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

Comprehensive bioinformatics-based annotation and functional characterization of bovine chymosin protein revealed novel biological insights

Chymosin, an aspartic protease present in the stomachs of young ruminants like cows (bovine), causes milk coagulation and cheese production through the breakdown of κ-casein peptide bonds at the Met105-Phe106 site. Bovine chymosin is first synthesized as a pre-prochymosin that is cleaved to produce the mature chymosin protein. Despite significant strides in research, our understanding of this crucial enzyme remains incomplete. The purpose of this work was to perform in silico evolutionary and functional analysis and to gain unique insights into the structure of this protein. For this, the sequence of Bos taurus chymosin from UniProt database was subjected to various bioinformatics analyses. We found that bovine chymosin is a low molecular weight and hydrophilic protein that has homologs in other Bovidae species. Two active sites of aspartic peptidases, along with a functional domain, were identified. Gene Ontology analysis further confirmed chymosin's involvement in proteolysis and aspartic endopeptidase activity. Potential disordered residues and post-translational modification sites were also uncovered. It was revealed that the secondary structure of bovine chymosin is comprised of beta strands (44.27%), coils (43.65%), and alpha helices (12.07%). A highly optimized 3D structure was also obtained. Moreover, crucial protein-protein interactions were unveiled. Altogether, these findings provide valuable insights that could guide future research on bovine chymosin and its biological roles.

Extent of κ-casein hydrolysis during renneting of bovine milk: A critical assessment of the analytical and estimation approaches

Renneting is an enzymatic process that turns milk into curd which is then transformed into cheese. Rennet-induced coagulation of caseins (CNs) is the critical step during this process and the key is the primary hydrolysis of κ-CN's Phe105-Met106 bond by chymosin. This article comprehensively reviews the existing data on the extent/degree of κ-CN hydrolysis during renneting of bovine milk and critically evaluates its determination methods. The data show that under normal cheese-making conditions, milk gelation occurs at a degree of κ-CN hydrolysis <80%, which varies due to several factors including analytical and estimation approaches. The common approach involves isolating the macropeptides released, by precipitating whey proteins and residual CN in 1%-12% trichloroacetic acid (TCA), then assuming that the maximum amount obtained is 100% κ-CN hydrolysis. The drawback is that the estimated degree of κ-CN hydrolysis may be higher than the actual value as TCA partially precipitates the macropeptide fractions. Moreover, macropeptide isolation seems unnecessary based on current advances in chromatographic and electrophoretic techniques. The present work proposes a simple mass balance-based approach that will provide accurate estimates in future studies. The accuracy of measuring the degree of κ-CN hydrolysis has implications on the precision of the data in relation to its partitioning (% distribution between the curd and whey) which is essential for improving whey quality.

Biochemical, microbiological, and structural evaluations to early detect age gelation of milk caused by proteolytic activity of Pseudomonas fluorescens

Heat–stable peptidase AprX, released by Pseudomonas species in raw milk during cold storage, can cause gelation of UHT milk since it is able to split caseinomacropeptides (CMPtot) from κ-casein, so inducing aggregation of casein micelles. Identifying raw milk susceptibility to gelation would allow UHT milk manufacturers to select appropriate processing conditions or give the milk a different destination. Two approaches, i.e., detection of free CMPtot and evidence of casein aggregates, were evaluated as possible indicators for early detecting milk destabilization. With this aim, microfiltered milk was inoculated with a P. fluorescence strain and incubated at either 4 or 25 °C. The presence of CMPtot was detected using capillary electrophoresis after 96 and 24 h at the two temperatures, respectively, when milk also became heat unstable and small flocks of protein appeared. Confocal laser scanning microscopy evidenced initial aggregates of casein micelles after 48 and 24 h at 4 and 25 °C, respectively. Keeping the milk at 25 °C/24 h could be a useful condition to accelerate milk destabilization. Despite the similar timing of instability detection, presence of CMPtot was the only trait specific for AprX activity.

Impact of Rodenticides on the Coagulation Properties of Milk

In this study, we investigated the impact of the rodenticides (strychnine, bromadiolone, and brodifacoum) on milk pH, rennet coagulation time (RCT), and coagulum strength. Sub-lethal amounts of strychnine and bromadiolone produced an unnaturally large change in milk pH, compared to brodifacoum and brodifacoum on milk coagulation properties. All three studied rodenticides significantly affected RCT and coagulum strength. The presence of sub-lethal amounts of each individual rodenticide increased RCT by an overall mean of 17% (p < 0.001). Rodenticide contamination decreased coagulum strength by an overall mean of 26% (p < 0.05). Our results suggest that such changes could be noticeable at the farm, thus, potentially averting the mixture of contaminated milk with the tanker supply, and preventing downstream distribution to consumers.

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.

A novel protein mixture containing vegetable proteins renders enteral nutrition products non-coagulating after in vitro gastric digestion

BACKGROUND & AIMS

Non-coagulation of protein from enteral nutrition (EN) in the stomach is considered to improve gastric emptying and may result in reduced upper gastrointestinal complications such as reflux and aspiration pneumonia. For the development of a new EN protein mixture with reduced gastric coagulation, the coagulating properties of individual proteins, a novel blend of four proteins (P4 protein blend) and commercial EN products were investigated.

METHODS

A semi-dynamic, computer controlled setup was developed to mimic gastric digestion. The coagulation behaviour of 150 ml protein solutions and EN products was investigated. These were heat-treated calcium caseinate, sodium caseinate, whey, soy and pea protein, and the P4 protein blend comprising of the latter four (all solutions 6% w/v protein), four new enteral nutrition product varieties (New Nutrison® .0 or 1.5 kcal/ml, with and without MultiFibre MF6™) based on the P4 protein blend and two other commercially available casein dominant EN products (T1 and T2).

RESULTS

Calcium caseinate and sodium caseinate yielded a total wet coagulate of 43.5 ± 0.7 g and 52.7 ± 6.2 g, respectively. Whey, soy, pea and the P4 protein blend did not produce any measurable coagulate. T1 and T2 resulted in a total wet coagulate of 37.5 ± 0.8 g and 57.3 ± 0.8 g, respectively, while all new EN product varieties based on the P4 protein blend did not produce any measurable coagulate.

CONCLUSIONS

The P4 protein blend renders EN product varieties non-coagulating after in vitro gastric digestion.

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.

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.