The Simulation Research Of Kinesin Neck-Linker's Docking Process

Kinesin,the smallest processive motor proteins known to date,carry out various tasks including cargo transport and mitosis.In kinesin motors,a basic question is about the mechanism by which ATP binding generates the force required for walking.The zipper-like docking of Neck-Linker onto motor head after ATP binding has been suggested as the force generating step.A tooth consists of a central amino acid and a group of amino acids which have weak interactions with the central amino acid.The weak interactions in the neck zipper include hydrophobic interaction,hydrogen bond and salt bridge.We analysed the weak interactions in every tooth and find that in the neck linker's docking process,weak interactions need cooperation to form a tooth.The formation of one tooth shortens the distance between the residues of the next tooth,so that makes conditions for the formation of the next tooth.NAMD is a kind of open source MD software.We simulated kinesin neck linker's docking process through NAMD and partly proved our analysis of the weak interactions in the neck zipper.