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The human N-glycosylases SMUG1 and MBD4 catalyze the removal of uracil residues from DNA resulting from cytosine deamination or replication errors. For polymorphic variants of SMUG1 (G90C, P240H, N244S, N248Y) and the MBD4^(cat) catalytic domain (S470L, G507S, R512W, H557D), the structures of enzyme-substrate complexes were obtained by molecular dynamic simulation. It was experimentally found that the SNP variants of SMUG1, N244S and N248Y, had increased catalytic activity compared to the wild-type enzyme, probably due to the acceleration of the dissociation of the enzyme-product complex and an increase in the enzyme turnover rate. All other SNP variants of SMUG1 (G90C, P240H) and MBD4^(cat), in which amino acid substitutions disrupted the substrate binding region and/or active site, had significantly lower catalytic activity than the wild-type enzymes.

In the repair of the damage to bases, human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a key participant via the DNA base excision repair pathway. APE1 cleaves AP sites in DNA, which are potentially cytotoxic and highly mutagenic if left unrepaired. According to existing structural data, this enzyme’s active site contains many polar amino acid residues, which form extensive contacts with a DNA substrate. A few alternative catalytic mechanisms of the phosphodiester bond hydrolysis by APE1 have been reported. Here, the kinetics of conformational changes of the enzyme and of DNA substrate molecules were studied during the recognition and cleavage of the abasic site in the pH range from 5.5 to 9.0 using stopped-flow fluorescence techniques. The activity of APE1 increased with an increase in pH because of acceleration of the rates of catalytic complex formation and of the catalytic reaction. Molecular dynamics simulation uncovered a significant increase in the pKₐ of His-309 located in the active site of the enzyme. This finding revealed that the observed enhancement of enzymatic activity with pH could be associated with deprotonation of not only Tyr-171 but also His-309. The obtained data allowed us to hypothesize that the ionized state of these residues could be a molecular switch between the alternative catalytic mechanisms, which involve different functionalities of these residues throughout the reaction.

Background Human apurinic/apyrimidinic endonuclease APE1 is one of participants of the DNA base excision repair pathway. APE1 processes AP-sites and many other types of DNA damage via hydrolysis of the phosphodiester bond on the 5′ side of the lesion. APE1 also acts as an endoribonuclease, i.e., can cleave undamaged RNA. Methods Using pre-steady-state kinetic analysis we examined the role of certain catalytically important amino acids in APE1 enzymatic pathway and described their involvement in the mechanism of the target nucleotide recognition. Results Comparative analysis of the cleavage efficiency of damaged DNAs containing an abasic site, 5,6-dihydrouridine, or α-anomer of adenosine as well as 3′-5′-exonuclease degradation of undamaged DNA and endonuclease hydrolysis of RNA substrates by mutant APE1 enzymes containing a substitution of an active-site amino acid residue (D210N, N212A, T268D, M270A, or D308A) was performed. Detailed pre–steady-state kinetics of conformational changes of the enzyme and of DNA substrate molecules during recognition and cleavage of the abasic site were studied. Conclusions It was revealed that substitution T268D significantly disturbed initial DNA binding, whereas Asn212 is critical for the DNA-bending stage and catalysis. Substitution D210N increased the binding efficacy and blocked the catalytic reaction, but D308A decreased the binding efficacy owing to disruption of Mg2+ coordination. Finally, the substitution of Met270 also destabilized the enzyme–substrate complex but did not affect the catalytic reaction. Significance It was found that the tested substitutions of the active-site amino acid residues affected different stages of the complex formation process as well as the catalytic reaction.

The aim of this study was to investigate the effect of daily walnut consumption on dyslipidemia in dietary. Within a year, the patients who have been suggested taking walnut or not in their individual dietary were scanned retrospectively and randomized into 2 groups. The first group consists of 72 cases (only those taken on the diet program) and the second group consists of 73 cases (walnut consumption in regulated diet). Baseline blood lipid parameters and anthropometric measurements were assessed in both groups and compared with values at 3rd month. p values

Milk gels (acid or rennet) are used by dairy industry to produce dairy products such as yogurt and cheese. Enrichment of milk with calcium salts and heat treatment are known to produce “calcium-milk coagulum” as a new type of milk gels, due to reduction of milk protein charges through calcium binding. The combination of heat treatment and calcium addition to milk results in gel structures, but the effect of calcium addition and pH adjustment during heating of milk is still unclear. The role of added calcium and decreasing pH were investigated by addition of calcium chloride (30 mM) to reconstituted skim milk followed by pH adjustment by hydrochloric acid and sodium hydroxide (4.6

The development of coagulation properties during cold storage of raw milks categorized as good or poorly coagulating is largely unknown. This was studied in the present investigation at individual cow’s milk level in addition to elucidating the impact of cheesemaking processing steps on the resulting coagulation properties of silo tank cheesemilk. Rennet coagulation time (RCT), curd firming rate (CFR) and gel firmness (G’max); Ca, P and Mg distribution; pH; and casein micelle size of raw skim milk from individual cows classified as “good” or “poor” in coagulation properties were investigated over 72 h storage at 4 °C. For the cheesemilk, the impact of overnight cold storage, thermization and standardization, pasteurization, and acidification to either pH 6.45 or 6.30 on the coagulation properties were studied. After 24 h of cold storage, RCT of both good and poorly coagulating milks was significantly prolonged though recovering somewhat after prolonged storage for good coagulating samples. In contrast, G’max was significantly reduced after 72 h of cold storage for good coagulating milk. Both total and colloidal Ca were higher in good compared with poorly coagulating milk, while mineral distribution and milk pH did not change during storage. For cheesemilk, up to 14 h, cold storage did not impair coagulation properties significantly, which was markedly improved by acidification. The study shows that rheological parameters of good and poorly coagulating milks are impacted differently by the cold storage. Conversely, cheesemilk coagulation properties were not impaired by the studied cheesemaking processing steps and, further, were enhanced by acidification steps.

A spectrophotometric assay for plasmin and plasminogen-derived activity in dairy products was optimised and extended to determine plasmin and plasminogen-derived activity in turbid samples of dairy products. The method was validated by assessing reproducibility, repeatability, level of detection and recovery of plasmin activity in different sample matrices. Plasmin activity in raw milk was not affected by skimming, but decreased by 30% in pasteurised and homogenised whole milk, leading to an underestimation of plasmin activity. The effects of dissociation of plasmin and caseins by epsilon-aminocaproic acid (EACA) plus NaCl on the plasmin activity were investigated. Comparison of pasteurised milk with a micellar casein solution showed that the dissociation of plasmin and caseins on adding EACA and NaCl decreases interference by caseins, but increases inhibition of plasmin with serum-based inhibitory components. The level of detection and repeatability of this method for plasmin activity analysis were improved compared with previous spectrophotometric assays. (C) 2014 Elsevier Ltd. All rights reserved. (Less)

Zinc finger proteins that bind Zn(II) using a Cys2His2 coordination motif within a ββα protein fold are the most abundant DNA binding transcription factor domains in eukaryotic systems. These classic zinc fingers are typically unfolded in the apo state and spontaneously fold into their functional ββα folds upon incorporation of Zn(II). These metal-induced protein folding events obscure the free energy cost of protein folding by coupling the protein folding and metal-ion binding thermodynamics. Herein, we determine the formation constant of a Cys2His2/ββα zinc finger domain, the C-terminal finger of the Wilms’ tumor suppressor protein (WT1-4), for the purposes of determining its free energy cost of protein folding. Measurements of individual conditional dissociation constants, Kd values, at pH values from 5 to 9 were determined using fluorescence spectroscopy by direct or competition titration. Potentiometric titrations of apo-WT1-4 followed by NMR spectroscopy provided the intrinsic pKa values of the Cys2His2 residues, and corresponding potentiometric titrations of Zn(II)–WT1-4 followed by fluorescence spectroscopy yielded the effective pKaeff values of the Cys2His2 ligands bound to Zn(II). The Kd, pKa, and pKaeff values were combined in a minimal, complete equilibrium model to yield the pH-independent formation constant value for Zn(II)–WT1-4, KfML value of 7.5 × 1012 M–1, with a limiting Kd value of 133 fM. This shows that Zn(II) binding to the Cys2His2 site in WT1-4 provides at least −17.6 kcal/mol in driving force to fold the protein scaffold. A comparison of the conditional dissociation constants of Zn(II)–WT1-4 to those from the model peptide Zn(II)–GGG–Cys2His2 over the pH range 5.0 to 9.0 and a comparison of their pH-independent KfML values demonstrates that the free energy cost of protein folding in WT1-4 is less than +2.1 kcal/mol. These results validate our GGG model system for determining the cost of protein folding in natural zinc finger proteins and support the conclusion that the cost of protein folding in most zinc finger proteins is ≤+4.2 kcal/mol, a value that pales in comparison to the free energy contribution of Zn(II) binding, −17.6 kcal/mol., The formation constant for a natural Cys2His2 ββα zinc finger peptide has been determined using a suite of equilibrium measurements. These data are compared to literature values for Zn(II)−Cys2His2 protein events to assess the free energy cost of protein folding in proteins with metal-induced protein folding events. The data lead to the conclusion that the free energy contribution of Zn(II) binding is far in excess of the minimal free energy cost of protein folding.

The effect of proteolysis on oxidation in low-fat cheese was investigated. The accumulation of dityrosine during storage increased significantly in the cheese with a high degree of proteolysis, while hexanal and heptanal were lower in the cheese with high proteolytic activity, indicating that the peptides/free amino acids acted as antioxidants on the propagating step in lipid oxidation. Dimethyl disulphide concentration was also lower in the cheese with a higher level of peptides. Therefore, oxidation of tyrosine residues seemed to function as antioxidants both regarding secondary lipid oxidation products and protein-derived oxidation products through formation of dityrosine, being a termination reaction.

Photo-oxidation of cheese products has become an issue due to the fact that packaging of cheeses in transparent materials is very frequently used. The present study aimed to give new aspects of the possible antioxidative activity of whey proteins in photo-oxidation of cheese and the whey proteins were expected to act as scavenger and thereby reduce lipid oxidation. Oxidation was investigated in low-fat model cheese with whey protein isolate (WPI) added and compared to a low-fat control cheese. The cheeses were packed in air or in vacuum, respectively, and stored under light. Accumulations of lipid hydroperoxides, pentanal, hexanal, heptanal, 1-hexanol, dimethyl disulfide and dityrosine were all found to be dependent on the availability of oxygen. The presence of WPI reduced the accumulation of both lipid and protein oxidation products. The consumption of the naturally occurring antioxidant α-tocopherol was not affected by the added WPI. After the seventh day of light-exposed storage during which all riboflavin was decomposed and the concentration of α-tocopherol had found a stable level, the presence of WPI resulted in an extension of the observed lag phase in the accumulation of secondary lipid oxidation products. As WPI reduced the accumulation of protein oxidation products as well, it is suggested that WPI is not a typical radical scavenger.

The initial stage of the Maillard reaction, protein lactosylation, occurs during heat treatment of milk and continues during subsequent storage. We compared the initial lactosylation as well as the rate of lactosylation of milk proteins during storage in UHT milk subjected to direct or indirect heat treatment using liquid chromatography (LC) coupled with electrospray injection mass spectrometry (ESI-MS). Furosine content was used as an overall marker to allow for a quantitative correlation of lactosylation measured by LC-ESI-MS in the UHT milks. Protein lactosylation increased during the storage period of 6months at 20 degrees C. Both the initial extent and the rate of lactosylation positively correlated with the number of lysine residues in the different proteins. An exponential or linear correlation with furosine concentration could be established for major and minor lactosylated proteins, respectively. (Less)

Chymosin-induced cleavage of κ-casein (κ-CN) occurs during the first enzymatic phase in milk coagulation during cheese manufacturing, where the hydrophilic C-terminal peptide of κ-CN, named caseino-macropeptide (CMP), is released into the whey. The CMP peptide is known for its rather heterogeneous composition with respect to both genetic variation and multiple posttranslational modifications, including phosphorylation and O-linked glycosylation. An approach of liquid chromatography coupled with mass spectrometry was used to investigate (1) the overall protein profile and (2) the release of various forms of CMP after addition of chymosin to individual cow milk samples from 2 breeds, Danish Jersey (DJ) and Danish Holstein-Friesian (DH). The cows were selected to represent distinct homo- and heterozygous types of the κ-CN genetic variants A, B, and E (i.e., genotypes AA, BB, AB, EE, and AE). Initially, investigation of the protein profile showed milk with κ-CN BB exhibited the highest relative content of κ-CN, whereas AE milk exhibited the lowest, and after 40min of renneting >90% of intact κ-CN was hydrolyzed by chymosin in milk representing all κ-CN genotype. By in-depth analysis of the CMP chromatographic profile, multiple CMP isoforms with 1 to 3 O-linked glycans (1-3 G) and 1 to 3 phosphate groups (1-3 P) were identified, as well as nonmodified CMP isoforms. The number of identified CMP isoforms varied to some extent between breeds (21CMP isoforms identified in DJ, 26CMP isoforms in DH) and between κ-CN genetic variants (CMP variant A being the most heterogeneous compared with CMP B and E), as well as between individual samples within each breed. The predominant forms of glycans attached to CMP were found to be the acidic tetrasaccharide {N-acetyl-neuraminic acid α(2-3)galactose β(1-3)[N-acetyl-neuraminic acid α(2-6)]N-acetyl galactose} or trisaccharides {N-acetyl-neuraminic acid α(2-3)galactose β(1-3)N-acetyl galactose and galactose β(1-3)[N-acetyl-neuraminic acid (α2-6)]N-acetyl galactose}. The CMP release was calculated to follow first-order kinetics and was determined by the measurement of CMP content during renneting. The highest rate of release for all CMP isoforms occurred from 0 to 2min after chymosin addition. Concurring results from both breeds showed that CMP variant A with 1-2 P had the highest reaction rate of CMP release, followed by CMP B 1-2 P and then by CMP E 1-2 P (only in DH). All the identified glycosylated CMP isoforms had lower reaction rates of release compared with that of nonglycosylated CMP, thus glycan modifications seemed to negatively influence the reaction rate of chymosin-induced hydrolysis of κ-CN.

Tyrosine phosphorylation of phospholipase Cgamma2 (PLCgamma2) is a crucial activation switch that initiates and maintains intracellular calcium mobilization in response to B cell antigen receptor (BCR) engagement. Although members from three distinct families of non-receptor tyrosine kinases can phosphorylate PLCgamma in vitro, the specific kinase(s) controlling BCR-dependent PLCgamma activation in vivo remains unknown. Bruton's tyrosine kinase (Btk)-deficient human B cells exhibit diminished inositol 1,4,5-trisphosphate production and calcium signaling despite a normal inducible level of total PLCgamma2 tyrosine phosphorylation. This suggested that Btk might modify a critical subset of residues essential for PLCgamma2 activity. To evaluate this hypothesis, we generated site-specific phosphotyrosine antibodies recognizing four putative regulatory residues within PLCgamma2. Whereas all four sites were rapidly modified in response to BCR engagement in normal B cells, Btk-deficient B cells exhibited a marked reduction in phosphorylation of the Src homology 2 (SH2)-SH3 linker region sites, Tyr(753) and Tyr(759). Phosphorylation of both sites was restored by expression of Tec, but not Syk, family kinases. In contrast, phosphorylation of the PLCgamma2 carboxyl-terminal sites, Tyr(1197) and Tyr(1217), was unaffected by the absence of functional Btk. Together, these data support a model whereby Btk/Tec kinases control sustained calcium signaling via site-specific phosphorylation of key residues within the PLCgamma2 SH2-SH3 linker.

The effect of enzymatic activity in direct steam infusion heat treated milk with ultra-short holding times (>150 degrees C for

The aim of the present investigation was to study the underlying causes of noncoagulating (NC) milk. Based on an initial screening in a herd of 53 Danish Holstein-Friesians, 20 individual Holstein-Friesian cows were selected for good and poor chymosin-induced coagulation properties; that is, the 10 cows producing milk with the poorest and best coagulating properties, respectively. These 20 selected cows were followed and resampled on several occasions to evaluate possible changes in coagulation properties. In the follow-up study, we found that among the 10 cows with the poorest coagulating properties, 4 cows consistently produced poorly coagulating (PC) or NC milk, corresponding to a frequency of 7%. Noncoagulating milk was defined as milk that failed to form a coagulum, defined as increase in the storage modulus (G') in oscillatory rheometry, within 45min after addition of chymosin. Poorly coagulating milk was characterized by forming a weak coagulum of low G'. Milk proteomic profiling and contents of different casein variants, ionic contents of Ca, P and Mg, κ-casein (CN) genotypes, casein micelle size, and coagulation properties of the 4 NC or PC samples were compared with milk samples of 4 cows producing milk with good coagulation properties. The studies included determination of production of caseinomacropeptide to ascertain whether noncoagulation could be ascribed to the first or second phase of chymosin-induced coagulation. Caseinomacropeptide was formed in all 8 milk samples after addition of chymosin, indicating that the first step (cleavage of κ-CN) was not the cause of inability to coagulate. Furthermore, the effect of mixing noncoagulating and well-coagulating milk was studied. By gradually blending NC with well-coagulating milk, the coagulation properties of the well-coagulating samples were compromised in a manner similar to titration. Milk samples from cows that consistently produced NC milk were further studied at the udder quarter level. The coagulation properties of the quarter milk samples were not significantly different from those of the composite milk sample, showing that poor coagulation traits and noncoagulation traits of the composite milk were not caused by the milk quality of a single quarter. The milk samples exhibiting PC or NC properties were all of the κ-CN variant AA genotype, and contained casein micelles with a larger mean diameter and a lower fraction of κ-CN relative to total CN than milk with good coagulation properties. Interestingly, the relative proportions of different phosphorylation forms of α-CN differed between well-coagulating milk and PC or NC milk samples. The PC and NC milk samples contained a lower proportion of the 2 less-phosphorylated variants of α-CN (α(S1)-CN-8P and α(S2)-CN-11P) compared with samples of milk that coagulated well.

The immunomodulatory activities of four sialic acid-containing milk proteins (kappa-casein, glycomacropeptide, lactoferrin, and proteose peptone-3 component) were determined, and the role of sialic acid was evaluated. Two in vitro models were used: murine splenocyte proliferation, where the effect on LPS-, Con A-, and PHA-stimulated proliferation was studied, and cytokine production in LPS-stimulated murine dendritic cells (DC). All four proteins inhibited LPS-induced splenocyte proliferation, though to different degrees, and independently of sialic acid. kappa-Casein strongly inhibited PHA-induced proliferation and had a weak inhibitory effect on Con A-induced proliferation, whereas lactoferrin stimulated Con A-induced proliferation. kappa-Casein, glycomacropeptide, and lactoferrin differentially affected cytokine production by DC: kappa-casein significantly inhibited production of TNF-alpha, IL-10, -12, -6, and -1beta, independent of sialic acid, whereas less-marked effects of glycomacropeptide and lactoferrin were seen. These findings thus point to important immunosuppressive effects of some milk proteins and indicate that they may function via different mechanisms.

Photo-oxidation of cheese products has become an issue due to the fact that packaging of cheeses in transparent materials is very frequently used. The present study aimed to investigate the effect of fat content and availability of oxygen on light-induced oxidation in cheese, as we expected that the fat content would affect the oxidation pathways. Two different model cheeses with 5.4% and 18% fat were packed in air and in vacuum, respectively. The contents of protein (dityrosine and dimethyl disulphide (DMDS)) and lipid (lipid hydroperoxides, pentanal, hexanal and heptanal) oxidation products were significantly reduced in vacuum-packed cheeses compared to cheeses packed in air. Protein oxidation correlated to the concentration of lipids in the cheeses, and interactions between the lipid radicals and proteins seemed to be decisive for the generation of dityrosine, whereas the influence of lipid radicals on the generation of the DMDS seemed more ambiguous. The higher levels of dityrosine and DMDS in the cheese with a high fat content indicated that transfer of radicals from the lipids to the proteins occurred. Even though the generation of DMDS was reduced in vacuum-packed cheese when compared to cheese packed in air, DMDS was formed in vacuum-packed cheese.