SMD Research Of The Force Genaration Process Of Kinesin

As the smallest and simplest motor，kinesins have served as the model for discoverying therelationship between protein structure and mechanochemical function of motor. In kinesinmotors, a fundamental question concerns: How the force generates which is required for forwardwalking continuously. The present conclusion is that neck-linker is a key component in forcegenerating of kinesin. Neck-linker was forced to unbind from motor head via our previous SMDsimulations. Those simulations demonstrate that the rates of H bonds breaking in all6teeth aredifferent. We start with zero force to explore what influence the neck-linker unbinding rateevents one by one. Using MD software NAMD we first simulate the free movement ofneck-linker of kinesin in water environment. The results indicate that the outermost H bond ofthe6th tooth in neck zipper domain unbinds while others keep stable. The attacks of the watermolecular on the H bond between from the neck linker and the motor domain have beenmonitored. The further statistical analysis show that the H bonds breaking are mainly caused byattacks of the water molecules and other factors play a minor role.