Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics...

Folding pathways of the B domain of staphylococcal protein A have been sampled with a distributed computing approach. Starting from an extended structure, the method employs an index measuring topological similarity to the native structure to selectively sample trajectory branches leading to the native fold. Unperturbed and continuous folding trajectories are drawn on a physics-based atomic potential energy surface with an implicit solvent. The sampled folding trajectories demonstrate a similar sequence of events: the earlier stage involves a partial formation of helix 2 and to a less extent of helix 1 at their N terminals, followed by the hydrophobic collapse between residues F14, I17, and L18 on helix 1 and residues R28, F31, and I32 on helix 2, which results in the rigidification of the helix turn from R28 to I32. Helix 2 is then able to extend, allowing for the formation to turn 2. The above description explains one experimental result why a G30A mutant of the protein was observed to be the fastest folder among proteins of its size. And the ensemble of structures right before the final collapse is in good agreement with the transition state ensemble mapped by another recent experiment with Fersht Phi values. We emphasize that because the approach here does not provide quantifications of the free energy landscape, our model of the transition state ensemble emerges from comparisons of simulations and previous experimental results rather from the simulation results alone. On the other hand, as our approach does not rely on a low-dimensional free energy surface, it can complement methods based on the construction of free energy surfaces.