Conformational Changes of the Protein Domains Upon Binding with Carbon Nanotubes Studied by Molecular Dynamics Simulations

The interactions between the nanoscale particles, such as the carbon nanotubes, and biomolecules are essential to the nanoscale particle based biotechnology and biomedical applications, such as gene delivery, cellular imaging, tumor therapy. However, how the structure changes and whether the functions of the biomolecules are affected due to the existence of nanoscale particles are still poorly understood. In this paper, we review some of our recent progresses, which are based on the large scale molecular dynamics simulations, towards this direction. In our studies, by using an all-α domain named HP35 and an all-β domain named YJQ8WW as the examples, we show that the single-walled carbon nanotube (SWCNT), a typical form of hydrophobic nanoscale particle, can considerably change both the secondary and the tertiary structures of the proteins and form the protein-SWCNT complexes, in which the unfolded part of the proteins wrap around the SWCNT. The hydrophobic interaction and π-π stacking interaction between the nanoscale particles and the hydrophobic residues are found to play important roles in our observation.