Paper Citing NAMD - Abstract
Geng, Yi-Zhao; Li, Tie; Ji, Qing; Yan, Shiwei
Simulation Study of Interactions Between Kinesin's Neck Linker and Motor Domain
CELLULAR AND MOLECULAR BIOENGINEERING, 7:99-105, MAR 2014
The docking movement of kinesin's neck linker to the motor domain is the force generation step of kinesin. This docking movement is achieved by various non-bonding interactions between neck linker and motor domain. However, the relative strength and the structural basis for these interactions are still unclear. To elucidate these problems, we unbind the docked neck linker from motor domain using steered molecular dynamics and mutation simulations. We find that the surprisingly high strength of a structure called the " asparagine latch" arises from exquisite cooperation between hydrogen bonds and hydrophobic interactions. A beta-sheet called the " cover-neck bundle" behaves like an elastic beam in its unbinding process. The hydrophobic interaction between ILE327 (amino acid sequence in 2KIN) and the hydrophobic pocket on the motor domain is strong and provides a fixed support for elastic bending of the cover-neck bundle.
