We address the problem of proteasomal protein translocation . Proteasomes are important for all aspects of the cellular metabolism but the mechanism of protein transport remains unknown. We introduce a new stochastic model of the proteasomal transport. We account for the protein translocation and the topology of the positioning of cleavage centers of a proteasome from first principles. We show by test examples and by a comparison with experimental data that our model allows reconstruction of the translocation  rates from mass spectroscopy data on digestion patterns and can be used to investigate the properties of transport in different experimental set-ups. Finally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids which enables more reliable determination of 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 .
R
. Proteasomes are important for all aspects of the cellular metabolism but the mechanism of protein transport remains unknown. We
and
R
transport. We
digestion (cleavage) of proteins. In this model we
D
topology of the
R
centers
sites
R
a comparison with
processing
A
and cleavage
R
Finally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids which enables more reliable determination of translocation rates
Detailed investigation with this model will enable theoretical quantitative prediction of the proteasomal activity