Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity

Details Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity

2003-10-20

arxiv.org/abs/cond-mat/0310455v2

Biophys. J. 86, 3373 (2004)

Physics

Condensed Matter

Statistical Mechanics

42 pages, 12 figures

Scientific paper

10.1529/biophysj.103.036152

The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or DNA is biased due to the different chemical environments on the two sides of the membrane, while the molecular motor motion is biased through a coupling to chemical energy. An externally applied force can oppose these biases. For both systems we solve lattice models exactly both with and without disorder. The models incorporate explicitly the coupling to the different chemical environments for polymer translocation and the coupling to the chemical energy (as well as nucleotide pairing energies) for molecular motors. Using the exact solutions and general arguments we show that the heterogeneity leads to anomalous dynamics. Most notably, over a range of forces around the stall force (or stall tension for DNA polymerase/exonuclease systems) the displacement grows sublinearly as t^\mu with \mu<1. The range over which this behavior can be observed experimentally is estimated for several systems and argued to be detectable for appropriate forces and buffers. Similar sequence heterogeneity effects may arise in the packing of viral DNA.

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