HUANG Yan-Bin1, PAN Zhang2,3, ZHANG Hui2, AN Li2, KONG De-Xin4, JI Qing2
1School of Science, Hebei University of Engineering, Handan 0560382School of Science, Hebei University of Technology, Tianjin 3001303Basic Courses Department, Tangshan College, Tangshan 0630004Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049
Water in the Neck-Zipper Region of Kinesin
HUANG Yan-Bin1, PAN Zhang2,3, ZHANG Hui2, AN Li2, KONG De-Xin4, JI Qing2
1School of Science, Hebei University of Engineering, Handan 0560382School of Science, Hebei University of Technology, Tianjin 3001303Basic Courses Department, Tangshan College, Tangshan 0630004Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049
摘要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 10Å, 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.
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 10Å, 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.
HUANG Yan-Bin;PAN Zhang;ZHANG Hui;AN Li;KONG De-Xin;JI Qing. Water in the Neck-Zipper Region of Kinesin[J]. 中国物理快报, 2009, 26(7): 78701-078701.
HUANG Yan-Bin, PAN Zhang, ZHANG Hui, AN Li, KONG De-Xin, JI Qing. Water in the Neck-Zipper Region of Kinesin. Chin. Phys. Lett., 2009, 26(7): 78701-078701.
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