  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.
