Exploring the Folding Mechanism of Small Proteins GB1 and LB1

The computational atomistic description
of the folding reactions
of the B1 domains, GB1 and LB1, of protein G and protein L, respectively,
is an important challenge in current protein folding studies. Although
the two proteins have overall very similar backbone structures (β-hairpin−α-helix−β-hairpin),
their apparent folding behaviors observed experimentally were remarkably
different. LB1 folds in a two-state manner with the single-exponential
kinetics, whereas GB1 folds in a more complex manner with an early
stage intermediate that may exist on the folding pathway. Here, we
used a new method of all-atom molecular dynamics simulations to investigate
the folding mechanisms of GB1 and LB1. With the Lorentzian energy
term derived from the native structure, we successfully observed frequent
folding and unfolding events in the simulations at a high temperature
(414 K for GB1 or 393 K for LB1) for both the proteins. Three and
two transition-state structures were predicted for the GB1 and LB1
folding, respectively, at the high temperature. Two of the three transition-state
structures of GB1 have a better formed second β-hairpin. One
of the LB1 transition states has a better formed first hairpin, and
the other has both hairpins equally formed. The structural features
of these transition states are in good agreement with experimental
transition-state analysis. At 300 K, more complex folding processes
were observed in the simulations for both the proteins. Several intermediate
structures were predicted for the two proteins, which led to the conclusion
that both the proteins folded through similar mechanisms. However,
the intermediate state accumulated in a sufficient amount only in
the GB1 folding, which led to the double-exponential feature of its
folding kinetics. On the other hand, the LB1 folding kinetics were
well fitted by a single-exponential function. These results are fully
consistent with those previously observed experimentally.