ABSTRACT
In the present work, we explored the diameter selectivity of dynamic self-assembly for the single-strand DNA (ssDNA) encapsulation in double-walled nanotubes (DWNTs) via molecular dynamics simulation method. Moreover, the pulling out process was carried out by steered molecular dynamics simulations. Considering π-π stacking and solvent accessibility together, base-CNT binding should be strongest on a graphene sheet and weakest on the inner CNT surface. When pulling the ssDNA out of the single-walled carbon nanotube (SWNT), the force exhibits characteristic fluctuations around a plateau about 300 pN. Each fluctuation force pulse to pull ssDNA corresponds to the exit of one base. In addition, the solvents used for the system are also of significant interest. Water does play an important role in encapsulation process but doesn't in the pulling out process.
Subject(s)
DNA, Single-Stranded/pharmacokinetics , Graphite/chemistry , Nanotubes, Carbon/chemistry , Adsorption , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/metabolism , Gene Transfer Techniques , Graphite/metabolism , Models, Biological , Molecular Dynamics Simulation , Polymers/chemical synthesis , Polymers/chemistry , Polymers/metabolism , Polymers/pharmacokinetics , ThermodynamicsABSTRACT
Steered molecular dynamics simulations are performed to explore the unfolding and refolding processes of CLN025, a 10-residue beta-hairpin. In unfolding process, when CLN025 is pulled along the termini, the force-extension curve goes back and forth between negative and positive values not long after the beginning of simulation. That is so different from what happens in other peptides, where force is positive most of the time. The abnormal phenomenon indicates that electrostatic interaction between the charged termini plays an important role in the stability of the beta-hairpin. In the refolding process, the collapse to beta-hairpin-like conformations is very fast, within only 3.6 ns, which is driven by hydrophobic interactions at the termini, as the hydrophobic cluster involves aromatic rings of Tyr1, Tyr2, Trp9, and Tyr10. Our simulations improve the understanding on the structure and function of this type of miniprotein and will be helpful to further investigate the unfolding and refolding of more complex proteins.
