ArticleBiophysical journal2005
A mathematical model of protein degradation by the proteasome.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Cryo-EM structure of the plant 26S proteasome.Plant communications · 2022Article
- Association with proteasome determines pathogenic threshold of polyglutamine expansion diseases.Biochemical and biophysical research communications · 2021Article
- Proteasome Biology: Chemistry and Bioengineering Insights.Polymers · 2020Review
- Article
- Proteasome properties of hemocytes differ between the whiteleg shrimp Penaeus vannamei and the brown shrimp Crangon crangon (Crustacea, Decapoda).Cell stress & chaperones · 2017Article
- Proteostasis, oxidative stress and aging.Redox biology · 2017Review
- Novel Proteasome Inhibitors and Histone Deacetylase Inhibitors: Progress in Myeloma Therapeutics.Pharmaceuticals (Basel, Switzerland) · 2017Review
- Degradation of oxidized proteins by the proteasome: Distinguishing between the 20S, 26S, and immunoproteasome proteolytic pathways.Molecular aspects of medicine · 2016Review
- Modelling proteasome and proteasome regulator activities.Biomolecules · 2014Review
- Proteasome inhibitors - molecular basis and current perspectives in multiple myeloma.Journal of cellular and molecular medicine · 2014Review
- A systems view of the protein expression process.Systems and synthetic biology · 2011Article
- Force spectroscopy of substrate molecules en route to the proteasome's active sites.Biophysical journal · 2011Article
- The 20S proteasome splicing activity discovered by SpliceMet.PLoS computational biology · 2010Article
- Crystallization and preliminary X-ray analysis of the Thermoplasma acidophilum 20S proteasome in complex with protein substrates.Acta crystallographica. Section F, Structural biology and crystallization communications · 2008Article
- Optimal length transportation hypothesis to model proteasome product size distribution.Journal of biological physics · 2006Article
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Authors and funding
5 authors.
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Abstract
The proteasome is the major protease for intracellular protein degradation. The influx rate of protein substrates and the exit rate of the fragments/products are regulated by the size of the axial channels. Opening the channels is known to increase the overall degradation rate and to change the length distribution of fragments. We develop a mathematical model with a flux that depends on the gate size and a phenomenological cleavage mechanism. The model has Michaelis-Menten kinetics with a V(max) that is inversely related to the length of the substrate, as observed in the in vitro experiments. We study the distribution of fragment lengths assuming that proteasomal cleavage takes place at a preferred distance from the ends of a protein fragment, and find multipeaked fragment length distributions similar to those found experimentally. Opening the gates in the model increases the degradation rate, increases the average length of the fragments, and increases the peak in the distribution around a length of 8-10 amino acids. This behavior is also observed in immunoproteasomes equipped with PA28. Finally, we study the effect of re-entry of processed fragments in the degradation kinetics and conclude that re-entry is only expected to affect the cleavage dynamics when short fragments enter the proteasome much faster than the original substrate. In summary, the model proposed in this study captures the known characteristics of proteasomal degradation, and can therefore help to quantify MHC class I antigen processing and presentation.
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