Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

2020 ◽  
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
Boronic Acid ◽  
Computational Study ◽  
Ubiquitin Proteasome System ◽  
Bayesian Optimization ◽  
Inhibition Mechanism ◽  
20S Proteasome ◽  
Acid Base ◽  
Ubiquitin Proteasome ◽  
Infection Cycles

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

2020 ◽  
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
Boronic Acid ◽  
Computational Study ◽  
Ubiquitin Proteasome System ◽  
Bayesian Optimization ◽  
Inhibition Mechanism ◽  
20S Proteasome ◽  
Acid Base ◽  
Ubiquitin Proteasome ◽  
Infection Cycles

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

scholarly journals Involvement of the Ubiquitin-Proteasome System in the Formation of Experimental Postsurgical Peritoneal Adhesions

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Clara Di Filippo ◽  
Pasquale Petronella ◽  
Fulvio Freda ◽  
Marco Scorzelli ◽  
Marco Ferretti ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
20S Proteasome ◽  
Intracellular Protein ◽  
Peritoneal Adhesions ◽  
Proteasome Subunit ◽  
Peritoneal Tissue ◽  
Intracellular Protein Degradation ◽  
Ubiquitin Proteasome

We investigated the Ubiquitin-Proteasome System (UPS), major nonlysosomal intracellular protein degradation system, in the genesis of experimental postsurgical peritoneal adhesions. We assayed the levels of UPS within the adhered tissue along with the development of peritoneal adhesions and used the specific UPS inhibitor bortezomib in order to assess the effect of the UPS blockade on the peritoneal adhesions. We found a number of severe postsurgical peritoneal adhesions at day 5 after surgery increasing until day 10. In the adhered tissue an increased values of ubiquitin and the 20S proteasome subunit, NFkB, IL-6, TNF-αand decreased values of IkB-beta were found. In contrast, bortezomib-treated rats showed a decreased number of peritoneal adhesions, decreased values of ubiquitin and the 20S proteasome, NFkB, IL-6, TNF-α, and increased levels of IkB-beta in the adhered peritoneal tissue. The UPS system, therefore, is primarily involved in the formation of post-surgical peritoneal adhesions in rats.

Abstract 5417: Inducible 20S β Subunit LMP-2 is Down-Regulated in db/db Mouse Hearts with Diabetic Cardiomyopathy

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Lingyun Zu ◽  
Djahida Bedja ◽  
Lewis C Becker ◽  
Zheqing P Cai
Keyword(s):  
Diabetic Cardiomyopathy ◽  
Ubiquitin Proteasome System ◽  
Left Ventricular ◽  
Heart Weight ◽  
20S Proteasome ◽  
Cardiac Atrophy ◽  
Ubiquitin Proteasome ◽  
And Control ◽  
Fractional Shortening

Background: The ubiquitin-proteasome system (UPS) plays an important role in cell growth, differentiation, and survival. Low molecular mass polypeptide (LMP)-2 is an inducible 20S beta subunit and its role in diabetic cardiomyopathy has not been previously studied. We investigated the hypothesis that LMP-2 is down-regulated in diabetic hearts and is involved in diabetic cardiomyopathy. Methods: db/db mice and control db/+ littermates were studied at 20 weeks of age. Cardiac function was measured by echocardiography. Chymotryptic-like activity of the 20S proteasome was analyzed by fluorogenic assay using the substrate Suc-LLVY-aminomethycoumarin (-AMC). Results: db/db mice had a severe increase in blood glucose and a decrease in heart weight compared with db/+ mice (135±6 vs. 168±7 mg, n = 4, p < 0.01). Left ventricular function was decreased with a lower fractional shortening in db/db mice (48.7±3.2 vs. 60.7±0.4 %, n = 4, p < 0.05). LMP-2 was constitutively expressed in both db/+ and db/db mouse hearts, but its level was severely depressed in the db/db hearts (78±11 vs. 245±18 AU, n = 4, p < 0.01). Consistent with the change in LMP-2, chymotryptic-like activity was also significantly down-regulated in these diabetic hearts (3286±112 vs. 3598±52 AU, n = 3, p < 0.05). Furthermore, the role of LMP-2 in regulating 20S proteasome function and cardiac mass was determined in LMP-2 knockout and wildtype mice. Chymotryptic-like activity was significantly decreased in LMP-2 knockout mouse hearts (11156±360 vs. 18280±454 AU, n = 4, p < 0.01), and cardiac atrophy was found in these knockout mice (147±7.1 vs 178±10.5 mg, n=10; p < 0.01). Taken together, these results suggest that LMP-2 is necessary for normal proteasome function in the heart and its down-regulation may contribute to the development of diabetic cardiomyopathy.

Autophagy and Ubiquitination as Two Major Players in Colorectal Cancer: A Review on Recent Patents

2020 ◽  
Vol 15 (2) ◽  
pp. 143-153
Author(s):  
Javad Saffari-Chaleshtori ◽  
Majid Asadi-Samani ◽  
Maryam Rasouli ◽  
Sayed Mohammad Shafiee
Keyword(s):  
Colorectal Cancer ◽  
Systematic Review ◽  
Protein Quality ◽  
Ubiquitin Proteasome System ◽  
Colorectal Carcinogenesis ◽  
20S Proteasome ◽  
Search Terms ◽  
Ubiquitin Proteasome ◽  
Main Protein

Background: As one of the most commonly diagnosed cancers among men and women, Colorectal Cancer (CRC) leads to high rates of morbidity and mortality across the globe. Recent anti- CRC therapies are now targeting specific signaling pathways involved in colorectal carcinogenesis. Ubiquitin Proteasome System (UPS) and autophagy are two main protein quality control systems, which play major roles in the carcinogenesis of colorectal cancer. A balanced function of these two pathways is necessary for the regulation of cell proliferation and cell death. Objective: In this systematic review, we discuss the available evidence regarding the roles of autophagy and ubiquitination in progression and inhibition of CRC. Methods: The search terms “colorectal cancer” or “colon cancer” or “colorectal carcinoma” or “colon carcinoma” in combination with “ubiquitin proteasome” and “autophagy” were searched in PubMed, Web of Science, and Scopus databases, and also Google Patents (https://patents.google .com) from January 2000 to Feb 2020. Results: The most important factors involved in UPS and autophagy have been investigated. There are many important factors involved in UPS and autophagy but this systematic review shows the studies that have mostly focused on the role of ATG, 20s proteasome and mTOR in CRC, and the more important factors such as ATG8, FIP200, and TIGAR factors that are effective in the regulation of autophagy in CRC cells have not been yet investigated. Conclusion: The most important factors involved in UPS and autophagy such as ATG, 20s proteasome and mTOR, ATG8, FIP200, and TIGAR can be considered in drug therapy for controlling or activating autophagy.

scholarly journals Intraperitoneal Oxygen/Ozone Treatment Decreases the Formation of Experimental Postsurgical Peritoneal Adhesions and the Levels/Activity of the Local Ubiquitin-Proteasome System

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Clara Di Filippo ◽  
Annalisa Capuano ◽  
Barbara Rinaldi ◽  
Margherita Luongo ◽  
Biagio Lettieri ◽  
...  
Keyword(s):  
Surgical Procedure ◽  
Ubiquitin Proteasome System ◽  
Ozone Treatment ◽  
20S Proteasome ◽  
Tissue Oxygen ◽  
Peritoneal Adhesions ◽  
Midline Laparotomy ◽  
Proteasome Subunit ◽  
Peritoneal Tissue ◽  
Ubiquitin Proteasome

We have investigated whether an oxygen/ozone (95%O2/5%O3) mixture would have potential against the formation of experimental postsurgical peritoneal adhesions. In two groups of rats, one control intraperitoneally injected with 3 mL/rat of O2and one intraperitoneally injected with oxygen/ozone mixture (3 mL/rat equivalent to 300 μg/kg ozone), we induced a midline laparotomy and an enterotomy at the level of the ileum to encourage the formation of peritoneal adhesions. Samples were taken from the parietal peritoneal tissue to assess the formation of adhesions 0 and 10 days after the surgical procedure and to assess the levels of ubiquitin and 20S proteasome. We found decreased formation of postsurgical peritoneal adhesions after treatment of the rats with 300 μg/kg ozone associated with a decreased levels of ubiquitin and 20S proteasome subunit within the adhered tissue. Oxygen/ozone mixture is potentially useful for approaching the post-surgical peritoneal adhesions, and the UPS system is involved in this.

Theoretical Studies of the Acid–Base Equilibria in a Model Active Site of the Human 20S Proteasome

2021 ◽  
Vol 61 (4) ◽  
pp. 1942-1953
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
20S Proteasome ◽  
Theoretical Studies ◽  
Acid Base

scholarly journals Application of SPRi Biosensors for Determination of 20S Proteasome and UCH-L1 Levels in the Serum and Urine of Transitional Bladder Cancer Patients

2021 ◽  
Vol 11 (17) ◽  
pp. 7835
Author(s):  
Anna Sankiewicz ◽  
Tomasz Guszcz ◽  
Ewa Gorodkiewicz
Keyword(s):  
Bladder Cancer ◽  
Cancer Progression ◽  
Transitional Cell ◽  
Ubiquitin Proteasome System ◽  
Clinicopathological Parameters ◽  
Control Group ◽  
20S Proteasome ◽  
Ubiquitin Proteasome ◽  
Serum And Urine

The ubiquitin–proteasome system (UPS) participates in the degradation of proteins which play an important role in regulating the cell cycle, apoptosis, and angiogenesis, as well as in the immune system. These processes are important in carcinogenesis. Transitional cell carcinoma (TCC) is one of the predominant types of bladder cancer. The relationship between the ubiquitin–proteasome system and cancer progression has become a topic of increasing interest among researchers. In this work, we propose an application of surface plasmon resonance imaging (SPRi)-based biosensors for the detection of 20S proteasome and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) in the blood serum and urine of patients with TCC. The aim of the study was to determine 20S proteasome and UCH-L1 concentrations and to correlate the results with clinicopathological parameters. The group of subjects consisted of 82 patients with confirmed TCC, in addition to a control group of 27 healthy volunteers. It was found that 20S proteasome and UCH-L1 concentrations were significantly elevated in both the serum and urine of TCC patients, compared with the healthy subjects. There was a correlation between 20S proteasome concentrations in serum and urine, as well as between serum proteasome and UCH-L1 concentration. The SPRi biosensor sensitive to 20S proteasome using PSI inhibitor as the receptor, and the SPRi biosensor sensitive to the UCH-L1 protein using the protein-specific antibody as the receptor is suitable for the determination of 20S proteasome and UCH-L1 in body fluids and can serve as useful tools in the investigation of cancer biomarkers.

The ubiquitin–proteasome system and skeletal muscle wasting

2005 ◽  
Vol 41 ◽  
pp. 173-186 ◽  
Author(s):  
Didier Attaix ◽  
Sophie Ventadour ◽  
Audrey Codran ◽  
Daniel Béchet ◽  
Daniel Taillandier ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Wasting ◽  
Proteolytic Enzymes ◽  
Cathepsin L ◽  
Ubiquitin Proteasome System ◽  
Complete Breakdown ◽  
Skeletal Muscle Proteins ◽  
Ubiquitin Proteasome ◽  
Tripeptidyl Peptidase Ii ◽  
F Box Protein

The ubiquitin–proteasome system (UPS) is believed to degrade the major contractile skeletal muscle proteins and plays a major role in muscle wasting. Different and multiple events in the ubiquitination, deubiquitination and proteolytic machineries are responsible for the activation of the system and subsequent muscle wasting. However, other proteolytic enzymes act upstream (possibly m-calpain, cathepsin L, and/or caspase 3) and downstream (tripeptidyl-peptidase II and aminopeptidases) of the UPS, for the complete breakdown of the myofibrillar proteins into free amino acids. Recent studies have identified a few critical proteins that seem necessary for muscle wasting {i.e. the MAFbx (muscle atrophy F-box protein, also called atrogin-1) and MuRF-1 [muscle-specific RING (really interesting new gene) finger 1] ubiquitin–protein ligases}. The characterization of their signalling pathways is leading to new pharmacological approaches that can be useful to block or partially prevent muscle wasting in human patients.

Sign in / Sign up

Export Citation Format

Share Document