Molecular Dynamics Simulations of Dynein Motor Domain in Explicit Water

Abstract

Dyneins are large microtubule motor proteins that play important roles in various biological movements. Cytoplasmic dynein is responsible for cell division, cell migration and other basic cellular functions. The motor domain of dynein consists of a ring-shaped six ATPases called AAA+ modules. Recently, ADP-bound high-resolution structures of cytoplasmic dynein have revealed the organization of the motor domain that comprises the AAA+ ring, the linker, stalk/strut and C sequence (PDB IDs = 3vkh and 3vkg). However, the high-resolution structure of an ATP-bound dynein remains unclear. Here, we carried out molecular dynamics (MD) simulations of both ADP and ATP-bound forms to examine their structures and dynamics. We built initial structures for MD as following. A high resolution structure (3vkg), which is a truncation mutant, was chosen. Then, we modeled missing residues and added a truncated domain from the wild type structure (3vkh). Four ADP molecules were placed to their original positions in the ADP bound form. One of ADP molecules in the AAA1 module, which is important for dynein function, was replaced to ATP in the ATP-bound form. A rectangular water box was placed around dynein. Finally, the systems consisted of approximately one million atoms. Electrostatic interactions were treated with the zero-dipole summation method, and their computations were accelerated by using GPGPUs. We carried out 200-ns MD simulation in each form, and investigated the effect of ATP on the structure and dynamics of dynein by comparing the trajectories between the ADP- and ATP-bound forms. The stalk of the ATP-bound form was more flexible than that of ADP-boud form. We observed directional fluctuation in the N-terminal subdomain of linker of the ATP-bound form. Interestingly, it coupled with the stalk motion along microtuble axis by principal component analysis for the MD trajectory.