How well does a funneled energy landscape capture the folding mechanism of spectrin domains?

ABSTRACT: Three structurally similar domains from ?-spectrin have been shown to fold very differently. First, there is a contrast in the folding mechanism, as probed by ?-value analysis, between the R15 domain and the R16 and R17 domains. Second, there are very different contributions from internal friction to folding: the folding rate of the R15 domain was found to be inversely proportional to solvent viscosity, showing no apparent frictional contribution from the protein, but in the other two domains, a large internal friction component was evident. Non-native misdocking of helices has been suggested to be responsible for this phenomenon. Here, I study the folding of these three proteins with minimalist coarse-grained models based on a funneled energy landscape. Remarkably, I find that, despite the absence of non-native interactions, the differences in folding mechanism of the domains are well captured by the model, and the agreement of the ?-values with experiment is fairly good. On the other hand, within the context of this model, there are no significant differences in diffusion coefficient along the chosen folding coordinate, and the model cannot explain the large differences in folding rates between the proteins found experimentally. These results are nonetheless consistent with the expectations from the energy landscape perspective of protein folding, namely, that the folding mechanism is primarily determined by the native-like interactions present in the G?-like model, with missing non-native interactions being required to explain the differences in "internal friction" seen in experiment.

SUBMITTER: Best RB 

PROVIDER: S-EPMC3808457 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature