title: Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes.
abstract: Proteasomal protein degradation is a key determinant of protein half-life and hence of cellular processes ranging from basic metabolism to a host of immunological processes. Despite its importance the mechanisms regulating proteasome activity are only incompletely understood. Here we use an iterative and tightly integrated experimental and modelling approach to develop, explore and validate mechanistic models of proteasomal peptide-hydrolysis dynamics. The 20S proteasome is a dynamic enzyme and its activity varies over time because of interactions between substrates and products and the proteolytic and regulatory sites; the locations of these sites and the interactions between them are predicted by the model, and experimentally supported. The analysis suggests that the rate-limiting step of hydrolysis is the transport of the substrates into the proteasome. The transport efficiency varies between human standard- and immuno-proteasomes thereby impinging upon total degradation rate and substrate cleavage-site usage.
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom.
authors.forename: Juliane
authors.initials: J
authors.lastname: Liepe
authors.affiliation: Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Hermann-Georg
authors.initials: HG
authors.lastname: Holzhütter
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Bellavista
authors.affiliation: Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Kloetzel
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom.
authors.forename: Michael P H
authors.identifier: http://orcid.org/0000-0002-3577-1222
authors.initials: MP
authors.lastname: Stumpf
authors.affiliation: Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany.|Luigi Galvani, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Mishto
mesh_terms: D000818:Animals; D002460:Cell Line; D005786:Gene Expression Regulation; D006801:Humans; D007700:Kinetics; D008099:Liver / Q000201:enzymology; D051379:Mice; D008954:Models, Biological; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D021381:Protein Transport; D059748:Proteolysis
chemical_list: D046988:Proteasome Endopeptidase Complex
keywords: Bayesian analysis; biophysics; computational biology; experimental design; functional analysis; human; mouse; proteasome regulation; proteasome structure; structural biology; systems biology