The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain,which may securely affect the original function of protein.Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.