Prediction of peptides in the fermented cocoa storage protein,with reference to the modelled 3D structure

The amino acid sequence and a model for the three-dimensional (3D) structure of the cocoa storage protein have been combined with available data from protease digestions to aid understanding of factors that contribute to the characteristic cocoa aroma. Data reported for the free amino acids liberated during extensive digestions, modelling the fermentation process, are compared to computer predictions. Since good agreement is obtained between experiment and theory for the free amino acids, the modelling can be used to study properties not yet reported experimentally. In particular, the peptides that remain after digestion are predicted, highlighting those sequences which may play important roles in the production of cocoa aroma. This approach could prove equally useful in understanding other such systems. © 1998 SCI.     

巴氏杜氏藻八氢番茄红素合成酶侧翼调控序列的克隆与分析

研究表明八氢番茄红素合成酶( PSY)是巴氏杜氏藻(Dunaliella bardawil)类胡萝卜素代谢途径中的第一个关键调节酶.本实验采用基于LAoPCR的基因组步移法分别设计两组基因特异引物pSP1-3及tSP1-3,克隆巴氏杜氏藻PSY( DbPSY)的启动子和终止子序列,并利用在线启动子分析软件分析其保守调控序列.最后利用生物信息学方法分析预测DbPSY的蛋白质结构.分析结果表明,DbPSY启动子具有两个保守调控序列:BOXLCOREDCPAL和GT1GMSCAM4,其中BOXLCOREDCPAL受紫外光诱导,上调下游基因的表达,GT1GMSCAM4受盐调控,促进下游基因的表达.蛋白结构分析表明,DbPSY的N端在邻近物种间具有较大的多样性.我们推测DbPSY的微调与启动子保守序列及蛋白质N端序列的多样性相关.     

Immunoproteomics to identify Staphylococcus aureus antigens expressed in bovine milk during mastitis

Staphylococcus aureus is an opportunistic pathogen affecting both human and animal species. An effective vaccine to prevent S. aureus bovine disease and transmission would have positive effects on animal well-being, food production, and human health. The objective of this study was to identify multiple antigens that are immunoreactive during udder colonization and disease for exploration as vaccine antigens to prevent bovine mastitis. Staphylococcus aureus produces several cell wall-anchored and surface-associated virulence factors that play key roles in the pathogenesis of mastitis. Many of these proteins are conserved between different strains of S. aureus and represent promising vaccine candidates. We used an immunoproteomics approach to identify antigenic proteins from the surface of S. aureus. The expression of cell wall and surface proteins from S. aureus was induced under low iron conditions, followed by trypsin extraction and separation by 2-dimensional electrophoresis. The separated proteins were blotted with antibodies from mastitic bovine milk and identified by liquid chromatography-mass spectrometry. Thirty-eight unique proteins were identified, of which 8 were predicted to be surface exposed and involved in S. aureus virulence. Two surface proteins, iron-regulated surface determinant protein C (IsdC) and ESAT-6 secretion system extracellular protein (EsxA), were cloned, expressed, and purified from Escherichia coli for confirmation of immune reactivity by ELISA. A PCR of 37 bovine S. aureus isolates indicated that the presence of esxA and isdC is conserved, and amino acid alignments revealed that IsdC and EsxA sequences are highly conserved. The immunoproteomics technique used in this study generated reproducible results and identified surface exposed and reactive antigens for further characterization.     

EVALUATION OF THE PROTEOLYTIC SUSCEPTIBILITY OF THREE LECTINS FROM SUBTRIBE DIOCLEINAE USING ENZYMATIC ACTION, HEAT TREATMENT AND MOLECULAR MODELING

The enzymatic digestion of the lectins from Canavalia brasiliensis, Dioclea grandiflora and Cratylia floribunda seeds was investigated by heat treatment and gel filtration chromatography. The potential sites of lectin cleavage by pepsin and trypsin was then determined by molecular modelling of the three-dimensional structure of D.grandiflora lectin. The lectins were shown to be susceptible to proteolytic cleavage using peptide mapping with the FPLC system. However, new peptides arose when hydrolysis was followed by heat treatment at 73C. According to the molecular model of D.grandiflora lectin, there are numerous sites for pepsin and trypsin proteolysis on the surface of the protein. It is suggested that when subjected to enzymatic action, the resulting peptides interact in order to retain the general folding of the protein. This is attributed, at least in part, to the numerous hydrogen bonds and hydrophobic interactions occurring within the inner protein structure. After heat treatment the additional cleavage sites become available and the lectins become completely inactivated .     

Enzymatic cross-linking of β-lactoglobulin in solution and at air-water interface: Structural constraints

Effective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular structure were determined at pH 6.8, 7.5 and 9.0 before and after high-temperature heat treatment. The conformational change was linked to efficiency of protein cross-linking. BLG was not susceptible to TrTyr without heat treatment. TG, however, induced inter-molecular cross-links at pH 7.5 and 9.0. After the heat treatments, BLG molecules adopted a molten-globule-like conformation. Both of the enzymes were able to form inter-molecular cross-links between heat-denatured BLG molecules. Electrophoretic mobility and broadness of the oligomer bands created by both enzymes on SDS-PAGE gels showed differences which were linked to the availability and number of target amino acid residues. Evidence for intra-molecular cross-linking was obtained. Once adsorbed to air/water interface, BLG formed a viscoelastic surface film which was characterized by surface shear rheology. Application of cross-linking enzymes under a dense layer of BLG molecules at the interface led to decreasing G′ with time. Intra-molecular links were most probably favored against inter-molecular on packed BLG layer leading to constrained molecules. Results in general emphasize the importance of structural and colloidal aspects of protein molecules in controlling inter/intra-molecular bond formation by cross-linking enzymes.     

DfrA12蛋白的结构分析及同源建模

本文通过分析DfrA12蛋白的初级结构和空间构型,为进一步了解该蛋白的结构与功能提供了理论依据。应用Expasy、TMHMM2.0、SignalP 4.0、SOPMA、GENO3D等生物信息学软件对DfrA12蛋白的初级和高级结构进行分析和预测。结果显示,DfrA12蛋白由165个氨基酸组成,富含α螺旋和无规则卷曲结构,不形成跨膜区域,无信号肽,定位于细胞内膜。应用同源建模的方法成功构建了该蛋白的三维模型。本研究为深入探讨DfrA12蛋白的结构与生物学功能奠定了理论基础。     

Characterization of carbohydrate structures of bovine MUC15 and distribution of the mucin in bovine milk

The present work reports the characterization of carbohydrate structures and the distribution of the newly identified mucin MUC15, a highly glycosylated protein associated with the bovine milk fat globule membrane (MFGM). Distribution of MUC15 was investigated in various fractions of bovine milk by densitometric scanning of Western blots. In raw milk, MUC15 was shown to constitute 0.08% (wt) of the protein and approximately 1.5% (wt) of the MFGM-associated proteins. Surprisingly, this study showed that in addition to the fat-containing fractions, such as MFGM and buttermilk, MUC15 was present in nonfat-containing fractions as well, such as skim milk and whey. Compositional and structural studies of the carbohydrates of bovine milk MUC15 showed that the glycans are composed of fucose, galactose, mannose, N-acetylgalactosamine, N-acetylglycosamine, and sialic acid. The carbohydrate was shown to constitute 65% of the total molecular weight, and the molar ratios of the individual sugars to protein of the O-linked glycans were determined. The glycan structures of MUC15 were further studied by enzymatic deglycosylation experiments using different endo- and exoglycosidases as well as a panel of lectins. The N-linked glycans were shown to contain mainly hybrid-type N-glycans. In addition, the N-glycans were shown to be sialylated and contain terminal poly-lactosamine structures. The O-linked glycans were found to constitute some unsubstituted Core-1 structures and a substantial number of sialylated Core-1 O-linked glycans. By comparing the results of peanut agglutinin lectin binding, enzymatic deglycosylation, and monosaccharide composition analysis, we concluded that bovine MUC15 also contains more complex O-glycans containing high amounts N-acetylglucosamine residues. Furthermore, a small subset of the O-linked glycans is decorated with lactosamine on their terminal ends.     

Enhanced antioxidant activity of Monascuspilosus fermented products by addition of ginger to the medium

The fermented products of Monascus sp. are known for their antihypercholesterolaemic effects, however, their antioxidant activities are different from those of many plant-derived foods. To evaluate the effect of ginger addition into the medium on the antioxidant activity of Monascuspilosus fermented products, we cultured uninoculated PDB medium (PDB), inoculated PDB medium (MP), uninoculated ginger-containing medium (PDBG), and inoculated ginger-containing medium (MPG). The broth and mycelia were collected, freeze-dried, and extracted to evaluate their free radical scavenging activities, inhibition of peroxidation, phenolic content, inhibition of DNA damage, cellular antioxidant activity, and expression of the antioxidant enzymes. The results showed that MPG had significantly higher antioxidant activity than PDB, MP, and PDBG at all fermentation time points. Moreover, the fermentation process significantly increased the antioxidant activities of MPG. After the inherent level of antioxidant capacity was increased, the modified M. pilosus fermented product demonstrated a higher anti-atherosclerotic value than the unmodified product.     

脱氮硫杆菌ATCC25259 SQR蛋白及突变体的结构分析与活性研究

本文研究了通过Discovery Studio 3.5利用同源建模法构建了脱氮硫杆菌ATCC25259的硫化物:醌氧化还原酶(Sulfide:quinone oxidoreductase,SQR)野生型蛋白及突变体蛋白模型,通过GROMACS 5.1.2对所有模型进行分子力学及分子动力学的优化,使蛋白模型处于能量较低且结构稳定的状态。使用PROCHECK,Verify 3D和Pro SA三种模型评价方法对模型进行评价,表明蛋白模型具有较高的合理性。使用该蛋白模型计算蛋白相互作用、SAS及能量值。将构建好的SQR及突变体的表达载体转入大肠杆菌BL21(DE3)诱导表达分子量约65 ku的蛋白。使用镍柱亲和层析纯化经大量表达含有6×His标签的野生型与突变体蛋白,采用已经建立的SQR活性测定方法,进行酶活性测定实验,结果表明突变体酶活性较低。从模拟计算与实验验证两方面说明SQR C端α螺旋结构对蛋白的结构稳定性具有重要影响,蛋白结构稳定性降低,从而酶活性降低。     

Properties of cellulose-degrading enzymes from Aspergillus oryzae and their contribution to material utilization and alcohol yield in sake mash fermentation

Four cellulose-degrading enzymes were identified in a solid-state culture of Aspergillus oryzae. The three major enzymes were purified and named Cel-1, Cel-2, and Cel-3, respectively. The molecular weights were determined to be 62, 120, and 34 kDa, respectively. The optimum temperature of Cel-3 activity was higher than that of the other enzymes. An acidic pH was found to be more suitable for Cel-1 activity than for the other enzymes, and Cel-3 was more stable under acidic conditions than the other two. These properties and the results of a protein homology search for N-terminal amino acid sequences suggest that Cel-1 and Cel-3 correspond to the previously isolated endo-1,4-beta-glucanase CelB and CelA, respectively. The analysis of substrate specificity suggested that Cel-2 is likely to be beta-glucosidase. The effect of Cel-1, Cel-2, and Cel-3 on the sake mash fermentation was determined and it was found that Cel-2 markedly improved material utilization and alcohol yield in sake mash fermentation.     

Cloning and characterization of the lactate-specific inducible gene KlCYB2, encoding the cytochrome b(2) of Kluyveromyces lactis

In yeast the utilization of lactate requires two enzymes, the D and L-lactate ferricytochrome c oxidoreductase (D and L-LCR), which stereospecifically oxidize D- and L-lactate to pyruvate. These enzymes are nuclearly encoded and localized in mitochondria. In the yeast Kluyveromyces lactis, a mutant devoid of D- and L-LCR activities and unable to grow on racemic lactate was isolated. Transformation of the mutant with a K. lactis genomic library allowed the isolation of the KlCYB2 gene, restoring the growth on lactate and the L-LCR activity. The KlCYB2 gene and its flanking regions were sequenced (Accession No. AJ243324; EMBL/GenBank databases). The deduced amino acid sequence is highly homologous to the corresponding Saccharomyces cerevisiae and Hansenula anomala protein sequences previously characterized. The homology is missed in the N-terminal region, corresponding to the presequence cleaved during import into mitochondria. Analysis of KlCYB2 gene expression indicated that, in contrast to S. cerevisiae, the major regulatory feature is induction by lactate.     

Folic acid complexes with human and bovine serum albumins

The interaction of folic acid with human serum (HSA) and bovine serum albumins (BSA) at physiological conditions, using constant protein concentration and various folic acid contents was investigated. FTIR, UV–visible and fluorescence spectroscopic methods as well as molecular modelling were used to analyse folic acid binding sites, the binding constant and the effect on HSA and BSA stability and conformations. Structural analysis showed that folic acid binds HSA and BSA via both hydrophilic and hydrophobic contacts with overall binding constants of K_{folic acid–HSA} = 8.1 (±0.5) × 10⁴ M⁻¹ and K_{folic acid–BSA} = 1.0 (±0.3) × 10⁵ M⁻¹. The number of bound acid molecules per protein was 1.7 (±0.4) for HSA and 1.5 (±0.3) for BSA complexes. Molecular modelling showed participation of several amino acids in folic acid–protein complexes stabilised by hydrogen bonding network. Folic acid complexation altered protein secondary structure by major reduction of α-helix from 59% (free HSA) to 35% (acid-complex) and 62% (free BSA) to 25% (acid-complex) with an increase in random coil, turn and β-sheet structures indicating protein unfolding. The results suggest that serum albumins might act as carrier proteins for folic acid in delivering it to target molecules.     

Identification of an Angiotensin I-converting Enzyme Inhibitory Peptides from Protein Hydrolysates by a Soybean Protease and the Antihypertensive Effects of Hydrolysates in 4 Spontaneously Hypertensive Model Rats

ABSTRACT: Our previous study demonstrated that, because of its substrate specificity, protein hydrolysates by protease D3, which is originated from soybean, exhibited the prominent property of being less bitter than other enzymatic hydrolysates. In the 1st experiment in this series, angiotensin I-converting enzyme (ACE) inhibitory peptides from soy protein hydrolysate by D3 were identified by the establishment of a novel and effective peptide identification method. The amino acid sequences of candidate ACE inhibitory peptides were determined by electrospray ionization mass/mass spectrometry (MS/MS) analysis after rough purification of the samples with gel filtration chromatography and reverse-phase chromatography. Some of the candidate peptides had amino acid sequences that showed homology with those of the reported ACE inhibitory peptides. Then, 8 types of novel candidate peptides were synthesized according to a solid-phase method, and their ACE inhibitory activity was confirmed as the IC₅₀ value. The most potent inhibitor was NWGPLV (IC₅₀= 21 μ M ). In the 2nd experiment, the antihypertensive activity of protein hydrolysates by D3 was investigated in spontaneously hypertensive model rats (SHRs). The dose-dependent antihypertensive effect of soy protein hydrolysate was confirmed, and systolic blood pressure was significantly reduced after the oral administration of doses exceeding 100 mg/kg. Casein hydrolysate was found to have the most potent effects on suppressing blood pressure as well as ACE inhibitory activity among the various food protein hydrolysates studied because of the primary structure of casein. These results indicate that hydrolysates by D3 could be a useful food ingredient because it has the physiological function (antihypertensive activity).     

Dromedary camel milk proteins,a source of peptides having biological activities – A review

Many useful properties are assigned to camel (Camelus dromedarius) milk, which is traditionally used for the treatment of tuberculosis, gastroenteritis, and allergy in many countries. Some amino acid sequences, which are encrypted in the camel proteins, may play a beneficial role in human health once they are released from milk either in vivo during normal digestion or by proteolysis with purified enzymes or during bacterial fermentation. Similar to the bovine milk counterparts, camel milk bioactive peptides may display a variety of potential activities that were almost always unveiled from in vitro analyses: anti-microbial, anti-oxidative, anti-hypertensive, anti-inflammatory, and immunomodulatory activities. Today, there is a growing interest for bioactive peptides generated from camel milk. This paper reviews available data on the potential biological activities of the camel milk proteins and their peptides liberated either during milk fermentation with proteolytic bacterial strains or by enzyme hydrolysis with specific proteases or simulated gastro-intestinal digestion.     

Construction of an additional metal-binding site in human metallothionein-2

We have constructed a new metal-binding site in the human metallothionein-2 (hMT-2), using the protein as a scaffold to investigate the structure and function of metal-binding. Potential metal-binding sites were designed within hMT-2 on the basis of structures generated by homology modeling. Amino acid residues D11, C13, C26 and S28 in the beta-domain of hMT-2 (hMT-2beta) were found, by computer search, to form a potential tetrahedral Cys4 metal-binding site. Six mutant proteins were constructed with the following amino acid substitutions: D11C, S28C and D11C/S28C in hMT-2 and the same mutations in hMT-2beta, respectively. These single-mutant and double-mutant proteins bound one gram atom of cadmium or zinc ions per gram molecule of protein more than the corresponding wild-type proteins. The circular dichroism spectra suggested that the structures of the single-mutant proteins that bound Cd or Zn were similar to that of the D11C/S28C double-mutant proteins. To evaluate the metal-binding affinity of the mutant proteins, we performed pH titrations of wild-type and mutant proteins. The stability with changes in pH of all the mutant proteins was higher than that of the wild-type proteins, and that of the double-mutant D11C/S28C protein was highest. Consequently, it appears that we were able to create novel proteins that bound metal ions at high density and with high affinity.     

甲醇芽孢杆菌凝乳酶的重组表达及其结构特性

为进一步了解微生物凝乳酶的结构特性,根据GenBank数据库中甲醇芽孢杆菌凝乳酶（I3EB99）的氨基酸序列和大肠杆菌密码子的偏爱性,设计合成此凝乳酶的全基因序列,构建原核表达载体,通过BL21（DE3）表达其融合蛋白,将获得的融合蛋白进行His标签特异性亲和纯化,并利用生物信息学方法研究凝乳酶的三维空间立体结构。结果表明,重组表达的甲醇芽孢杆菌凝乳酶质量浓度为0.7 mg/mL,凝乳活力为（15 870±1.17）SU/g,蛋白水解活力为（263.81±0.94）U/g,凝乳活力与蛋白水解活力比值为60.16,符合干酪生产加工的要求。结构特性研究表明,经重组表达后的甲醇芽孢杆菌凝乳酶呈现疏水特性,具有跨膜结构和信号肽,二级结构中α-螺旋少于β-折叠,在分离纯化过程中结构不稳定易降解,该凝乳酶与来自甲醇芽孢杆菌的一种未知蛋白酶是同源蛋白,高级结构与PDB蛋白数据库中的模板蛋白2ra1.1.A相似度最高。通过对甲醇芽孢杆菌凝乳酶结构特性的研究,为深入分析该凝乳酶作用机理及其功能性奠定了理论基础。     

Proteomic and peptidomic insights on myofibrillar protein hydrolysis in a sausage model during fermentation with autochthonous starter cultures

The hydrolysis of myofibrillar proteins during fermentation of sausage models by an autochthonous starter culture was investigated. In order to provide a whole map of the generated products, proteomic and peptidomic were used and complemented with the amino acid profile. Beaker sausages (BS) were used as models which were inoculated or not with Lactobacillus curvatus CRL705 and Staphylococcus vitulinus GV318 as starter cultures. The hydrolysis of actin, myosin light chain 1/3 (MLC 1/3), myosin regulatory light chain-2 (MRLC-2) and myosin heavy chain (MHC) was evidenced by two-dimensional gel electrophoresis (2-DE). In addition, a total of 33 peptides arisen from troponin T, MRLC-2 and particularly from actin were identified by LC–MS/MS. These results showed that the starter culture significantly enhanced the proteolysis of the proteins named above, even when the endogenous enzymes induced a clear breakdown. L. curvatus CRL705 highly enriched both peptide pattern and amino acid concentrations. When the autochthonous starter culture was inoculated, although proteolysis was remarkably reinforced, a reduction in peptide and amino acid composition was observed. Regarding actin primary structure, three regions of this protein were highly susceptible to degradation by the starter culture. Additionally, the essential role of exopeptidases – from meat and bacteria – in diversity of actin peptides during fermentation was shown. This study improved the knowledge of the proteolysis of myofibrillar proteins and the involved enzymes, as well as, completed the previously reported degradation of sarcoplasmic proteins by the same autochthonous starter culture. The singular peptides and amino acids pattern generated might contribute to the uniqueness of produced fermented sausages while they may be used as quality markers.     

Three-dimensional molecular modeling of bovine caseins: alpha s1-casein.

Structures derived from X-ray crystallography are extremely important in elucidating functional relationships for many proteins. However, the caseins of bovine milk are one class of noncrystallizable proteins. The complete primary and partial secondary structures of these proteins are known, but homologous proteins of known crystallographic structure cannot be found. Therefore, sequence-based predictions of secondary structure were made and adjusted to conform with global secondary structures determined by Raman spectroscopy. With this information, a three-dimensional structure for alpha s1-casein was constructed using molecular modeling programs. The predicted structure of alpha s1-casein contains a hydrophobic and a hydrophilic domain, which are connected by a segment of alpha-helix. This unrefined structure shows good agreement with global biochemical and chemical information concerning alpha s1-caseins A, B, and C.     

MasterCAM在零件数控加工编程中的应用

针对复杂曲面零件形状不规则、造型复杂、不易加工等问题,结合泵体端盖底板的设计与加工模拟,运用MasterCAM软件的造型技术和数控编程功能,建立了零件的三维模型,生成了零件的粗、精加工走刀路径,实现了实体的加工模拟,并通过后置处理生成NC代码,为类似零件的数控编程加工提供了一种方法和依据.