Dominant folding pathways of a WW domain

Abstract

We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways approach. We find evidence for the existence of two folding pathways, which differ by the order of formation of the two hairpins. This result is consistent with the analysis of the experimental data on the folding kinetics of WW domains and with the results obtained from large-scale molecular dynamics simulations of this system. Free-energy calculations performed in two coarse-grained models support the robustness of our results and suggest that the qualitative structure of the dominant paths are mostly shaped by the native interactions. Computing a folding trajectory in atomistic detail only required about one hour on 48 Central Processing Units. The gain in computational efficiency opens the door to a systematic investigation of the folding pathways of a large number of globular proteins.

Fig. 1.

Native structure of Fip35, a WW domain of the fip mutant of protein human pin1 (pdb code: pin1). The primary sequence of fip35 is: EEKLPPGWEKRMSADGRVYYFNHITNASQWERPSG.

Fig. 2.

Schematic representation of the structure of the two folding pathways obtained in our DRP simulations.

Fig. 3.

The free energy at T = 300 K as a function of the rmsd to native of the two hairpins, obtained from the Monte Carlo simulations in two coarse-grained models, described in Methods . In the upper box the model accounts for both native and nonnative interaction, in the lower box the model contains only native interactions. In the insert of the upper box, we show the corresponding plot of the specific heat. The two shaded regions in the lower box identify the average location of the transition states obtained from DRP simulations.

Fig. 4.

Upper box: the set of dominant folding paths for Fip35, obtained from atomistic DRP simulations, projected on the plane defined by the rmsd of the two hairpins to the corresponding native structures. The dark spots represent a few typical configurations in the two transition states, evaluated by the requesting a probability 1/2 to reach the native state. Lower box: evolution of the rmsd to native of the full protein and of the hairpins along a dominant trajectory. The shaded area is the reactive region and the dashed line identifies the transition state configuration obtained according to Eq. 10.

Fig. 5.

The set of trial paths connecting a given denatured configuration to the native state, used in the search for the dominant paths, projected on the plane defined by the rmsd to native of the two hairpins. The darker path is the selected dominant reaction pathways.