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Based on our recent study on physical origin of hydrophobic effects, this is applied to investigate the dependence of hydrophobic interactions on the solute size. As two same hydrophobic solutes are dissolved into water, the hydration free energy is determined, and the critical radius (Rc) is calculated to be 3.2 Å. With reference to the Rc, the dissolved behaviors can be divided into initial and hydrophobic solvation processes. These can be demonstrated by the molecular dynamics simulations on C 60 -C 60 fullerenes in water, and CH 4 -CH 4 molecules in water. In the association of C 60 fullerenes in water, with decreasing the separation between C 60 fullerenes, hydrophobic interactions can be divided into H1w and H2s hydrophobic processes, respectively. In addition, it can be derived that maximizing hydrogen bonding provides the driving force in the association of hydrophobic solutes in water.

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 forceextension 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.

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