Restrained molecular dynamics study of the interaction between bovine kappa-casein peptide 98-111 and bovine chymosin and porcine pepsin

Exploring Potential Bioactive Peptides in Fermented Bactrian Camel's Milk and Mare's Milk Made by Mongolian Nomads

To date, bioactive proteins and peptides from minor livestock milks and their fermented products have been scarcely reported. In Mongolia, nomads are commonly rearing five livestock animal species (i.e., cow, camel, goat, horse, and sheep) for milking and other purposes. In this study, we analyzed the peptide composition in fermented milks of Bactrian camels (Camelus bactrianus) and horses, produced by Mongolian nomads for self-consumption. Peptides from skimmed fermented milks were separated by ultrafiltration and reverse-phase high-performance liquid chromatography. Then, their amino acid sequences were determined by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry. Consequently, eleven peptides were identified in the fermented camel’s milk including four from β-casein (β-CN), three from α_s1-CN, and two from both κ-CN and lactophorin. On the other hand, twenty-four peptides were identified in the fermented mare’s milk including nineteen from β-CN, three from α_s1-CN, and one from both κ-CN and α_s2-CN. According to previous reports on the bioactivities of milk-derived peptides, antibacterial and antihypertensive activities were promising in both the fermented camel’s milk and mare’s milk. In addition, potential antioxidant activity was conjectured in the fermented camel’s milk. Further investigations are currently needed to clarify the potential role of immunomodulatory peptides in the two fermented milks.

Modification of protein structures by altering the whey protein profile and heat treatment affects in vitro static digestion of model infant milk formulas

Heat treatments induce changes in the protein structure in infant milk formulas (IMFs). The present study aims to investigate whether these structural modifications affect protein digestion. Model IMFs (1.3% proteins), with a bovine or a human whey protein profile, were unheated or heated at 67.5 °C or 80 °C to reach 65% of denaturation, resulting in six protein structures. IMFs were submitted to in vitro static gastrointestinal digestion simulating infant conditions. During digestion, laser light scattering was performed to analyze IMF destabilization and SDS-PAGE, OPA assay and cation exchange chromatography were used to monitor proteolysis. Results showed that, during gastric digestion, α-lactalbumin and β-lactoglobulin were resistant to hydrolysis in a similar manner for all protein structures within IMFs (p > 0.05), while the heat-induced denaturation of lactoferrin significantly increased its susceptibility to hydrolysis. Casein hydrolysis was enhanced when the native casein micelle structure was modified, i.e. partially disintegrated in the presence of lactoferrin or covered by heat-denatured whey proteins. The IMF destabilization at the end of the gastric digestion varied with protein structures, with larger particle size for IMF containing native casein micelles. During intestinal digestion, the kinetics of protein hydrolysis varied with the IMF protein structures, particularly for IMFs containing denatured lactoferrin, exhibiting higher proteolysis degree (67.5 °C and 80 °C vs. unheated) and essential amino acid bioaccessibility (67.5 °C vs. unheated). Overall, the protein structures, generated by modulating the whey protein profile and the heating conditions, impacted the IMF destabilization during the gastric phase and the proteolysis during the entire simulated infant digestion.

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.

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.

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.

Characterization and study of a κ-casein-like chymosin-sensitive linkage

The present report is dealing with the identification, in various unrelated proteins, of protein fragments sharing local sequence and structure similarities with the chymosin-sensitive linkage surrounding the Phe-Met/Ile bond of kappa-caseins. In all these proteins, this linkage is observed within an exposed beta-strand-like structure, as also predicted for kappa-caseins. The structure of one of these fragments, included in glutamine synthetase, particularly superimposes well with the conformation observed for a chymosin inhibitor (CP-113972) within the complex it forms with chymosin and can be similarly accommodated by specificity pockets within the enzyme substrate binding cleft. The effect of the enzyme activity of chymosin was thus tested on glutamine synthetase. Chymosin cut the latter at the Phe-Met linkage, suggesting that this system may locally resemble the kappa-casein/chymosin complex.

Detection of a single nucleotide polymorphism in the human α-lactalbumin gene: implications for human milk proteins

Variability in the protein composition of breast milk has been observed in many women and is believed to be due to natural variation of the human population. Single nucleotide polymorphisms (SNPs) are present throughout the entire human genome, but the impact of this variation on human milk composition and biological activity and infant nutrition and health is unclear. The goals of this study were to characterize a variant of human alpha-lactalbumin observed in milk from a Filipino population by determining the location of the polymorphism in the amino acid and genomic sequences of alpha-lactalbumin. Milk and blood samples were collected from 20 Filipino women, and milk samples were collected from an additional 450 women from nine different countries. alpha-Lactalbumin concentration was measured by high-performance liquid chromatography (HPLC), and milk samples containing the variant form of the protein were identified with both HPLC and mass spectrometry (MS). The molecular weight of the variant form was measured by MS, and the location of the polymorphism was narrowed down by protein reduction, alkylation and trypsin digestion. Genomic DNA was isolated from whole blood, and the polymorphism location and subject genotype were determined by amplifying the entire coding sequence of human alpha-lactalbumin by PCR, followed by DNA sequencing. A variant form of alpha-lactalbumin was observed in HPLC chromatograms, and the difference in molecular weight was determined by MS (wild type=14,070 Da, variant=14,056 Da). Protein reduction and digestion narrowed the polymorphism between the 33rd and 77th amino acid of the protein. The genetic polymorphism was identified as adenine to guanine, which translates to a substitution from isoleucine to valine at amino acid 46. The frequency of variation was higher in milk from China, Japan and Philippines, which suggests that this polymorphism is most prevalent in Asia. There are SNPs in the genome for human milk proteins and their implications for protein bioactivity and infant nutrition need to be considered.

Multispecies comparison of the casein gene loci and evolution of casein gene family

Caseins, the major milk proteins, are present in a genomic cluster spanning 250-350 kb. The divergence at the coding level between human, rodent, and cattle sequences is rather extensive for most of the genes in this region. Nevertheless, comparative analysis of genomic sequences harboring the casein gene cluster region of these species (with equal evolutionary distances 79-88 Myr) shows that the organization and orientation of the genes is highly conserved. The conserved gene structure indicates that the molecular diversity of the casein genes is achieved through variable use of exons in different species and high evolutionary divergence. Comparative analysis also revealed the presence within two species of uncharacterized casein family members and ruled out the previously held notion that another gene family, located in this region, is primate-specific. Several other new genes as well as conserved noncoding sequences with potential regulatory functions were identified. All genes identified in this region are, or are predicted to be, secreted proteins involved in mineral homeostasis, nutrition, and/or host defense, and are mostly expressed in the mammary and/or salivary glands. These observations suggest a possible common ancestry for the genes in this region.

ADSA Foundation Scholar Award. Formation and physical properties of milk protein gels

Gelation of milk proteins is the crucial first step in both cheese and yogurt manufacture. Several types of milk gels are discussed, with an emphasis on recent developments in our understanding of how these gels are formed and some of their key physical properties. Areas discussed include the latest dual-binding model for casein micelles; some recent developments in rennet-induced gelation; review of the methods that have been used to monitor milk coagulation; and a discussion of some of the possible causes for the wheying-off defect in yogurts. Casein micelles are the primary building blocks of casein-based gels; however, controversy about its structure continues. The latest model proposed for the formation of casein micelles is the dual-binding model proposed by Horne, 1998, which suggests that casein micelles are formed as a result of two binding mechanisms, namely hydrophobic attraction and colloidal calcium phosphate (CCP) bridging. Most previous models for the casein micelle have treated milk gelation from the viewpoint of simple particle destabilization and aggregation, but they have not been able to explain several unusual rheological properties of milk gels. Although there have been many techniques used to monitor the milk gelation process over the past few decades, only a few appear attractive as possible in-vat coagulation sensors. Another important aspect of milk gels is the defect in yogurts called wheying-off, which is the appearance of whey on the gel surface. The factors responsible for its occurrence are still unclear, but they have been investigated in model acid gel systems.

Solution structures of casein peptides: NMR, FTIR, CD, and molecular modeling studies of alphas1-casein, 1-23

To determine its potential for interacting with other components of the casein micelle, the N-terminal section of bovine alphas1-casein-B, residues 1-23, was investigated with nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies, and molecular modeling. NMR data were not consistent with conventional alpha-helical or beta-sheet structures, but changes in N-H proton chemical shifts suggested thermostable structures. Both CD and FTIR predicted a range of secondary structures for the peptide (30-40% turns, 25-30% extended) that were highly stable from 5 degrees C to 25 degrees C. Other conformational elements, such as loops and polyproline II helix, were indicated by FTIR only. Molecular dynamics simulation of the peptide predicted 32% turns and 27% extended, in agreement with FTIR and CD predictions and consistent with NMR data. This information is interpreted in accord with recent spectroscopic evidence regarding the nature of unordered conformations, leading to a possible role of alphas1-casein (1-23) in facilitating casein-casein interactions.

SSCP analysis at the bovine CSN3 locus discriminates six alleles corresponding to known protein variants (A, B, C, E, F, G) and three new DNA polymorphisms (H, I, A1)

A high resolution SSCP protocol was developed for simultaneous discrimination of the known CSN3 alleles A, B, C, E, F and G. Furthermore, three new DNA polymorphisms were identified in different Bos taurus and Bos indicus breeds or crosses. Mendelian segregation was shown for two of these polymorphisms (named CSN3*H and 1), and the third (named CSN3*A1) was found in unrelated animals, thus indicating the presence of three additional alleles at the bovine CSN3 locus. DNA sequencing revealed single mutations that led to a Thr/Ile substitution in amino acid position 135 for CSN3*H and to a Ser/Ala substitution in position 104 of the deduced amino acid sequence of CSN3*1 (GenBank accession numbers AF105260 and AF121023) compared to CSN3*A. In CSN3*A1, a silent mutation in the third codon position of Pro150 was found (GenBank accession number AF092513).

Micelle stability: kappa-casein structure and function

The stability of the casein micelle is dependent on the presence of kappa-casein (CN) on the surface of the micelle where it functions as an interface between the hydrophobic caseins of the micelle interior and the aqueous environment. kappa-Casein is also involved in thiol-catalyzed disulfide interchange reactions with the whey proteins during heat treatments and, after rennet cleavage, in the facilitation of micelle coagulation. These functions of kappa-CN are regulated by the three-dimensional structure of the protein on the micelle surface. The usual means of determining structure are not available for kappa-CN because this protein is strongly self-associating and has never been crystallized. Instead, algorithms were used to predict selected secondary structures and circular dichroism spectroscopy on kappa-CN and the macropeptide released by chymosin. Three peptides were synthesized to cover the chymosin-sensitive site (His98-Lys111), the region in the macropeptide that could be helical (Pro130-Ile153), and the region between. Nuclear magnetic resonance spectroscopy showed that the peptide His98-Lys111 was probably a beta-strand with tight turns at each end. This hypothesis was confirmed by a study of the molecular dynamics showing that the C variant of kappa-CN interacted less strongly with chymosin; consequently, the slow renneting time of milk that contains this protein was explainable. Both circular dichroism and nuclear magnetic resonance indicated that the peptide Pro130-Ile153 was probably helical under normal physiological conditions. A preliminary study using nuclear magnetic resonance showed that the intervening peptide had no discernible secondary structure. Consequently, most of the beta-sheet structure of kappa-CN is likely in the para-kappa-CN region.