ArticleThe journal of physical chemistry. B2020
Exploring the Proteolysis Mechanism of the Proteasomes.
Article in The journal of physical chemistry. B, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Copper Dyshomeostasis Affects α-Synuclein Clearance Mechanisms in Parkinson's Disease: Insights from In Vitro Models and Translational Evidence.International journal of molecular sciences · 2026Review
- Proteasome Dysregulation in Parkinson's Disease: Insights from Blood-Based Analyses.Molecular neurobiology · 2025Article
- The Role of the Ubiquitin System in Eye Diseases.Life (Basel, Switzerland) · 2025Review
- Structural comparison of human and Plasmodium proteasome β5 subunits: informing selective inhibitor design for anti-malaria agents.Malaria journal · 2025Article
- Distinct substrate specificities of the three catalytic subunits of the Trichomonas vaginalis proteasome.Protein science : a publication of the Protein Society · 2024Article
- Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits.ACS catalysis · 2024Article
- Drug Combination Studies of Isoquinolinone AM12 with Curcumin or Quercetin: A New Combination Strategy to Synergistically Inhibit 20S Proteasome.International journal of molecular sciences · 2024Article
- Article
- Elucidation of theACS catalysis · 2023Article
- Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities.European journal of medicinal chemistry · 2021Article
- Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies.International journal of molecular sciences · 2021Review
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Authors and funding
4 authors.
Funding
Abstract
The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.
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