  How ATP binding initiates the docking process of kinesin's neck linker is a
key question in understanding kinesin mechanism. It is believed that the
formation of an extra turn structure by the first three amino acids of neck
linker (LYS325, THR326, ILE327 in 2KIN) is crucial for initiating the docking
process. But the initial conformation of neck linker (specially the three amino
acids of the extra turn) and the neck linker docking initiation mechanism
remain unclear. By using molecular dynamics method, we investigate the initial
conformation of kinesin's neck linker in the docking process. We find that, in
the initial state of NL docking process, NL still has interactions with
{\beta}0 and forms a conformation similar to the "cover-neck bundle" structure
proposed by Hwang et al. [Structure 2008, 16(1): 62-71]. From this initial
structure, the docking of the "cover-neck bundle" structure can be achieved.
The motor head provides a forward force on the initial cover-neck bundle
structure through ATP-induced rotation. This force, together with the
hydrophobic interaction of ILE327 with the hydrophobic pocket on the motor
head, drives the formation of the extra turn and initiates the neck linker
docking process.
