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Proteinase K (proteinase + k)
Selected AbstractsHigh-resolution structure of proteinase K cocrystallized with digalacturonic acidACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Steven B. Larson Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32,Å resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions. [source] Influence of the SCGE protocol on the amount of basal DNA damage detected in the Mediterranean mussel, Mytilus galloprovincialisENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 8 2006Nicola Machella Abstract Genotoxicity studies using the single cell gel electrophoresis (SCGE) assay indicate that basal levels of DNA strand breaks (SBs) in marine invertebrates are higher and more variable than those in marine vertebrates. This elevated level of DNA damage was attributed to a large number of alkali-labile sites, which are characteristic of the tightly-packaged DNA in invertebrate cells. To investigate if altering the SCGE protocol can artificially modulate high levels of SBs, SCGE experiments were performed on haemocytes from the Mediterranean mussel (Mytilus galloprovincialis) using proteinase K (PK) digestion in combination with assay buffers containing various concentrations of EDTA. In addition, the effects of Trolox® (soluble antioxidant) and aurintricarboxylic acid (ATA; inhibitor of Ca2+/Mg2+ -dependent nucleases) also were tested. The levels of SBs in M. galloprovicialis cells were compared with SBs in cells from a terrestrial mollusk (the snail Helix aspersa), and a teleost fish (the seabass Dicentrarchus labrax). The integrity of M. galloprovincialis DNA isolated with phenol extractions using EDTA, Trolox, and ATA was further assayed by gel electrophoresis. High SBs in mussel cells were reduced by combining EDTA with PK digestion, or using Trolox® or ATA during cell processing for the SCGE assay. Snails and seabass had lower levels of SBs in the SCGE assay, and the levels were not affected by the protocol modifications. Adding EDTA, Trolox®, or ATA to phenol extractions of M. galloprovincialis genomic DNA also reduced the extent of DNA fragmentation. These results suggest that the internal fluids of M. galloprovincialis may increase the basal levels of DNA SBs through oxidative and/or enzyme-mediated pathways. M. galloprovincialis is used extensively as a sentinel species for assessing the genotoxic hazard of marine pollutants. Our data suggest that the SCGE protocol should be carefully considered when assessing DNA damage in these species. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source] Stepwise proteolytic removal of the , subdomain in ,-lactalbuminFEBS JOURNAL, Issue 15 2001The protein remains folded, can form the molten globule in acid solution Bovine ,-lactalbumin (,-LA) is an ,/, protein which adopts partly folded states when dissolved at low pH (A-state), by removal of the protein-bound calcium at neutral pH and low salt concentration (apo-state), as well as in aqueous trifluoroethanol. Previous spectroscopic studies have indicated that the A-state of ,-LA at pH 2.0, considered a prototype molten globule, has a native-like fold in which the helical core is mostly retained, while the , subdomain is less structured. Here, we investigate the conformational features of three derivatives of ,-LA characterized by a single peptide bond fission or a deletion of 12 or 19/22 amino-acid residues of the , subdomain of the native protein (approximately from residue 34 to 57). These ,-LA derivatives were obtained by limited proteolysis of the protein in its partly folded state(s). A nicked ,-LA species consisting of fragments 1-,3,40 and 41,123 (nicked-LA) was prepared by thermolytic digestion of the 123-residue chain of ,-LA in 50% (v/v) aqueous trifluoroethanol. Two truncated or gapped protein species given by fragments 1,40 and 53,123 (des,1-LA) or fragments 1,34 and 54-,57,123 (des,2-LA) were obtained by digestion of ,-LA with pepsin in acid or with proteinase K at neutral pH in its apo-state, respectively. The two protein fragments of nicked or gapped ,-LA are covalently linked by the four disulfide bridges of the native protein. CD measurements revealed that, in aqueous solution at neutral pH and in the presence of calcium, the three protein species maintain the helical secondary structure of intact ,-LA, while the tertiary structure is strongly affected by the proteolytic cleavages of the chain. Temperature effects of CD signals in the far- and near-UV region reveal a much more labile tertiary structure in the ,-LA derivatives, while the secondary structure is mostly retained even upon heating. In acid solution at pH 2.0, the three ,-LA variants adopt a conformational state essentially identical to the molten globule displayed by intact ,-LA, as demonstrated by CD measurements. Moreover, they bind strongly the fluorescent dye 8-anilinonaphthalene-1-sulfonate, which is considered a diagnostic feature of the molten globule of proteins. Therefore, the , subdomain can be removed from the ,-LA molecule without impairing the capability of the rest of the chain to adopt a molten globule state. The results of this protein dissection study provide direct experimental evidence that in the ,-LA molten globule only the , domain is structured. [source] Insect silk contains both a Kunitz-type and a unique Kazal-type proteinase inhibitorFEBS JOURNAL, Issue 7 2001Xavier Nirmala Insect silk is made up of structural fibrous (fibroins) and sticky (sericins) proteins, and contains a few small peptides of hitherto unknown functions. We demonstrate that two of these peptides inhibit bacterial and fungal proteinases (subtilisin, proteinase K and pronase). These ,silk proteinase inhibitors' 1 and 2 (SPI 1 and 2) are produced in the middle section of the silk-secreting glands prior to cocoon spinning and their production is controlled at transcription level. The full length cDNA of pre-SPI 1 contains 443 nucleotides and encodes a peptide of 76 amino-acid residues, of which 20 make up a signal sequence. The mature SPI 1 (6056.7 Da, 56 residues) is a typical thermostable Kunitz-type proteinase inhibitor with Arg in P1 position. The cDNA of pre-SPI 2 consists of 260 nucleotides and yields a putative secretory peptide of 58 amino-acid residues. The functional SPI 2 (3993 Da, 36 residues) is a single-domain Kazal-type proteinase inhibitor with unique structural features: free segment of the N-terminus is reduced to a single amino-acid residue, lack of CysI and CysV precludes formation of the A-ring and provides increased flexibility to the C-ring, and absence of several residues around the normal position of CysV shortens and changes the , helix segment of the protein. The structure reveals that the length and arrangement of the B-ring, including exposure of the P1 residue, and the position of the C-terminus relative to the B-loop, are essential for the activity of the Kazal-type inhibitors. [source] Extensive deproteinization of Dictyostelium discoideum RNase P reveals a new catalytic activityFEBS JOURNAL, Issue 7 2001Constantinos Stathopoulos Nuclear Dictyostelium discoideum RNase P was subjected to vigorous deproteinization procedures. After treatment with proteinase K followed by phenol extraction of samples containing D. discoideum RNase P activity, a new enzymatic activity was recovered. The proteinase K/phenol/SDS treated enzyme cleaves Schizossacharomyces pombe tRNAser (supS1), D. discoideum tRNASer and tRNALeu precursors several nucleotides upstream of the cleavage site of RNase P, liberating products with 5,-hydroxyl ends. This activity seems to be associated with one or two RNA molecules copurifying with D. discoideum RNase P activity as judged by its inhibition in the presence of micrococcal nuclease, which is in contrast to its resistance to proteinase K/phenol/SDS treatment. [source] Purification and characterization of two bacteriocins produced by lactic acid bacteria isolated from Mongolian airagJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2006B. Batdorj Abstract Aims:, The aim of this study was to isolate and identify bacteriocin-producing lactic acid bacteria (LAB) issued from Mongolian airag (traditional fermented mare's milk), and to purify and characterize bacteriocins produced by these LAB. Methods and Results:, Identification of the bacteria (Enterococcus durans) was carried out on the basis of its morphological, biochemical characteristics and carbohydrate fermentation profile and by API50CH kit and 16S rDNA analyses. The pH-neutral cell-free supernatant of this bacterium inhibited the growth of several Lactobacillus spp. and food-borne pathogens including Escherichia coli, Staphylococcus aureus and Listeria innocua. The antimicrobial agent (enterocin A5-11) was heat stable and was not sensitive to acid and alkaline conditions (pH 2,10), but was sensitive to several proteolytic enzymes. Its inhibitory activity was completely eliminated after treatment with proteinase K and , -chymotrypsin. The activity was however not completely inactivated by other proteases including trypsin and pepsin. Three-step purification procedure with high recovery yields was developed to separate two bacteriocins. The applied procedure allowed the recovery of 16% and 64% of enterocins A5-11A and A5-11B, respectively, present in the culture supernatant with purity higher than 99%. SDS-PAGE analyses revealed that enterocin A5-11 has a molecular mass of 5000 Da and mass spectrometry analyses demonstrates molecular masses of 5206 and 5218 Da for fractions A and B, respectively. Amino acid analyses of both enterocins indicated significant quantitative difference in their contents in threonine, alanine, isoleucine and leucine. Their N -termini were blocked hampering straightforward Edman degradation. Conclusions:, Bacteriocins A5-11A and B from Ent. durans belong to the class II of bacteriocins. Significance and Impact of the Study:, Judging from molecular masses, amino acid composition and spectrum of activities, bacteriocins A5-11A and B from Ent. durans show high degree of similarity with enterocins L50A and L50B isolated from Enterococcus faecium (Cintas et al. 1998, 2000) and with enterocin I produced by Ent. faecium 6T1a, a strain originally isolated from a Spanish-style green olive fermentation (Floriano et al. 1998). [source] Characterization of spore appendages from Bacillus cereus strainsJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2001T. Stalheim Aims:,Further characterization and comparison of spore appendages from Bacillus cereus strains. Methods and Results:,Appendages were isolated from 10 B. cereus strains from the food industry and food-borne outbreaks. The appendage proteins were dissolved in sample buffer containing 2% SDS and 5% mercaptoethanol at 100°C, and subjected to SDS-PAGE. None of the appendages showed identical protein patterns. Western blots, using antibodies raised against a 3·5 kDa appendage protein, showed that the majority of the appendage proteins reacted with the antibody. Removal of the appendages by sonic treatment of the spores did not alter their heat resistance. The appendages were digested by proteinase K, pepsin, and the enzymes in the detergent Paradigm 10, but not by trypsin or chymotrypsin. Spore adhesion to stainless steel was scarcely affected by removal of the appendages. Digestion of adhered intact spores (with appendages) with Paradigm 10 showed a high degree of variation. Conclusions:,Spore appendages from B. cereus are complex proteinaceous structures that differ among strains. Significance and Impact of the Study:,Information about spore appendages and their involvement in spore adhesion is crucial for improving cleaning methods used for control of bacterial spores in the food industry. [source] Enzymatic degradation of poly(L -lactic acid) fibers: Effects of small drawingJOURNAL OF APPLIED POLYMER SCIENCE, Issue 3 2007Hideto Tsuji Abstract The enzymatic degradation of poly(L -lactic acid) (PLLA) fibers with different low draw ratios (1.0, 1.2, and 1.4 times) was investigated in tris-HCl buffer solution (pH = 8.6) with proteinase K by the use of gravimetry, scanning electron microscopy (SEM), gel permeation chromatography (GPC), differential scanning calorimetry (DSC), and tensile testing. Surprisingly, even the small drawings (1.2 and 1.4 times) disturbed the proteinase K catalyzed enzymatic degradation of the PLLA fibers. This should have been because the enzyme could not attach to the extended (strained) chains in the amorphous regions of the uniaxially oriented PLLA fibers or could not catalyze the cleavage of the strained chains. The accumulation of crystalline residues formed as a result of selective cleavage, and removal of the amorphous chains was not observed, even for as-spun PLLA fibers. This indicated the facile release of formed crystalline residues from the surface of the as-spun PLLA fibers during enzymatic degradation. Such release may have been because the crystalline regions of the as-spun PLLA fibers were oriented with their c axis parallel to the machine direction, as reported for biaxially oriented PLLA films. Gravimetry, SEM, and tensile testing could trace the enzymatic degradation of the PLLA fibers, although the enzymatic degradation of the PLLA fibers was untraceable by GPC and DSC. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 2064,2071, 2007 [source] ISOLATION AND PARTIAL CHARACTERIZATION OF A NOVEL BACTERIOCIN PRODUCED BY LACTOCOCCUS LACTIS SSP.JOURNAL OF FOOD SAFETY, Issue 1 2007LACTIS MC3 ABSTRACT This work presents the isolation and partial characterization of a new lactococcal bacteriocin produced by Lactococcus lactis ssp. lactis MC38. The bacteriocin demonstrated broad spectrum of inhibition activity against both pathogenic and food spoilage organisms, and various lactic acid bacteria. This antimicrobial substance appeared to be proteinaceous because its activity was completely inactivated by proteinase K and ,-chymotrypsin. It was heat and pH stable. The apparent molecular mass of the purified bacteriocin, determined by sodium dodecyl sulfate,polyacrylamide gel electrophoresis, was 8.0 kDa. The amino acid composition of the studied bacteriocin was found to be quite different from known lactococcal bacteriocins. The calculation of the number of amino acid residues in the bacteriocin molecule revealed that it contained 62 amino acids. [source] SIMPLE METHOD FOR RNA PREPARATION FROM CYANOBACTERIA,JOURNAL OF PHYCOLOGY, Issue 5 2006Byung-Hyuk Kim A simple and rapid method is presented for the preparation of RNA from various cyanobacteria. Unlike other methods that require a lysis solution, lysozymes, or proteinase K, the proposed method, called the bead,phenol,chloroform (BPC) method, uses silica/zirconia beads, phenol, and chloroform to break the cells and extract RNA more efficiently. Experiments confirm that the BPC method can successfully isolate total RNA from various cyanobacterial strains without DNA contamination, and the extracted RNA samples have a relatively high purity, concentration, and yield. Furthermore, the BPC method is more rapid, simple, and economical when compared with previously reported methods. [source] Synthesis of poly(lactide- ran -MOHEL) and its biodegradation with proteinase KJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 9 2001Hiroyuki Shirahama Abstract Homopoly(L -lactide) and homopoly(D,L -lactide) were almost inert for biodegradation with tricine buffer or normal enzymes such as bromelain, pronase, and cholesterol esterase but biodegradable with proteinase K. Significantly enhanced biodegradation was observed when an optically active (R)- or (S)-3-methyl-4-oxa-6-hexanolide (MOHEL) unit was introduced into poly(L -lactide) [poly(L -LA)] or poly(D,L -lactide) [poly(D,L -LA)] sequences. Poly[L -LA- ran -(R)-MOHEL] in molar ratios of 86/14 to 43/57 showed good biodegradability that was independent of crystallinity. The biodegradation of polymers with proteinase K increased in the following order: poly[D,L -LA- ran -(R)-MOHEL] > poly[L -LA- ran -(R)-MOHEL] > poly[D,L -LA- ran -(S)-MOHEL] > poly[L -LA- ran -(S)-MOHEL] > poly(R)-MOHEL > poly(D,L -LA). The number-average molecular weight, molecular weight distribution, glass-transition temperature, and melting temperature did not change before and after the biodegradation of poly[L -LA- ran -(R)-MOHEL], indicating that the degradation occurred from the polymer surface. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1374,1381, 2001 [source] Enzymatic Degradation of Biodegradable Polyester Composites of Poly(L -lactic acid) and Poly(, -caprolactone)MACROMOLECULAR MATERIALS & ENGINEERING, Issue 10 2006Hideto Tsuji Abstract Summary: Two different types of biodegradable polyester composites, PLLA fiber-reinforced PCL and PCL/PLLA blend films were prepared at PCL/PLLA ratio of 88/12 (w/w), together with pure PCL and PLLA films. Their enzymatic degradation was investigated by the use of Rhizopus arrhizus lipase and proteinase K as degradation enzymes for PCL and PLLA chains, respectively. In the FRP film, the presence of PLLA fibers accelerated the lipase-catalyzed enzymatic degradation of PCL matrix compared with that in the pure PCL film, whereas in the blend film, the presence of PLLA chains dissolved in the continuous PCL-rich domain retarded the lipase-catalyzed enzymatic degradation of PCL chains. In contrast, in the FRP film, the proteinase K-catalyzed enzymatic degradation of PLLA fibers was disturbed compared with that of the pure PLLA film, whereas in the blend film, the proteinase K-catalyzed enzymatic degradation rate of particulate PLLA-rich domains was higher than that of pure PLLA film. The reasons for aforementioned enhanced and disturbed enzymatic degradation are discussed. Normalized PCL weight loss of pure PCL, FRP, and blend films as a function of Rhizopus arrhizus lipase-catalyzed enzymatic degradation time. [source] An , -amylase (At4g25000) in Arabidopsis leaves is secreted and induced by biotic and abiotic stressPLANT CELL & ENVIRONMENT, Issue 4 2007ELIZABETH A. DOYLE ABSTRACT Leaves are reported to contain a secreted , -amylase that accumulates during senescence or after biotic or abiotic stress; however, a gene encoding this enzyme has not been described. Because a secreted amylase is isolated from plastidic starch, the function of this enzyme is difficult to predict, but circumstantial evidence suggests that it may degrade starch after cell death. The Arabidopsis thaliana genome contains three , -amylase genes, one of which, AMY1 (At4g25000), has a putative signal sequence suggesting that the protein may be secreted. Two independent T-DNA insertion mutants in AMY1 lacked an amylase band on starch zymograms, which was previously named ,A1'. Washed leaf protoplasts contained reduced A1 activity suggesting that the enzyme is secreted. Native AMY1, fused to a weakly fluorescent form of GFP, was sensitive to proteinase K infiltrated into leaf apoplastic spaces, while a cytosolic form of GFP was unaffected until cell breakage, confirming that the AMY1 protein is secreted. Amylase A1 was transcriptionally induced in senescing leaves and in leaves exposed to heat stress, treated with abscisic acid or infected with Pseudomonas syringae pv. tomato expressing avrRpm1. The A1 amylase was also extremely heat resistant and its expression was up-regulated in cpr5-2, an activated defence response mutant. [source] Multiple genotyping in bovine pre-implantation embryos with whole genome amplificationANIMAL SCIENCE JOURNAL, Issue 5 2008Hiroki HIRAYAMA ABSTRACT This study examined genetic diagnosis using whole genome amplification (WGA) in bovine embryos. The first experiment was conducted to compare the WGA efficiency of primer extension preamplification-PCR (PEP-PCR) and multiple displacement amplification (MDA), and to optimize the DNA extraction method. The sensitivity of SRY -specific PCR from MDA products increased when DNA of fibroblasts was extracted by a NaOH treatment instead of the conventional method (heat treatment). The detectability of SRY from PEP-PCR products was lower than that in MDA regardless of the DNA extraction method (proteinase K or NaOH treatment). Sexing and genotyping were performed using MDA products from embryo biopsy. The accuracy of PCR-based and LAMP-based sexing was 100% regardless of the amounts of biopsy. Genotyping of CL16, BND3, SCD and F11 in MDA products from 10 to 20% of trophectoderm was successful 97, 97, 95 and 95% of the time, respectively, but reduced biopsy amount (<10% of trophectoderm) decreased the accuracies (33,83%). Microsatellite markers were analyzed using MDA products from 10 to 20% of trophectoderm. In eight out of 16 microsatellites, genotypes were not contradictory among the dam, sire and embryos. In the other eight microsatellites, the inconsistency rates were 17,83%. These results indicate that MDA is useful for multiple genetic diagnoses in bovine embryos. [source] Serotonin content of normal and inflamed appendix: a possible role of serotonin in acute appendicitis,APMIS, Issue 11 2008MOHAMMAD VASEI The appendix is lined by a mucosa which has many neuroendocrine cells containing serotonin. Local release of serotonin can act as a mediator of inflammation. In this study we explored the serotonin content of the neuroendocrine cells of the appendixes removed for clinical diagnosis of appendicitis. Appendix specimens were divided into three groups: Acute appendicitis (AA), non-appendicitis (NA), and follicular hyperplasia (FH). Normal appendix specimens from patients undergoing elective abdominal surgery were used as the control group (NL). All sections were exposed to proteinase K, incubated with anti-serotonin, chromogranin A, and synaptophysin antibodies, and treated with the LSAB kit. Polygonal cells were seen within the crypt epithelium (enterochromaffin cell, EC) and within the lamina propria (subepithelial neuroendocrine cell, SNC). In AA, only 16 cases (64%) showed serotonin staining in non-destructed glands. There was a significant reduction in the number of ECs in AA compared to the FH (96%), NA (100%) and NL (100%) groups (P<0.001). Chromogranin and synaptophysin immunostaining also showed a significant reduction in the number of ECs in AA compared with the other three groups (P<0.001). SNC serotonin reactivity was lower in the AA group compared with the other groups (p<0.001). The inflamed appendix is markedly depleted of serotonin in the epithelium and lamina propria. Local serotonin release from ECs and SNCs in the appendix may act as an inflammatory mediator in appendicitis and is likely to be the source of raised blood serotonin in AA. [source] The magic triangle goes MAD: experimental phasing with a bromine derivativeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Tobias Beck Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br,K edge was successfully carried out. Radiation damage to the bromine,carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out. [source] High-resolution structure of proteinase K cocrystallized with digalacturonic acidACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Steven B. Larson Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32,Å resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions. [source] A preliminary neutron crystallographic study of proteinase K at pD 6.5ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Anna S. Gardberg A preliminary neutron crystallographic study of the proteolytic enzyme proteinase K is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the vapor-diffusion method. Data were collected to a resolution of 2.3,Å on the LADI-III diffractometer at the Institut Laue,Langevin (ILL) in 2.5,d. The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure with the aim of providing relevant information on the location of H atoms, particularly at the active site. This information will contribute to further understanding of the molecular mechanisms underlying the catalytic activity of proteinase K and to an enriched understanding of the subtilisin clan of serine proteases. [source] | ||||||||||||||||