Paper Citing NAMD - Abstract
Geng Yi-Zhao; Ji Qing; Liu Shu-Xia; Yan Shi-Wei
Initial conformation of kinesin's neck linker
CHINESE PHYSICS B, 23 Art. No. 108701, OCT 2014
How ATP binding initiates the docking process of kinesin's neck linker is a key question in understanding kinesin mechanisms. By exploiting a molecular dynamics method, we investigate the initial conformation of kinesin's neck linker in its docking process. We find that, in the initial conformation, the neck linker has interactions with beta 0 and forms a 'cover-neck bundle' structure with beta 0. From this initial structure, the formation of extra turns and 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. Based on these findings, a pathway from ATP binding-induced motor head rotation to neck linker docking is proposed.
