The Study On Correlation Of Backbone Hydrogen Bonds On Necklinker Of Kinesin With Water

As the smallest molecular motor,kinesin plays an extremely important role in cell transport and it strongly influences cell mitosis.Kinesin converts the chemical energy of ATP hydrolysis into mechanical energy which can be directly applied and used to carry cargo along a microtubule for hundreds of steps in unique direction.During the process of walking,kinesin is in the different nucleotide cyclic states.The two motor domains,which are in an unsynchronized state simultaneously,alternate their relative positions while walking along the microtubule.At this point,the two motor domains undergo mild conformational change correspondingly.The process of kinesin’s neck-linker docking to the motor domain is a key factor in the force generation activity of kinesin.(1)By using molecular dynamics simulation,the interactions of the backbone hy-drogen bonds between the kinesin’s neck-linker and motor domain were assessed.It was found that four zipper-like backbone hydrogen bonds in the area between β 10 of the neck-linker and the motor domain were formed.It showed that the difference on strengths of these four backbone hydrogen bonds were large.Hence,the bond rate of each bond was evaluated.In the MD simulation,we used explicit water molecular model to observe the interaction between amino acids and water molecules.We believe that the strength difference of these backbone hydrogen bonds was mainly due to the relationship among these backbone hydrogen bonds and water molecules around them The attack activities from water molecules to hydrogen bonds depend on the surround-ing environment.Once water molecules approach backbone hydrogen bonds and attack them,they are likely to help break the hydrogen bonds and promote the undocking pro-cess of the neck-linker from the motor domain.Water molecules can get close to the backbone hydrogen bonds via water channels which are paths that particularly allow the water molecules enter.Therefore,water molecules can directly attack hydrogen bonds and weaken their strength.On the other terminus of the zipper,the backbone hydrogen bonds are well protected by the hydrophobic side chain of the amino acids and are rel-atively difficult to break.Thus,the intensity of the hydrogen bonds of the zipper is in a gradient distribution(2)The kinesin’s neck-linker at the C-terminus of kinesin is considered to be the key to the force generation process of kinesin.The neck-linker consists of approxi-mately 14 amino acid residues and can be divided into three parts:three starting amino acids at the N-terminus of the neck-linker,β 9 and β 10.Respectively,the neck-linker is also connected to the motor domain in three steps:the first three amino acids form an extra turn structure;the β 9 is docked to the motor domain;and,the β 10 is docked to the motor domain.In these processes,kinesins are docking and undocking by the effect of various external forces and internal forces.This study focuses on the third step.The β 10 is docked to the motor domain to form zipper-like four hydrogen bonds Moreover,the gradient strength of the hydrogen bonds of the zipper helps the docking and undocking processesThe neck-linker docking process is a force generating process that drives the rear motor domain to the front so that allows the motor to move forward.In the process,once the ASN latch at the β 10 N-terminus is locked,the next docking process is rela-tively easy to implement.The undocking process of the neck-linker is the reverse of the docking process.The C-terminus backbone has a low hydrogen bond strength and is easily to be broken by attack from water molecules.As the backbone hydrogen bonds open one by one from C-terminus,subsequent backbone hydrogen bonds are exposed to the aqueous environment and increasing the likelihood of opening.All processes indicate that protein application uses less energy to achieve better results(3)We investigated the coordination relationship of several non-bonding interac-tions involved in the mechanical function of kinesin.The spatial structure of the protein is linked by hydrogen bonding between the amino acid main chain or the side chain of the peptide chain,and has interactions such as salt bond,hydrophobic interaction,and water bridge.Apparently,the docking process of β 10 at the C-terminus of the neck-linker is driven by backbone hydrogen bonds.However,the arrangement of the hy-drophobic and hydrophilic amino acid side chains in the relevant part of β 10 is critical for the formation and stabilization of the backbone hydrogen bond.By mutating sev-eral key hydrophobic amino acid,we investigated the relationship between hydrophobic interactions and the backbone hydrogen bonds of β 10 in the neck-linker and found a positive relationship between them.These findings deepen our understanding of kinesin structural design.The researches in this paper reveal various bond energy relationships of kinesin docking and undocking process.And,it suggests that the importance of the effective strength of the protein backbone hydrogen bonds and non-bond interactions with the surrounding water environment should be considered in future studies of the conforma-tional changes of similar proteins.