Steered Molecular Dynamics Simulation Of Three Biosystems

During the past few years, merging biotechnology and materialsscience has been paid extraordinary attention. In particular, the carbonnanotube (CNT) with nucleic acids has been extensively studied due toapplications in bioengineering and clinical medicine. CNT were used todeliver plasmid DNA into cells. Since ssDNA could bind to outer surfacesof CNTs through π π stacking, resulting in helical wrapping to thesurface, it can assist dispersion and separation of CNTs. It is well-knownthat most proteins are functional in vivo because they fold intocharacteristic three-dimensional structures. Under some conditions,protein will unfold into random coil that loses biochemical function. Thusfolding and unfolding are essential to life.In this paper, we study the interaction between nanotube and DNA, aswell as the unfolding of proteins by mechanical stretching using steeredmolecular dynamics (SMD) simulation, which mimics AFM experimentand reveals the molecular mechanisms underlying mechanical function.Our simulations improve the understanding on the structure and function of biomolecules and will be helpful to further investigate the unfoldingand refolding of more complex proteins.