A numerical algorithm for investigating the role of the motor–cargo linkage in molecular motor-driven transport

We extend the numerical algorithm developed by Wang et al. (2003. J. Theor. Biol. 221, 491–511) for studying biomolecular transport processes to include the linkage that connects molecular motors to their cargo. The new algorithm is used to investigate how the stiffness of the linkage affects the average velocity, effective diffusion coefficient, and randomness parameter. Three different models for molecular motors are considered: (1) a discrete stepping motor (2) a motor moving in a tilted-periodic potential and (3) a motor driven by a flashing potential. We demonstrate that a flexible motor–cargo linkage can make inferences on motor behavior based on measurements of the cargoʹs position difficult. We also show that even for the case of a tilted-periodic potential there exists an optimal stiffness of the linkage at which transport is maximized. The MATLAB code used in this paper is available at: http://www.unc.edu/~telston/code/.