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At least 19 recordsLinked to original sources
PubMed2026

Oncogene activation mechanism determines the limits of targeted protein degradation.

Protein degrader drugs such as PROTACs are being advanced as therapeutics targeted against oncogenic proteins. During tumorigenesis, oncogenic proteins can become constitutively activated via mechanisms including gene amplification, which increases protein production, and point mutations, which can extend protein half-life. Few experimental studies have addressed how disease-associated changes in target protein homeostasis influence PROTAC activity. We developed orthogonal methods to increase production or enhance stability of β-catenin, an important oncoprotein and target for degrader therapeutics, and used the dTAG system to evaluate the consequences for PROTAC activity. Stabilizing oncogenic missense mutations increase protein expression up to 5-fold but do not alter the PROTAC-imposed minimal steady-state level. In contrast, transcriptional upregulation increases both pre- and post-treatment target levels, revealing a synthesis-dependent ceiling on achievable depletion. Our results highlight distinct constraints on PROTAC activity arising from different mechanisms of oncogene activation, with potential implications for preclinical modeling, drug resistance and personalized medicine.

Humans↗
PubMed1979

Application of liver perfusion as an in vitro model in studies of intracellular protein degradation.

Amino acids appear to be prime regulators of autophagy and proteolysis in liver. They both attain a maximum rapidly when livers from fed rats are perfused in the single-pass mode without amino acids and are suppressed to basal levels by amino acid additions. The fact that their greatest responsiveness to amino acids occurs slightly below normal plasma levels suggests that these cellular processes could play a role in regulating plasma amino acid concentrations in vivo. Autophagy and proteolysis are also inhibited by insulin and stimulated by glucagon. In the latter instance the hormonal action is not direct but mediated indirectly by depletion of intracellular glutamine, probably as a consequence of enhanced gluconeogenesis. Close correlations among (1) rates of intracellular proteolysis, (2) the aggregate volume of lysosomal elements, and (3) estimates of degradable protein internalized within lysosomes indicate that lysosomal function can explain total intracellular protein degradation (with the possible exception of rapidly turning over fractions) over the full range of proteolysis from maximum down to and including the basal state. Since ratios of degradable intralysosomal protein to corresponding rates of proteolysis in intact liver are constant over this range, protein internalization may be the rate-limiting step in lysosomal proteolysis.

Amino Acids↗
PubMed2026

Post-translational chemical modification of E3 ligase for efficient target protein degradation.

Targeted protein degradation (TPD) has emerged as a powerful therapeutic strategy, with proteolysis-targeting chimeras (PROTACs) leading efforts to address previously undruggable targets. However, PROTACs face challenges such as low bioavailability and poor pharmacokinetic properties which limit their biological applications. Here, we report a strategy termed post-translational chemical modification targeting chimera (PTcM-TAC), which integrates ligand-directed chemistry into the PROTAC framework to achieve sustained target protein degradation through covalent modification of E3 ligases. PTcM-TAC incorporates an electrophilic dibromophenyl benzoate warhead into the linker connecting the E3 ligase ligand and the protein-of-interest (POI) ligand, enabling selective transfer of the POI ligand onto the recruited E3 ligase while releasing the E3-binding moiety. Mechanistic studies, including LC-MS/MS peptide mapping, pull-down assays, and structural modeling, demonstrated site-selective modification of CRBN by the PTcM-TAC. The resulting ligand-labeled E3 ligase enables sustained pseudo-catalytic target recognition through a simplified binary interaction, thereby maintaining degradation activity even after compound washout. Furthermore, we successfully applied the PTcM-TAC strategy to another representative E3 ligase, von Hippel-Lindau (VHL), which exhibited substantially sustained degradation activity compared with conventional PROTACs. To our knowledge, PTcM-TAC represents the first ligand-directed chemical strategy that converts transient PROTAC-mediated ternary complex formation into binary target recognition via post-translational chemical modification of an E3 ligase. We believe that PTcM-TAC could provide a platform for next-generation targeted protein degraders to overcome the current limitation of PROTAC approach.

Ubiquitin-Protein Ligases↗
PubMed1979

Protein degradation and the regulation of protein balance in muscle.

The rate of of protein degradation in muscle changes in many states but the nature of these changes is often paradoxical. Thus there can be increases during growth (anabolic increases) as well as during wasting (catabolic increases). Decreases can occur during growth (anabolic decreases) as well as during wasting (catabolic decreases). These changes are observed in man (as judged by changes in 3-methylhistidine excretion) and in experimental animals. The nature of the changes is not understood but it is possible that muscle growth induces increased degradation as part of the accompanying myofibre remodelling. The rate of protein degradation can also be influenced by thyroid status, since in thyroid deficiency degradation is reduced and can be stimulated by triiodothyronine. This response is independent of changes in muscle growth. Finally, acute exercise suppresses protein degradation in vivo in man as well as suppressing protein synthesis (in vivo in rats). When protein degradation rates change, acid proteinase activities also change in muscle. The anabolic increase in degradation appears to involve increases in mainly cathepsin D whereas catabolic increases in degradation are associated with an increase mainly in pepstatin-insensitive acid autolytic activity.

Adult↗
PubMed1979

Protein metabolism in lung: use of isolated perfused lung to study protein degradation.

This study investigates the use of the isolated perfused lung to study protein degradation. Proteins were labeled in vivo for 10 min or for 5 h using L-[U-14C]phenylalanine. When prelabeled lungs were perfused in vitro virtually all of the acid-soluble and acid-insoluble radioactivity in the tissue and perfusate remained as phenylalanine. Protein degradation was measured as the accumulation of free [14C]phenylalanine in ther perfusate; during the time this accumulated the amount of intracellular free phenylalanine and the free phenylalanine space remained constant. Proteins labeled during 10 min had a constant rate of degradation between 45 and 90 min of perfusion (about 11%.h-1); those labeled during 5 h had a constant rate of degradation for 90 (about 3%.h-1). The percent dry lung weight did not change during the perfusion. We conclude that measurable rates of proteolysis of "rapid" and "slowly" turning over proteins can be obtained while the lung is virtually free of edema. This system should allow studies on the modulation of proteolysis in intact lung under defined conditions.

Animals↗
PubMed1979

Protein metabolism in lung. II. Influence of amino acids and glucose on protein degradation.

We used the isolated perfused lung to study protein degradation. Proteins were labeled in vivo during 10 min (fast) or 5 h (slow). The absence of exogenous amino acids lowered the rate of proteolysis of fast but not of slowly turning over proteins. Addition of normal rat plasma levels of amino acids, after 45 min of perfusion without amino acids, returned the rate of proteolysis to control levels. The absence of exogenous glucose increased the rate of degration of rapidly turning over proteins but decreased the degradation rate of slowly turning over proteins. These changes took place in the absence of any measurable effect of amino acids or glucose on the amount of lung water, the rate of perfusate flow, the lung concentration of ATP or the intracellular concentration of free phenylalanine. We conclude that these substrates influence proteolysis in our system and that the degradation of rapidly and slowly turning over proteins are regulated independently in the isolated perfused lung.

Adenosine Triphosphate↗
PubMed1978

The effect of protein degradation on cellular growth characteristics.

The role of protein degradation in cellular proliferation was investigated by measurements of the rates of degradation of labile and stable proteins for a number of cell types under various growth conditions. The rate of protein degradation was found to be a relatively invariant parameter in that it did not change after strong inhibition of protein synthesis with cychloheximide or histidinol, it was the same in both exponential and stationary phase, and it did not correlate with the presence or absence of malignant transformation. Using three different cell types with widely differing division rates, the rate of cell division and DNA synthesis (in %/hr) was found to be precisely equal to the rate of protein accumulation (in %/hr) , i.e., to the rate of protein synthesis minus the rate of protein degradation. Division rates between the different cell types appeared to be determined chiefly by the rate of protein synthesis though, especially at low division rates, the rate of protein degradation could represent a large component of the protein accumulation rate.

Cell Division↗
PubMed1979

Muscle protein degradation in premature human infants.

1. Myofibrillar protein degradation has been measured by the rate of 3-methylhistidine excretion in premature infants weighing between 635 g and 1295 g. Analyses were made in conjunction with 1--3 day nitrogen balance studies. 2. In 56 balance studies in 36 infants, total muscle protein breakdown varied between 0.70 and 2.58 (mean 1.05) g day-1 kg-1 body weight while the percentage of total muscle protein degraded each day was between 3.3 and 8.3 (mean 4.8). 3. Both total and fractional rates of protein breakdown showed highly significant negative correlations with nitrogen retention but no relationship to total energy input. 4. Protein degradation was higher than average in infants who were losing weight at the time of the balance study, lower in infants who were gaining weight and higher in those who died within 2 weeks of the analysis. 5. Myofibrillar protein breakdown was not different between infants fed orally and those receiving total parenteral nutrition. 6. Generally the effects of nitrogen and evergy status on muscle protein degradation in the premature infants are different from changes reported in adult human beings or adult rats. We suggest that this difference may be a consequence of the very limited energy reserves of the premature infant.

Aging↗
PubMed1979

Intracellular protein degradation in Neurospora crassa.

In exponentially growing cultures of Neurospora crassa, the basal rate of protein degradation increases as the constant of the rate of growth decreases, so that in slow growing cells (mu = 0.13) the rate of protein degradation is about 25% of the rate of protein accumulation. During glucose starvation and shift-down transition of growth, the rate of protein degradation is greatly enhanced, and a moderate reduction (about 30%) of the ATP level is observed. Treatment of glucose-starved cells with 2-deoxyglucose reduces the ATP content by 70% and blocks protein degradation. The addition of cycloheximide, given at the onset of glucose starvation, prevents the enhancement of protein degradation; instead cycloheximide is without effect if added when proteolysis has already started. At a supraoptimal temperature (42 degrees C) the basal rate of protein degradation is not stimulated, contrary to the behavior observed in bacteria. Guanosine nucleotides, which appear to have a regulatory role for protein degradation in bacteria, are not found in N. crassa.

Amino Acids↗
PubMed1977

Regulation of protein degradation in normal and transformed human cells. Effects of growth state, medium composition, and viral transformation.

In WI-38, a normal human fibroblast, the rates of degradation of short lived and long lived proteins are identical whether the cultures are growing exponentially or are density-inhibited. Replacement of the growth medium with fresh medium does not alter these rates. In VA-13, an SV-40 transformed derivative of WI-38, the rates of protein degradation are also independent of growth rate and fresh medium. However, in both WI-38 and VA-13 the rate of long lived protein degradation increases as the serum concentration is reduced below 5%. After complete serum withdrawal, the rate increases by 60 to 100% in both cell types. Withdrawal of arginine and phenylalanine triples the rate of long lived protein degradation, while addition of 10% dialyzed serum to this amino acid-deficient medium reduces the effect to twice that of the controls. Incubation of both types of cells in phosphate-buffered saline also increases protein degradation. This effect is reduced by glucose, albumin, and dialyzed serum. Therefore, the rate of protein degradation is independent of growth rate in normal and transformed human cells. However, the rate of degradation is closely coupled to certain medium alterations.

Cell Division↗
PubMed2026

Intestinal content accelerates muscle protein degradation in red shrimp (Solenocera crassicornis) during refrigeration: Insights from metagenomics and metabolomics.

This study systematically explored the effects of intestinal components on muscle quality deterioration and protein degradation of red shrimp during refrigerated storage. The results demonstrated that refrigeration induced continuous quality degradation and muscle protein breakdown in red shrimp, whereas eliminating intestinal tissues effectively retarded muscle spoilage and protein degradation, and optimized muscle texture. The intestinal microorganisms could secrete extracellular proteases to promote muscle protein degradation were primarily Vibrio, Bacillus, Pseudomonas, Photobacterium, and Shewanella. These microorganisms promote protein degradation by secreting zinc proteases, serine proteases, and aspartyl proteases. This study elucidates the molecular mechanisms of intestinal microbial metabolism influences the muscle protein degradation of red shrimp during refrigeration. The findings provide a theoretical foundation for precise regulation of intestinal-targeted microorganisms, thereby maintaining optimal quality of shrimps during refrigeration.

Animals↗
PubMed1977

The role of lysosomal enzymes in protein degradation in different types of rat liver cells.

Highly purified suspensions of parenchymal, endothelial and Kupffer cells were prepared from the rat liver. The respective roles of these cell classes in the degradation of proteins was investigated by analysing the cellular distribution of two lysomal proteases. The specific arginine naphthylamidase activity was 2 times higher in Kupffer cells compared with the nearly equal activities in endothelial and parenchymal cells. The specific activity of the important endopeptidase cathepsin D in endothelial and Kupffer cells was about 12 and 36 times higher, respectively, than the activity in parenchymal cells. These results are in agreement with an important role of Kupffer and endothelial cells in the degradation of proteins and protein containing material of exogenous origin.

Aminopeptidases↗
PubMed1978

General characteristics of protein degradation in diabetes and starvation.

The enhanced protein degradation associated with diabetes and starvation is fundamentally different from normal protein catabolism. In normal eukaryotic cells large molecular weight proteins tend to be degraded more rapidly than small proteins, acidic proteins tend to be degraded more rapidly than neutral or basic proteins, and glycoproteins tend to be degraded more rapidly than nonglycoproteins. All three of these general correlations are absent or markedly reduced in liver and muscle of diabetic and starved rats. In contrast, the correlations between proteins size and half-life, between protein net charge and half-life, and between protein carbohydrate content and half-life are not affected in brain of diabetic or starved animals. These results suggest that diabetes and starvation alter the general characteristics of intracellular protein degradation in target tissues of insulin. Degradation of serum proteins is also affected in diabetes and starvation. In normal animals a general correlation exists between isoelectric points of serum proteins and their degradative rates. This relationship is abolished in diabetes and starvation, as it is among liver and muscle proteins. The implications of our findings are discussed with regard to possible mechanisms of the enhanced protein breakdown.

Animals↗
PubMed2025

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice.

Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function. An appealing platform among these technologies is the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity due to the high concentrations of auxin required in the original AID1 system is no longer a concern, making it possible to study protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and silencing of the OsTIR1 adaptor protein. Resistance to auxin degradation was also acquired in mouse primary CtcfminiAID/miniAID knock-in B-ALL cells through missense mutations of the OsTIR1(F74G) protein in vivo and ex vivo. In summary, our innovative study expands our understanding of the AID system and cautions careful consideration of design for future applications in mammalian system.

CTCF↗
PubMed1977

Cystinotic fibroblasts accumulate cystine from intracellular protein degradation.

Fibroblasts derived from patients with cystinosis, an autosomal recessive condition, accumulate the disulfide amino acid cystine within lysosomes. The metabolic defect leading to the cystine accumulation and the source from which the cystine is derived are unknown. In this report we present data showing that cystine in these cells accumulates from the degradation of endogenous protein. This conclusion is based upon: (i) no demonstrable synthesis of cystine from serine; (ii) no difference in cystine reaccumulation between glutathione-depleted and non-glutathione-depleted cystinotic cells; (iii) recovery of labeled cystine only when the protein pool is labeled; (iv) reversible inhibition of cystine reaccumulation by known inhibitors of lysosomal protein degradation (chloroquine and NH4Cl).

Biodegradation, Environmental↗