Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.4.21.64 (proteinase K)
 4,071 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We describe a new method for lipopolysaccharide (LPS) preparation by water extraction at 100 degrees C and subsequent digestion with proteinase K. The crude LPS could be reliably used for immunoblotting since it retained a high level of antigenicity, and was free of SDS and proteinase K, both of which can cause problems. Two monoclonal antibodies which failed to react with LPS prepared by two conventional methods reacted well with our preparation. We used the new method to prepare LPS from 44 strains of bacteria formerly classified as Bacteroides, some of which have been reclassified as Porphyromonas or Prevotella. In general, yields were good, and electrophoretic profiles obtained with SDS-PAGE and silver staining enabled strains to be rated rough, semi-rough, or smooth.
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PMID:A rapid method for preparation of rough and smooth lipopolysaccharide from Bacteroides, Porphyromonas and Prevotella. 834 89

The combined effect of several sensitizers and light on H2O or D2O solutions of DNA-histone complexes, as well as the significance of singlet oxygen (1O2), in this photosensitizing reaction has been studied. On H2O solutions, the production of 1O2, as well as the formation of DNA-protein cross-links (DPCs), were found to be dependent on light dose for all the sensitizers. Mesotetra (4N-methylpyridyl) porphine (T4MPyP), methylene blue (MB), and toluidine blue (TB) were the best photosensitizers with regard to tryptophan photolysis, followed by hematoporphyrin (HP), thioflavine T (TT), and pyronin G (PG). The formation of DPCs showed high initial rates, reaching a plateau at doses over 90 J/cm2. Under these irradiation conditions, the percentage of DPCs induced by the sensitizers decreases in the order T4MPyP > MB > TB >> HP approximately TT >> PG (approximately 0). These DPCs were totally destroyed with proteinase K (15 micrograms/ml). The irradiation of the DNA-histone-sensitizer solutions in the presence of L-carnosine (5 x 10(-4) M) produced approximately a 50% of DPCs inhibition for T4MPyP, MB, and TB, and a total inhibition for HP, TT, and PG. The substitution of H2O by D2O as solvent significantly increased the photodegradation of tryptophan, as well as the photoinduction of DPCs by the sensitizers. The results obtained indicate that singlet oxygen is the main agent responsible in the DNA-protein cross-linking formation.
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PMID:Photodynamic induction of DNA-protein cross-linking in solution by several sensitizers and visible light. 848 98

Hot water extract prepared from the mycelial culture of mushroom Phellinus linteus stimulated polyclonal antibody production in an in vitro culture system. The active fraction PLP was purified from the extract ca. 1030-fold by ethanol precipitation followed by DEAE-cellulose and gel permeation chromatography. PLP contained 13.2% (w/w) peptide and 82.5% (w/w) carbohydrate. About 6.8% (w/w) of the total carbohydrate was uronic acid. The molecular weight distribution of PLP was found to be nearly homogeneous (153 kDa) in gel permeation HPLC analysis. Neutral sugar composition analysis revealed Ara (7.5%), Xyl (3.7%), Glc (21.1%), Gal (24.1%) and Man (44.2%). Uronic acid was identified as a glucuronic acid by gas chromatography. Ten amino acids were detected and Asp and Glu were the major components. In our assay system, the half-maximal concentration of PLP for B-lymphocyte stimulation was ca. 3 micrograms/ml. Partial acid hydrolysis as well as sodium periodate treatment of PLP decreased the activity significantly, suggesting that both the full molecular size and the sugar moiety were essential. However, proteinase K treatment for up to 48 h did not affect the activity.
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PMID:B-lymphocyte-stimulating polysaccharide from mushroom Phellinus linteus. 858 12

The crystal structure of a ternary complex of proteinase K, Hg(II) and a hexapeptide N-Ac-Pro-Ala-Pro-Phe-Pro-Ala-NH2 has been determined at 2.2 A resolution and refined to an R factor of 0.172 for 12,910 reflections. The mercury atom occupies two alternate sites, each of which was assigned an occupancy of 0.45. These two sites are bridged by Cys-73 S gamma which forms covalent bonds to both. Both mercury sites form regular polyhedrons involving atoms from residues Asp-39, His-69, Cys-73, His-72, Met-225, and Wat-324. The complex formation with mercury seems to disturb the stereochemistry of the residues of the catalytic triad Asp-39, His-69, and Ser-224 appreciably, thus reducing the enzymatic activity of proteinase K to 15%. The electron density in the difference Fourier map shows that the hexapeptide occupies the S1 subsite predominantly and the standard recognition site constituted by Ser-132 to Gly-136 and Gly-100 to Tyr-104 segments is virtually empty. The hexapeptide is held firmly through a series of hydrogen bonds involving protein atoms and water molecules. As a result of complex formation, Asp-39, His-69, Met-225, Ile-220, Ser-219, Thr-223, and Ser-224 residues move appreciably to accommodate the mercury atoms and the hexapeptide. The largest movement is observed for Met-225 which is involved in multiple interactions with both mercury and the hexapeptide. The activity results indicate an inhibition rate of 95%, as a result of the combined effect of mercury and hexapeptide.
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PMID:Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 A resolution. 881 35

Surface iodinated larvae of Haemonchus contortus were incubated in the presence of the fungal protease, proteinase K, and proteolysis quantified by scintillation counting of released radioactivity. No radioactivity was released from live ensheathed infective-stage larvae (L3(2M)). In contrast, 58% of the radioactivity was released from ecdysed, second molt (2M) cuticles (sheaths) of L3(2M) and 48% from live exsheathed third-stage larvae (L3). When L3(2M) larvae were killed by heat (80 degrees C for 10 min) prior to proteinase K incubation, 61% of the radioactivity was released, whereas less than 7% was released from larvae killed by the metabolic inhibitors NaN3 or KCN. Proteinase K released 44% of the radioactivity from live L3(2M) larvae which had been preincubated with 1% sodium dodecylsulfate (SDS), whereas no radioactivity was released from L3(2M) larvae preincubated with either 1% Triton X-100, 0.2% CTAB, 50% methanol, 50% ethanol, or water. Following incubation with proteinase K, only L3(2M) larvae which had been heat-killed or preincubated with SDS showed visible damage to the sheath. Material released from L3(2M) larvae by exposure to either heat or SDS contained a 98,000 M(r) protein by SDS-PAGE autoradiography. These results indicate that viable L3(2M) larvae are resistant to attack by proteinase K and that this resistance is dependent on structural properties of the sheath.
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PMID:The role of the sheath in resistance of Haemonchus contortus infective-stage larvae to proteolytic digestion. 889 81

The crystal structure of a complex formed by the interaction between proteinase K and a designed octapeptide amide, N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2, has been determined at 2.5 A resolution and refined to an R-factor of 16.7% for 7,430 reflections in the resolution range of 8.0-2.50 A. The inhibitor forms a stable complex through a series of hydrogen bonds and hydrophobic interactions with the protein atoms and water molecules. The inhibitor is hydrolyzed between Phe4I and DAla5I (I indicates the inhibitor). The two fragments are separated by a distance of 3.2 A between the carbonyl carbon of Phe4I and the main-chain nitrogen of DAla5I. The N-terminal tetrapeptide occupies subsites S1-S5 (S5 for acetyl group), whereas the C-terminal part fits into S1'-S5' region (S5' for amide group). It is the first time that such an extended electron density for a designed synthetic peptide inhibitor has been observed in the prime region of an enzyme of the subtilisin family. In fact, the inhibitor fills the recognition site completely. There is only a slight rearrangement of the protein residues to accommodate the inhibitor. Superposition of the present octapeptide inhibitor on the hexapeptide inhibitor studied previously shows an overall homology of the two inhibitors, although the individual atoms are displaced significantly. It suggests the existence of a recognition site with flexible dimensions. Kinetic studies indicate an inhibition rate of 100% by this specifically designed peptide inhibitor.
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PMID:Strategy to design peptide inhibitors: structure of a complex of proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5 A resolution. 897 53

With the objective of monitoring xenobiotic degrading bacteria in soil, a method for rapid extraction of DNA from soil, amenable to amplification by PCR, was developed. The method was based on lysis by freeze-thawing and subsequent addition of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide and proteinase K. The extraction method required 2 h and was tested on six different soils differing in organic content, water holding capacity and pH, including ones from which DNA extraction is difficult. DNA yields from the soils ranged from 6.1 to 54.0 micrograms of DNA per g soil. The efficiency and reproducibility of the DNA extraction method were evaluated by competitive PCR. The organic content in the soils was a major factor affecting the amount of obtained DNA amenable for amplification by PCR. A PCR primer-pair was designed on the basis of the known nucleotide sequences of several catechol 2,3-dioxygenase genes. The specificity of the primer-pair was demonstrated on different sequenced catechol 2,3-dioxygenase genes and on site-specific bacterial isolates from polycyclic aromatic hydrocarbon (PAH)-contaminated soil. The concentration of catechol 2,3-dioxygenase DNA in PAH-contaminated sediment undergoing an ex situ compost process was quantified by competitive PCR over a period of 16 weeks. The concentration of PAHs and catechol 2,3-dioxygenase DNA in the soil samples, was found to correlate.
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PMID:DNA recovery and PCR quantification of catechol 2,3-dioxygenase genes from different soil types. 908 10

Parameters of fluorescence of three single-tryptophan-containing proteins and of two log-normal components of proteinase K (2 tryptophans) were analyzed in relation to the microenvironment characteristics of indolic atoms in crystal structures of the proteins. For this purpose, it was constructed a system of microenvironment description including accessibility of the atoms to the bulk and bound water; the density, polarity and mobility of environment within radii of 5.5 and 7.5 A from each indolic atom; and the existence of eventual partners in hydrogen bonding with excited fluorophore. The analysis showed that, in the cases of the most shorter-wavelength emission bands (those structured at 308 nm for azurin and at 316 nm for L-asparaginase), as well as of the monomer melittin band at 350 nm, the microenvironment characteristics well agreed to those predicted in the model of discrete states of tryptophan in proteins [1,3,7] and can be used for assignment of protein fluorescence spectral components to individual tryptophan residues. However, differences of the microenvironment parameters included in the system are little discernible for the component bands of proteinase K emission at ca. 330 and 340 nm. In order to reliably assign such components of tryptophan fluorescence, it seems to be sufficient to take into account some additional structural characteristics, which could be revealed in a comprehensive analysis of a great number of proteins possessing such spectral components.
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PMID:[Assignment of a component of protein fluorescence spectra to tryptophan residues by their three-dimensional microoenvironmental properties]. 917 73

A presumptive diagnosis of tuberculosis can be made if a tissue has characteristic histopathologic changes and acid-fast organisms. However, definitive diagnosis requires culture and species identification of the causative mycobacterium, a process that takes several weeks to complete. The purpose of work reported here was to determine if formalin-fixed, paraffin-embedded tissues could be tested by polymerase chain reaction (PCR) to provide a more rapid diagnosis of tuberculosis. Nondecalcified tissues from cases of tuberculosis in cattle and elk (Cervus elaphus) were examined. The primers used for PCR amplified a 123-bp fragment of IS6110, an insertion sequence that is specific for organisms in the Mycobacterium tuberculosis complex (M. tuberculosis, M. bovis, M. microti, M. africanum). The PCR test detected this sequence in tissues from 92 of 99 (93%) tuberculosis cases, including 3 of 4 elk. In 80 tissues, the positive results were obtained using material prepared by immersion of paraffin sections in water containing a detergent, followed by alternating boil/freeze cycles. The remaining positive results were obtained with DNA isolated from the crude tissue extracts by proteinase K digestion and phenol/chloroform purification. Accuracy of the IS6110 PCR test was demonstrated by negative test results on 31 tissues that had either nonmycobacterial granulomas or granulomatous lesions caused by other mycobacteria (M. paratuberculosis or M. avium). The findings of this study show that a PCR test usually can provide a rapid diagnosis of tuberculosis when it is applied to paraffin sections that have characteristic lesions and acid-fast organisms.
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PMID:Detection of Mycobacterium bovis in formalin-fixed, paraffin-embedded tissues of cattle and elk by PCR amplification of an IS6110 sequence specific for Mycobacterium tuberculosis complex organisms. 924 62

Staphylococcal alpha-toxin is a single-chain protein with a molecular mass of 33.2 kDa, which can form large water-filled pores both in lipid bilayers and in erythrocyte membranes. Limited proteolysis of the purified toxin with proteinase K led to time-dependent changes of all the functional features of the channels formed by the toxin. Single-channel conductance in planar bilayers was decreased about threefold. The anion selectivity of the channel was replaced with cation selectivity and the asymmetry in the current-voltage relationship of the channel became more pronounced. At the same time the nicked toxin kept its full ability to form ion channels in lipid bilayers, although it lost a considerable part of its hemolytic activity. In planar bilayers and in erythrocyte membranes, the proteolytically nicked toxin actually formed channels with a slightly smaller diameter (approximately 1.2 times) than that formed by the native toxin. This decrease was not marked enough to explain changes in the biological effects of the nicked toxin. The change in channel selectivity induced by the cleavage is considered to be the major determinant of the changes in the biological effects of the nicked toxin.
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PMID:Pore-forming properties of proteolytically nicked staphylococcal alpha-toxin: the ion channel in planar lipid bilayer membranes. 925 67


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