Paper Citing NAMD - Abstract
Liu Ying-Zhe; Cai Wen-Sheng; Shao Xue-Guang
Molecular Dynamics Simulation of Hydrophobin Proteins on the Surface of Single-walled Carbon Nanotubes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 33:2013-2018, SEP 10 2012
Carbon nanotubes (CNTs) coated by hydrophobin proteins through noncovalent interactions were shown to be soluble and dispersed in water. However, the detail of the microscopic structure and underlying interaction mechanism is fragmentary. In the present work, atomistic molecular dynamics (MD) simulations have been conducted to elucidate the adsorption mechanism of hydrophobin HFBI on the surface of single-walled carbon nanotubes (SWNTs) in an aqueous environment. Three initial orientations of HFBI towards SWNTs were taken into account, and the relative binding free energies were calculated. Different adsorption conformations were obtained from MD simulation trajectories with an aggregate time of 240 ns. The present results reveal that the adsorption mode, where the adsorption sites fully come from the hydrophobic patch of the protein, is the most energetically favored. Furthermore, the main secondary structures of protein are preserved in the entire course of adsorption due to four disulfide bonds.
