KINESIN MODEL FOR BROWNIAN DYNAMICS SIMULATIONS OF STEPPING EFFICIENCY

The motor protein kinesin plays an integral role in cell function, transporting, for example, cargo from the center to the periphery of a cell. Kinesin molecules have been shown experimentally to walk along microtubules in a hand-over-hand stepping motion, carrying their cargo eight nanometers per step. However, details of the stepping process are still under investigation. Kinesins are difficult to study with atomistic simulations due to the size of the proteins and the long time-scales involved. In this work we develop a 3D model of kinesin stepping on a rigid microtubule substrate that can be simulated efficiently with Brownian dynamics simulations. The interactions governing the motor protein conformations and the interactions between kinesin sites and the microtubule sites are designed to reproduce important aspects of the biological system. We perform simulations spanning many kinesin steps to investigate the stepping efficiency of the motor protein for different neck linkers. We find that neck linkers close to the wild-type length yield a stepping efficiency of about 90%, in agreement with experimental data. In addition, we find that increasing the neck-linker length leads to a decrease in efficiency, as has also been observed in experiments