Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation |
Results of SMD simulation of GB1 and gpW proteins. (a) The force–extension curves of the unfolding process of protein GB1 show an force peak at the extension of ∼ 3.19 nm and forces all above 600 pN (710 pN, 714 pN, and 600 pN, respectively), which indicates the unfolding transition state. Three force–extension curves of the unfolding process of GB1 show very small difference in its unfolding process. (b) Six typical force–extension curves of the unfolding process of the protein gpW show multiple random force peaks. The peak forces are all below 200 pN, much smaller than that of GB1, which demonstrates that gpW is less mechanically resistant. In all SMD simulations, spring constant k = 100 kJ/mol/nm2 and pulling velocity v = 0.001 nm/ps. |