Water Soluble Modified Carbon Nanotubes Interact With Ww Function Protein Molecular Dynamics Simulations

Nano-scale materials have been widely used in various fields, including nano-devices and nano-biomedicine. In recent years, it has been found that the nano-materials may be toxic to the living beings. The understanding of the mechanism of the possible toxicity or non-toxicity is of importance in the applications. As one of the promising nano-particles, carbon nanotube (CNT) has attracted special attentions. It has been recognized that CNT will affect the structure and function of protein. In2011, Guanghong Zuo et. al. from Fudan University found that single-walled carbon nanotubes(SWCNTs) could plug into the hydrophobic cores of the YAP65WW domain to form stable complexes, which would destroy the structure of the protein and thus lead to the loss of its original biological function. Their studies provide theoretical progress on the understanding of the mechanism of the possible toxicity of nano-particles at the molecular level. Because of the property of aggregation of hydrophobic SWCNTs, the SWCNTs that widely used in bio-medicine are usually functionalized with water soluble groups. In this thesis we focused on the interaction between the functionalized SWCNT and YAP65WW domain protein.Firstly, we study the interaction between the SWCNT functionalized with three arginine side chains (f-SWCNT) and YAP65WW domain. Our simulation results show that the functionalized SWCNT can adsorb on the hydrophobic core of the YAP65WW domain because of the hydrophobic interaction between the naked wall of SWCNT and the YAP65WW domain, which affects the structure of the protein. The functional groups can form hydrogen bonds with some residues of the protein, which will stabilize the f-SWCNT-protein complex.Then we study the binding competition between the f-SWCNT and the ligand on the target protein. The results show that f-SWCNT has a large probability to adsorb on the active site of the YAP65WW domain before the ligand. Because of the active site being occupied, the protein will lose its original biological function. This result shows that the nano-particle functionalized with soluble groups is still probably toxic to the proteins because of the strong hydrophobic interaction, the hydrogen bonds and other complex factors.