Reverse Engineering of Proteasomal Translocation Rates

We address the problem of proteasomal protein translocation and introduce a new stochastic model of the proteasomal digestion (cleavage) of proteins. In this model we account for the protein translocation and the positioning of cleavage sites of a proteasome from first principles. We show by test examples and by processing experimental data that our model allows reconstruction of the translocation and cleavage rates from mass spectroscopy data on digestion patterns and can be used to investigate the properties of transport in different experimental set-ups. Detailed investigation with this model will enable theoretical quantitative prediction of the proteasomal activity.