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)

Ubiquitination plays an essential role in maintaining cellular homeostasis by regulating a multitude of essential processes. The ability to identify ubiquitinated proteins by MS currently relies on a strategy in which ubiquitinated peptides are identified by a 114.1 Da diglycine (GG) tag on lysine residues, which is derived from the C-terminus of ubiquitin, following trypsin digestion. In the following study, we report a more comprehensive approach for mapping ubiquitination sites by trypsin digestion and MS/MS analysis. We demonstrate that ubiquitination sites can be identified by signature peptides containing a GG-tag (114.1 Da) and an LRGG-tag (383.2 Da) on internal lysine residues as well as a GG-tag found on the C-terminus of ubiquitinated peptides. Application of this MS-based approach enabled the identification of 96 ubiquitination sites from proteins purified from human MCF-7 breast cancer cells, representing a 2.4-fold increase in the number of ubiquitination sites that could be identified over standard methods. Our improved MS-based strategy will aid future studies which aim to identify and/or characterize ubiquitinated proteins in human cells.
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PMID:Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. 1737 Feb 65

The ubiquitin-proteasome pathway degrades the majority of proteins in mammalian cells and plays an essential role in the generation of antigenic peptides presented by major histocompatibility class I molecules. Proteasome inhibitors are of great interest as research tools and drug candidates. Most work on proteasome inhibitors has focused on the inhibition of the chymotryptic-like (beta5) sites; little attention has been paid to the inhibition of two other types of active sites, the trypsin-like (beta2) and the caspase-like (beta1). We report here the development of the first cell-permeable and highly selective inhibitors (4 and 5) of the proteasome's caspase-like site. The selectivity of the compounds is directly and unambiguously established by Staudinger-Bertozzi labeling of proteasome subunits covalently modified with azide-functionalized inhibitor 5. This labeling reveals that the caspase-like site of the immunoproteasome (beta1i) is a preferred target of this compound. These compounds can be used as tools to study roles of beta1 and beta1i sites in generation of specific antigenic peptides and their potential role as co-targets of anti-cancer drugs.
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PMID:A cell-permeable inhibitor and activity-based probe for the caspase-like activity of the proteasome. 1744 66

There is a growing need for the large-scale identification of the ubiquitinated proteins and ubiquitin attachment sites. As part of this effort, we generated a transgenic mouse expressing a tagged ubiquitin in the heart. We found that the majority of ubiquitinated proteins in mouse heart are insoluble in detergent-free buffer and were chemically cleaved after methionine with CNBr. CNBr cleaved the proteins into smaller polypeptides while preserving the ubiquitin chains. Ubiquitin-conjugated polypeptides were then purified under denaturing conditions, digested with Lys-C and trypsin, and analyzed by liquid chromatography-tandem mass spectrometry. We identified 121 proteins that were ubiquitinated in mouse heart, and we detected 33 ubiquitination sites in 21 of the proteins. Components of cardiac muscle and many mitochondrial proteins were identified as substrates for ubiquitination, strongly suggesting that proteins related to major heart functions such as contraction and energy production are under continuous quality control by the ubiquitin system.
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PMID:A proteomics approach to identify the ubiquitinated proteins in mouse heart. 1745 54

Huntington's disease (HD) is a progressive, autosomal dominant neurodegenerative disease caused by an abnormally expanded CAG repeat in the HD gene. Ubiquitylated aggregates containing mutant huntingtin protein in neurons are hallmarks of HD. Misfolded mutant huntingtin monomers, oligomers, or aggregates may be a result of, and cause, ubiquitin- proteasome dysfunction. To investigate the ubiquitin-proteasome system we designed a series of firefly luciferase reporters targeted selectively to different points along this pathway. These reporters were used to monitor ubiquitin-proteasome system function in a striatal cell culture model of HD. Ubiquitylation processes were not reduced in mutant huntingtin cells but recognition or degradation of ubiquitylated substrates was decreased. We also found mutant huntingtin expressing cells had slight but significant decreases in chymotrypsin-like and caspase-like activities, and an unexpected increase in trypsin-like activity of the proteasome core. General proteasome core inhibitors, as well as selective caspase-like activity inhibitors, were less effective in mutant cells. Finally, treatment with 3-nitropropionic acid, a succinate dehydrogenase inhibitor, had opposite effects on the ubiquitin-proteasome system with activation in wild-type and decreased activity in mutant huntingtin expressing cells. The results of these experiments show clearly selective disruption of the ubiquitin-proteasome system in this cell culture model of HD. The high throughput tools that we have designed and optimized will also be useful in identifying compounds that alter ubiquitin-proteasome system function and to investigate other neurodegenerative diseases such Alzheimer's disease and Parkinson's disease.
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PMID:Ubiquitin-proteasome system alterations in a striatal cell model of Huntington's disease. 1745 94

Incubation of rat brain mitochondria with ubiquitin and ATP followed by subsequent mitochondria sedimentation was accompanied by reduction of ubiquitin content in the supernatant. This decrease was more pronounced in the presence of ATP-regenerating system in the incubation medium (creatine phosphate/creatine phosphokinase). This ubiquitin incorporation into brain mitochondria observed only in the presence of ATP in the incubation medium increased sensitivity of monoamine oxidases (MAO) A and B to proteolytic inactivation by trypsin and papain, respectively. (Ubiquitin did not influence sensitivity of MAO B to trypsin and MAO A to papain). The data obtained suggest that ubiquitin incorporation into rat brain mitochondria increases susceptibility of MAOs to certain exogenous proteases, however, it remains unclear whether these changes stem from direct MAO-ubiquitin conjugation or reflect alterations in the membrane environment of these enzymes.
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PMID:[Ubiquitin causes selective increase in the sensitivity of rat brain mitochondrial monoamine oxidases to various proteases]. 1807 75

Protein degradation is mediated predominantly through the ubiquitin-proteasome pathway. The importance of the proteasome in regulating degradation of proteins involved in cell-cycle control, apoptosis, and angiogenesis led to the recognition of the proteasome as a therapeutic target for cancer . The importance of the proteasome for general cell homeostasis has been established, and the 2004 Nobel Prize for Chemistry honored the researchers that discovered the ubiquitin-proteasome pathway. Robust, sensitive assays are essential for monitoring proteasome activity and for developing inhibitors of the proteasome. Peptide-conjugated fluorophores are widely used as substrates for monitoring proteasome activity, but fluorogenic substrates can exhibit significant background and can be problematic for screening because of cellular autoflorescence or fluorescent library compounds. To address these issues, we developed a homogeneous, bioluminescent method that combines peptide-conjugated aminoluciferin substrates and a stabilized luciferase. We have developed homogeneous, bioluminescent assays for all three proteasome activities, the chymotrypsin-like, trypsin-like, and caspase-like, using purified proteasome. We have also applied this technology to a cellular assay using the substrate for the chymotrypsin-like activity in combination with a selective membrane permeabilization step (patent pending). The proteasome assays are designed in a simple "add and read" format and have been tested in 96-and 384-well plates. The bioluminescent, coupled-enzyme format enables sensitive and rapid protease assays ideal for inhibitor screening.
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PMID:Homogeneous, bioluminescent proteasome assays. 1817 19

In mammals, the ubiquitin-proteasome proteolytic pathway is a major route of protein degradation and has been shown to be regulated by the feeding status via the protein kinase B (PKB)-Forkehead box-O transcription factor signaling pathway-mediated transcription regulation of atrophy-related ubiquitin ligases, atrogin1 and muscle RING finger 1. In contrast, in rainbow trout (Oncorhynchus mykiss), the activity of the proteasome in muscle was not affected during starvation-induced muscle degradation. The aim of this study was therefore to explore the molecular basis for this lack of induction of this proteolytic route during starvation. In this study, rainbow trout were food deprived for 7 and 14 d, refed ad libitum, and the effect of the nutritional status was assessed on the different steps involved in the regulation of the ubiquitin-proteasome system in muscle. We observed that starvation reduced the phosphorylation of PKB and enhanced the expression of atrogin1 in muscle, whereas refeeding led to the opposite effects. The level of polyubiquitinated proteins in muscle increased to over 2 times the initial value on d 0 after 14 d of starvation and decreased significantly at 12 h after refeeding, but there were no major changes in the activity of the main proteasomal peptidases (chymotrypsin-like and trypsin-like). Altogether, these results indicate that in rainbow trout muscle, the polyubiquitination step of the ubiquitin-proteasome route is regulated by the feeding status similarly to what is observed in mammals.
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PMID:Feeding status regulates the polyubiquitination step of the ubiquitin-proteasome-dependent proteolysis in rainbow trout (Oncorhynchus mykiss) muscle. 1828 54

Sarcopenia is one of the most striking effects of age, the causes and the pathogenic mechanisms being largely unknown. Unfortunately, there is limited information on the effect of aging on muscle protein breakdown in basal conditions. The present study aimed at investigating if skeletal muscle ubiquitn mRNA levels and proteasome activities vary with age in healthy individuals. Ub mRNA levels were measured by northern blot analysis whereas proteasome activities were determined by evaluating the cleavage of specific fluorogenic substrates in the rectus abdominis muscle of 14 healthy male individuals. Patients were divided in three groups according to the age: (1) 20-30 years (N = 3); (2) 31-64 years (N = 5); (3) > or = 65 years (N = 6). Quantitation of the ubiquitin mRNA levels (expressed in arbitrary units) (mean (SD) showed no differences among the three groups of age (20-30 years: 1352 +/- 441; 31-64 years: 1324 +/- 439; > or = 65 years: 884 +/- 400; P = 0.33). The correlation between age and muscle ubiquitin mRNA levels was not statistically significant (r = -0.4, P = 0.26). The three proteasome activities, chymotrypsin-like (CTL), trypsin-like (TL) and peptidyl-gutamyl-peptidase (PGP), expressed as nkatal x 10(-3)/mg protein, were similar in the three groups of patients stratified according to the age. There was no correlation between age with either CTL (r = 0.22, P = 0.4), PGP (r = 0.002, P = 0.9), and TL (r = 0.28, P = 0.33) activities. In conclusion, the present study shows that the skeletal muscle proteasome activities do not differ with age in healthy male individuals.
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PMID:Proteasome activities in the rectus abdominis muscle of young and older individuals. 1833 Jul 17

Ubiquitin (Ub) is a 76 amino acid polypeptide that modifies a wide range of proteins in the types of monomer or polymers, and functional consequence of ubiquitination is modulated by the length and topologies of polyUb chains. Whereas polyUb chains are usually analyzed by fully trypsin digestion and mass spectrometry (MS), we present here a middle-down strategy to characterize the structure of polyUb chains by high-resolution mass spectrometry (MS). Under optimized condition, native folded polyUb is partially trypsinized exclusively at the R74 residue, generating a large Ub fragment (1-74 residues termed UbR74) and its ubiquitinated form with a diglycine tag (UbR74-GG). The molar ratio between UbR74 and UbR74-GG reflects the length of homogeneous polyUb chains (i.e., 1:1 for the dimer, 1:2 for the trimer, 1:3 for the tetramer, and so on). Moreover, lysine residues in ubiquitin used for chain linkages are detectable by MS/MS and MS/MS/MS of large GG-tagged Ub fragments. The strategy was validated using a number of ubiquitin polymers, including K48-linked human di-Ub, K63-linked human tetra-Ub, as well as His-tagged polyUb chains purified from yeast under native condition. The potential of this strategy to analyze polyUb chains with mixed linkages (e.g., forked chains) is also discussed. Together, this middle-down MS strategy provides a novel complementary method for studying the length and linkages of complex polyUb chain structures.
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PMID:Characterization of polyubiquitin chain structure by middle-down mass spectrometry. 1835 85

Plant proteolytic system includes proteases, mainly localized inside the organelles, and the ubiquitin-proteasome pathway in both, the cytoplasm and the nucleus. It was recently demonstrated that under severe Cd stress sunflower (Helianthus annuus L.) proteasome activity is reduced and this results in accumulation of oxidized proteins. In order to test if under other heavy metal stresses sunflower proteolytic system undergoes similar changes, an hydroponic experiment was carried out. Ten days old sunflower plants were transferred to hydroponic culture solutions devoid (control) or containing 100 microM of AlCl(3), CoCl(2), CuCl(2), CrCl(3), HgCl(2), NiCl(2), PbCl(2) or ZnCl(2) and analyzed for protein oxidative damage and proteolytic activities. After 4 days of metal treatment, only Co(2+), Cu(2+), Hg(2+), and Ni(2+) were found to increase carbonyl groups content. Except for Al(3+) and Zn(2+), all metals tested significantly reduced all proteasome activities (chymotrypsin-like, trypsin-like and PGPH) and acid and neutral proteases activities. The effect on basic proteases was more variable. Abundance of 20S protein after metal treatments was similar to that obtained for control samples. Co(2+), Cu(2+), Hg(2+), Ni(2+), Cr(3+), and Pb(2+) induced accumulation of ubiquitin conjugated proteins. It is concluded that heavy metal effects on proteolytic system cannot be generalized; however, impairment of proteasome functionality and decreased proteases activities seem to be a common feature involved in metal toxicity to plants.
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PMID:Heavy metals effects on proteolytic system in sunflower leaves. 1846 79


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