Proteasome transport model

Finally for effects where both the translocation and kinetic properties are important one can merge both models. This can be done by including the transport corrections in the kinetic model described here. In this case different transport rate functions result in different influx coefficients and, hence, different kinetic properties of the proteasome. This modeling approach is especially important for the... 

Considering the highly processive mechanism of the protein degradation by the proteasome, a question naturally arises what is a mechanism behind such translocation rates Let us discuss one of the possible translocation mechanisms. In [52] we assume that the proteasome has a fluctuationally driven transport mechanism and we show that such a mechanism generally results in a nonmonotonous translocation rate. Since the proteasome has a symmetric structure, three ingredients are required for fluctuationally driven translocation the anisotropy of the proteasome-protein interaction potential, thermal noise in the interaction centers, and the energy input. Under the assumption that the protein potential is asymmetric and periodic, and that the energy input is modeled with a periodic force or colored noise, one can even obtain nonmonotonous translocation rates analytically [52]. Here we... 

Next let us show how one can compute the proteasome output if the transport rates are given. In our model we assume that the proteasome has a single channel for the entry of the substrate with two cleavage centers present at the same distance from the ends, yielding in a symmetric structure as confirmed by experimental studies of its structure. In reality a proteasome has six cleavage sites spatially distributed around its central channel. However, due to the geometry of its locations, we believe that a translocated protein meets only two of them. Whether the strand is indeed transported or cleaved at a particular position is a stochastic process with certain probabilities (see Fig. 14.5). 

A. Zaikin and J. Kurths. Optimal length transportation hypothesis to model proteasome product size distribution. Journal of Biological Physics, 2006. (in press, DOI 10.1007/sl0867-006-9014-z). 

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