Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.4.21.4 (trypsin)
42,187 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Incubation of GST pi from human placenta with 8 mM PLP resulted in a rapid loss of activity during the first 10 min, concomitant with a Schiff base formation. This inactivation was probably due to the formation of a reversible adduct between PLP and the enzyme. After sodium borohydride treatment this adduct was reduced and stabilized. Stoichiometry and peptide isolation studies showed that three lysine residues were modified during reaction of GST and PLP. Protection of the enzyme against inactivation was achieved in the presence of 4 mM GSH suggesting that at least one lysyl residue is associated with the substrate binding site. Peptide mapping by digesting the enzyme with trypsin revealed that lysine shielded by GSH is Lys-127. Our results suggest that this residue may play an important role in enzymatic activity.
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PMID:Chemical modification of human placental glutathione transferase by pyridoxal 5'-phosphate. 159 39

Pyridoxal 5'-diphospho-5'-adenosine (PLP-AMP), an adenine nucleotide affinity analog, was found to bind in a saturable fashion to isolated alpha-subunit from Escherichia coli F1-ATPase with a stoichiometry of one mol/mol and a Kd approximately 150 microM. The binding was shown to be specific by the following criteria: 1) ATP reduced the binding of PLP-AMP by 80%, and 2) PLP-AMP, like ATP, induced a conformational change which increased the mobility of alpha-subunit in nondenaturing polyacrylamide gel electrophoresis and rendered alpha-subunit resistant to mild trypsin proteolysis. A stable adduct was formed between isolated alpha-subunit and [3H] PLP-AMP after reduction with NaBH4. alpha-Subunit labeled to the extent of 0.4-0.7 mol/mol was digested with trypsin and subjected to high pressure liquid chromatography purification, yielding a single labeled peptide. Automated amino acid sequencing showed that residue alpha-Lys-201 was specifically labeled. The results suggest that Lys-201 occupies a position proximate to the phosphate groups of bound ATP in the alpha.ATP complex. PLP-AMP did not support repolymerization of isolated alpha-, beta-, and gamma-subunits, consistent with previous reports that subunit repolymerization in vitro is dependent upon the presence of nucleoside triphosphate. Further, PLP-AMP-labeled alpha-subunit could not be reconstituted with isolated beta- and gamma-subunits in the presence of ATP, showing that occupation of the alpha-subunit nucleotide site by PLP-AMP impairs normal subunit-subunit interaction.
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PMID:Pyridoxal 5'-diphospho-5'-adenosine binds at a single site on isolated alpha-subunit from Escherichia coli F1-ATPase and specifically reacts with lysine 201. 289 72

Pyridoxine-5-P oxidase, the flavoprotein involved in the oxidation of pyridoxamine-5-P and pyridoxine-5-P to pyridoxal-5-P, has been isolated and purified to homogeneity using sheep brain tissues. Inactivation of the oxidase by bis-pyridoxal-5-P results in binding of the inhibitor to specific lysyl residues. After NaBH4 reduction of the inactivated enzyme, it was found that 1 P-pyridoxyl-pyridoxine-P residue was incorporated per enzyme dimer. After trypsin digestion of the bis-PLP modified enzyme, only one peptide absorbing at 320 nm, was separated by reverse-phase high performance liquid chromatography. The amino acid sequence of the labeled peptide was determined by automated Edman degradation. The observations reported in this paper are relevant to the mechanisms underlying the regulation of the catalytic function of pyridoxines-5-P oxidase by the product pyridoxal-5-P. It is postulated that the catalytic function of the oxidase is modulated by binding of pyridoxal-5-P to a specific lysyl residue of the dimeric structure of the protein.
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PMID:Brain pyridoxine-5-phosphate oxidase. Modulation of its catalytic activity by reaction with pyridoxal 5-phosphate and analogs. 311 57

The adenine nucleotide analog, [3H]pyridoxal 5'-diphospho-5'-adenosine (PLP-AMP), is shown to be a potent and specific inhibitor of yeast hexokinase PII. Evidence that the analog binds specifically at the ATP binding site includes the demonstration that glucose binding enhances PLP-AMP binding and that PLP-AMP and ATP bind competitively with an apparent Ki(PLP-AMP) = 23 microM. In addition, from the relationship between the degree of inhibition and extent of modification, it is estimated that the incorporation of 1 mol of PLP-AMP/mol of subunit is required for complete inhibition. Borohydride reduction of the Schiff's base complex formed between hexokinase and [3H]PLP-AMP gives a stable product. The reduced derivative was digested with trypsin and a single radioactive peptide was isolated by reversed-phase high-pressure liquid chromatography. Amino acid sequence analysis identified Lys-111 as the modified residue. Taking into account the known structures of the binary complexes (Shoham, M., and Steitz, T. A. (1980) J. Mol. Biol. 140, 1-14), the results suggest that Lys-111, located in the smaller of the two lobes of hexokinase, moves into the active site upon formation of the ternary complex.
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PMID:The adenine nucleotide binding site on yeast hexokinase PII. Affinity labeling of Lys-111 by pyridoxal 5'-diphospho-5'-adenosine. 313 29

Tryptophanase purified from Escherichia coli B/1t7-A is inactivated by mild ozonization following pseudo-first-order kinetics. Previous data from the authors suggest that one out of two tryptophan residues (Trp's) in the enzyme subunit is preferentially oxidized concomitant with the ozone inactivation and has a direct interaction with the coenzyme, pyridoxal phosphate [PLP (M. Tokushige, Y. Fukuda, and Y. Watanabe, 1979, Biochem. Biophys. Res. Commun. 86, 976-981)]. To determine which Trp is more susceptible to ozonization and interacts with PLP, the native and ozonized enzyme proteins were cleaved by trypsin and the two Trp-containing peptides were analyzed by reverse-phase HPLC equipped with a dual-monitoring system consisting of an uv and a fluorescence monitor connected in tandem for selective detection of Trp-containing peptides. This device facilitated rapid detection and quantitation of the Trp-containing peptides which decreased upon ozonization. The results showed that Trp preferentially oxidized upon ozonization and involved in the interaction with PLP was the one in peptide T-15 rather than that in T-23, which Kagamiyama et al. originally designated (H. Kagamiyama, H. Wada, H. Matsubara, and E. E. Snell, 1972, J. Biol. Chem. 247, 1576-1585).
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PMID:Assignment of ozone-sensitive tryptophan residue in tryptophanase by a dual-monitoring high-performance liquid chromatography system. 389 14

Mechanism-based inactivators were used to probe the active site of the broad specificity amino acid racemase from Pseudomonas striata. Kinetic parameters for the inactivation of the racemase with both stereoisomers of beta-fluoroalanine, beta-chloroalanine, and O-acetylserine were determined. By use of 14C-labeled O-acetylserines, the stoichiometry of inactivator binding was found to be one inactivator bound per enzyme subunit. The PLP-dependent enzyme contains one coenzyme per subunit, and after NaB3H4 reduction of the PLP-imine bond, followed by trypsin digestion of the protein, the amino acid sequence of the PLP-binding peptide was determined. Trypsin digestion of the enzyme labeled with either L or D isomer of O-acetylserine and sequencing of the labeled peptide revealed that the inactivators bind to the same lysine residue which binds PLP in native enzyme. The characterization of a PLP adduct released from inactivated enzyme under some conditions is also described. Implications of the formation of this compound with respect to the overall reaction mechanism of inactivation are discussed.
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PMID:Inactivation of the Pseudomonas striata broad specificity amino acid racemase by D and L isomers of beta-substituted alanines: kinetics, stoichiometry, active site peptide, and mechanistic studies. 643 37

This study was initiated to characterize PHI (peptide histidine isoleucine amide)-27-like peptides (PLPs) in rat and porcine brain in comparison with other members of the vasoactive intestinal polypeptide (VIP) family and to investigate their distribution by radioimmunoassay. The peptidic nature of the rat brain PLP was indicated by its trypsin sensitivity. On Sephadex chromatography rat brain PLP has the same molecular weight as synthetic (porcine intestinal) PHI-27. High pressure liquid chromatographic separations revealed that PLP in rat and porcine brain extracts elutes as a single peak distinct from VIP or secretin. Porcine brain PLP elutes in the same position as synthetic PHI-27, whereas rat brain PLP immunoreactivity consistently separates from synthetic PHI-27. This suggests that porcine brain PLP is identical to synthetic PHI-27, in agreement with the reported sequence of Tatemoto et al. (Tatemoto, K., M. Carlquist, T. McDonald, and V. Mutt (1983) FEBS Lett. 153: 248-252), whereas PLP may have a different amino acid sequence (or may be post-translationally modified). Using specific PHI and VIP radioimmunoassays, the distribution of PLP was found to parallel that of VIP in rat and porcine brain, being highest in cerebral cortex, amygdala, and hippocampus. PLP, like VIP, is abundant in rat retina and can be included in the growing list of retinal peptides. This highly correlated distribution of VIP and PLP may be explained by the recent discovery that they are derived from the same precursor (Itoh, N., K. Obata, N. Yanaihara, and H. Okamoto (1983) Nature 304: 547-549).(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:The distribution and chromatographic characterization of PHI (peptide histidine isoleucine amide)-27-like peptides in rat and porcine brain. 654 67

Fourteen popular scoring functions, i.e., X-Score, DrugScore, five scoring functions in the Sybyl software (D-Score, PMF-Score, G-Score, ChemScore, and F-Score), four scoring functions in the Cerius2 software (LigScore, PLP, PMF, and LUDI), two scoring functions in the GOLD program (GoldScore and ChemScore), and HINT, were tested on the refined set of the PDBbind database, a set of 800 diverse protein-ligand complexes with high-resolution crystal structures and experimentally determined Ki or Kd values. The focus of our study was to assess the ability of these scoring functions to predict binding affinities based on the experimentally determined high-resolution crystal structures of proteins in complex with their ligands. The quantitative correlation between the binding scores produced by each scoring function and the known binding constants of the 800 complexes was computed. X-Score, DrugScore, Sybyl::ChemScore, and Cerius2::PLP provided better correlations than the other scoring functions with standard deviations of 1.8-2.0 log units. These four scoring functions were also found to be robust enough to carry out computation directly on unaltered crystal structures. To examine how well scoring functions predict the binding affinities for ligands bound to the same target protein, the performance of these 14 scoring functions were evaluated on three subsets of protein-ligand complexes from the test set: HIV-1 protease complexes (82 entries), trypsin complexes (45 entries), and carbonic anhydrase II complexes (40 entries). Although the results for the HIV-1 protease subset are less than desirable, several scoring functions are able to satisfactorily predict the binding affinities for the trypsin and the carbonic anhydrase II subsets with standard deviation as low as 1.0 log unit (corresponding to 1.3-1.4 kcal/mol at room temperature). Our results demonstrate the strengths as well as the weaknesses of current scoring functions for binding affinity prediction.
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PMID:An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. 1555 82

Apyrase/ATP-diphosphohydrolase hydrolyzes di- and triphosphorylated nucleosides in the presence of a bivalent ion with sequential release of orthophosphate. We performed studies of substrate specificity on homogeneous isoapyrases from two potato tuber clonal varieties: Desiree (low ATPase/ADPase ratio) and Pimpernel (high ATPase/ADPase ratio) by measuring the kinetic parameters K(m) and k(cat) on deoxyribonucleotides and fluorescent analogues of ATP and ADP. Both isoapyrases showed a broad specificity towards dATP, dGTP, dTTP, dCTP, thio-dATP, fluorescent nucleotides (MANT-; TNP-; ethene-derivatives of ATP and ADP). The hydrolytic activity on the triphosphorylated compounds was always higher for the Pimpernel apyrase. Modifications either on the base or the ribose moieties did not increase K(m) values, suggesting that the introduction of large groups (MANT- and TNP-) in the ribose does not produce steric hindrance on substrate binding. However, the presence of these bulky groups caused, in general, a reduction in k(cat), indicating an important effect on the catalytic step. Substantial differences were observed between potato apyrases and enzymes from various animal tissues, concerning affinity labeling with azido-nucleotides and FSBA (5'-p-fluorosulfonylbenzoyl adenosine). PLP-nucleotide derivatives were unable to produce inactivation of potato apyrase. The lack of sensitivity of both potato enzymes towards these nucleotide analogues rules out the proximity or adequate orientation of sulfhydryl, hydroxyl or amino-groups to the modifying groups. Both apyrases were different in the proteolytic susceptibility towards trypsin, chymotrypsin and Glu-C.
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PMID:Potato tuber isoapyrases: substrate specificity, affinity labeling, and proteolytic susceptibility. 1589 65

In this work, we designed highly sensitive and selective luminescent detection method for alkaline phosphatase using bovine serum albumin functionalized gold nanoclusters (BSA-AuNCs) as the nanosensor probe and pyridoxal phosphate as the substrate of alkaline phosphatase. We found that pyridoxal phosphate can quench the fluorescence of BSA-AuNCs and pyridoxal has little effect on the fluorescence of BSA-AuNCs. The proposed mechanism of fluorescence quenching by PLP was explored on the basis of data obtained from high-resolution transmission electron microscopy (HRTEM), dynamic light scattering (DLS), UV-vis spectrophotometry, fluorescence spectroscopy, fluorescence decay time measurements and circular dichroism (CD) spectroscopy. Alkaline phosphatase catalyzes the hydrolysis of pyridoxal phosphate to generate pyridoxal, restoring the fluorescence of BSA-AuNCs. Therefore, a recovery type approach has been developed for the sensitive detection of alkaline phosphatase in the range of 1.0-200.0U/L (R² =0.995) with a detection limit of 0.05U/L. The proposed sensor exhibit excellent selectivity among various enzymes, such as glucose oxidase, lysozyme, trypsin, papain, and pepsin. The present switch-on fluorescence sensing strategy for alkaline phosphatase was successfully applied in human serum plasma with good recoveries (100.60-104.46%), revealing that this nanosensor probe is a promising tool for ALP detection.
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PMID:Sensitive detection of alkaline phosphatase by switching on gold nanoclusters fluorescence quenched by pyridoxal phosphate. 2839 45


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