Carbon nanotubes can interact with proteins or enzymes upon penetration into cell membranes of living organisms that may affect the protein-protein interactions in vivo. Here, three structural models composed of fourchain esterase from Hungatella hathewayi with and without pristine or carboxylated single-walled carbon nanotube (SWCNT) are constructed to investigate the changes in protein-protein interactions and SWCNT orientations by molecular dynamics simulations. The results show that the protein-protein interact very tightly to protect them from the separation by the carboxylated or pristine SWCNTs, as shown by the calculations of binding affinity and the distances between the centers of mass of different protein chains. Both pristine and carboxylated SWCNTs cause structural changes in the esterase. In addition, functionalization (e. g., carboxylation) can regulate the SWCNT orientation when positioned near the esterase.