Biology – Quantitative Biology – Subcellular Processes
Scientific paper
2008-06-16
J. Stat. Mech.: Theory Exp., P01009 (2009)
Biology
Quantitative Biology
Subcellular Processes
14 pages, 4 figures, submitted to J. Stat. Mech. (Special issue for proceedings of 5th Intl. Conf. on Unsolved Problems on Noi
Scientific paper
10.1088/1742-5468/2009/01/P01009
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic model of the proteasomal degradation of proteins, which accounts for the protein translocation and the topology of the positioning of cleavage centers of a proteasome from first principles. For this model we develop the mathematical description based on a master-equation and techniques for reconstruction of the cleavage specificity inherent to proteins and the proteasomal translocation rates, which are a property of the proteasome specie, from mass spectroscopy data on digestion patterns. With these properties determined, one can quantitatively predict digestion patterns for new experimental set-ups. Additionally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids, which enables especially reliable determination of translocation rates.
Goldobin Denis S.
Zaikin Alexey
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