Modeling the in Vitro 20S Proteasome Activity: The Effect of PA28-αβ and of the Sequence and Length of Polypeptides on the Degradation Kinetics

Michele Mishto, Fabio Luciani, Hermann Georg Holzhütter, Elena Bellavista, Aurelia Santoro, Kathrin Textoris-Taube, Claudio Franceschi, Peter M. Kloetzel, Alexey Zaikin

Research output: Contribution to journalArticle

Abstract

Proteasomes are fundamental for the degradation of intracellular proteins, having a key role in several important metabolic and signaling pathways, in the cell cycle and in antigen presentation. In vitro proteasomal digestion assays are widely used in molecular biology and immunology. We developed a model, ProteaMAlg (proteasome modeling algorithm) that describes the kinetics of specific protein fragments generated by 20S proteasomes in different conditions, once the substrate cleavage strengths are provided. ProteaMAlg was tested on a variety of data available in the literature as well as on new degradation experiments performed with polypeptides of different sequences and lengths. The comparison between in vitro and in silico experiments was used to quantify the effect on degradation of the sequence and the length of target polypeptides, of the presence of regulatory molecules such as PA28-αβ, and of the type of 20S proteasome (constitutive- or immunoproteasome). The model showed that the effect of the PA28 regulatory subunit results in a modification of the gating functions of the proteasome core particle. Immunoproteasome digestion experiments suggested that this form of proteasome, which is involved in generating MHC-class I epitopes, presents modified cleavage and gating activities. Our analysis improves the current understanding of the kinetics of proteasome functioning, and provides a tool to quantify and predict the effect of key parameters during in vitro digestion. ProteaMAlg is publicly available on the web (http://www.proteamalg.com).

Original languageEnglish
Pages (from-to)1607-1617
Number of pages11
JournalJournal of Molecular Biology
Volume377
Issue number5
DOIs
Publication statusPublished - Apr 11 2008

Keywords

  • digestion kinetics
  • mathematical modeling
  • MHC class I antigen
  • prediction algorithm
  • proteasome degradation

ASJC Scopus subject areas

  • Virology

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    Mishto, M., Luciani, F., Holzhütter, H. G., Bellavista, E., Santoro, A., Textoris-Taube, K., Franceschi, C., Kloetzel, P. M., & Zaikin, A. (2008). Modeling the in Vitro 20S Proteasome Activity: The Effect of PA28-αβ and of the Sequence and Length of Polypeptides on the Degradation Kinetics. Journal of Molecular Biology, 377(5), 1607-1617. https://doi.org/10.1016/j.jmb.2008.01.086