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ABSTRACT: Neck linker (NL) is one of the most important mechanical elements of kinesin motors. The zipping up process of the neck-zipper (NZ) formed by NL and the related secondary structure elements is one of the major parts of kinesin's power stroke. All the weak interactions that are responsible for the formation of NZ are sensitive to or dependent on water. To investigate the role of water in the NZ region, a molecular dynamics (MD) model is set up with a crystal structure of kinesin 2KIN surrounded by a 10 Å water layer, and minimization is performed to determine the positions of hydrogen atoms and other atoms. It is revealed that water molecules can assist the docking process of NL by forming hydrogen bonds at those positions where direct hydrogen bonding between the two sides of NZ is hindered and then acts as a constructive component of NZ at the docked state of NL. This result may improve the understanding of the mechanism for the docking of NL of kinesin wherein the function of water has not been comprehended sufficiently.
Chinese Physics Letters 01/2009; 26(7). · 0.81 Impact Factor