Figure 3.

Folding of a three-helix bundle protein. (A) A folding trajectory started from a fully unfolded conformation of the three-helix bundle protein (B domain of Staphylococcus aureus protein A, Protein Data Bank code 1BDD) using the all-atom sequence-based potential described in the text. The plot shows the time course of both energy and drms from crystal structure. The trajectory reaches drms values as low as 1 Å. (B) The lowest-energy structure from a folding trajectory superimposed on the native crystal structure. The drms between the two structures is 1.9 Å.