Motor proteins frequently interact with obstacles in the crowded cellular environments. We consider systems in which two degrees of freedom---motor and obstacle---affect each other's motion. Examples include helicase unwinding of DNA, a polymerizing filament which grows near a wall, and two motor proteins colliding on a microtubule. This talk describes a simplified model of the motor protein-obstacle interaction, where an interaction potential describes how the protein and obstacle affect each other's motion. We present results on helicases---the motor proteins which unwind double-stranded DNA in cells. For the specific class of helicase proteins which translocate on a DNA single strand as well as unwinding double-stranded DNA, the DNA single-strand/double-strand junction acts as an obstacle to the helicase. We show that the form of the interaction between helicase and junction strongly affects the overall DNA unwinding rate.
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