bovine chymosin. The crystal structure of a doubly glycosylated variant of camel chymosin was determined at a resolution of 1.6 Å and the crystal structure of unglycosylated bovine chymosin was redetermined at a slightly higher resolution (1.8 Å) than previously determined structures. Camel and bovine chymosin share the same overall fold, except for the antiparallel central β-sheet that connects the N-terminal and C-terminal domains. In bovine chymosin the N-terminus forms one of the strands which is lacking in camel chymosin. This difference leads to an increase in the flexibility of the relative orientation of the two domains in the camel enzyme. Variations in the amino acids delineating the substrate-binding cleft suggest a greater flexibility in the ability to accommodate the substrate in camel chymosin. Both enzymes possess local positively charged patches on their surface that can play a role in interactions with the overall negatively charged C-terminus of κ-casein. Camel chymosin contains two additional positive patches that favour interaction with the substrate. The improved electrostatic interactions arising from variation in the surface charges and the greater malleability both in domain movements and substrate binding contribute to the better milk-clotting activity of camel chymosin towards bovine milk.

Camel and bovine chymosin hydrolysis of bovine α(S1)- and β-caseins studied by comparative peptide mapping

In many cheese varieties, the general proteolytic activity of the coagulant is of great importance to the development of flavor and texture during ripening. This study used capillary electrophoresis and LC-MS/MS to compare the in vitro proteolytic behavior of camel and bovine chymosin (CC/BC) on bovine α(S1)- and β-casein (CN) at pH 6.5 and 30 °C. β-CN hydrolysis was also studied at pH 5.2 and in the presence of 0, 2, and 5% (w/v) NaCl. A total of 25 α(S1)- and 80 β-CN peptides were identified, and initial rates of early peptide formation were determined. The modes of proteolytic action of CC and BC shared a high degree of similarity generally. However, except for a few peptide bonds, CC was markedly less active, the magnitude of which varied widely with cleavage site. Preferential α(S1)-CN (Phe23-Phe24) and β-CN (Leu192-Tyr193) hydrolysis by CC proceeded at an estimated 36 and 7% of the initial rate of BC, respectively. The latter rate difference was largely pH and NaCl independent. Several cleavage sites appeared to be unique to CC and especially BC action, but qualitative differences were often predetermined by quantitative effects. In particular, negligible CC affinity to α(S1)-CN₁₆₄/₁₆₅ and β-CN₁₈₉/₁₉₀ prevented further exposure of the N-terminal products. β-CN hydrolysis by either enzyme was always stimulated at the lower pH, yet either inhibited or stimulated by the presence of NaCl, depending mainly on the predominating type of molecular substrate interactions involved at the specific site of cleavage. The potential impact of this proteolytic behavior on cheese quality is discussed.

Comparison of the hydrolysis of bovine κ-casein by camel and bovine chymosin: a kinetic and specificity study

Bovine chymosin constitutes a traditional ingredient for enzymatic milk coagulation in cheese making, providing a strong clotting capacity and low general proteolytic activity. Recently, these properties were surpassed by camel chymosin, but the mechanistic difference behind their action is not yet clear. We used capillary electrophoresis and reversed-phase liquid chromatography-mass spectrometry to compare the first site of hydrolysis of camel and bovine chymosin on bovine κ-casein (CN) and to determine the kinetic parameters of this reaction (pH 6.5; 32 °C). The enzymes showed identical specificities, cleaving the Phe105-Met106 bond of κ-CN to produce para-κ-CN and caseinomacropeptide. Initial formation rates of both products validated Michaelis-Menten modeling of the kinetic properties of both enzymes. Camel chymosin bound κ-CN with ∼30% lower affinity (K(M)) and exhibited a 60% higher turnover rate (k(cat)), resulting in ∼15% higher catalytic efficiency (k(cat)/K(M)) as compared to bovine chymosin. A local, less dense negatively charged cluster on the surface of camel chymosin may weaken electrostatic binding to the His-Pro cluster of κ-CN to simultaneously impart reduced substrate affinity and accelerated enzyme-substrate dissociation as compared to bovine chymosin.