Consensus for the Fip35 folding mechanism?

TL;DR

This study uses network analysis on extensive atomistic simulation data to clarify the folding pathways of the Fip35 WW-domain, revealing two major pathways with intermediates, resolving conflicting interpretations from previous analyses.

Contribution

It introduces a network-based analysis method to interpret long-timescale folding simulations, providing clearer insight into the folding mechanism of Fip35.

Findings

Folding occurs via two main pathways.

One pathway is significantly more populated.

Intermediates involve native hairpin configurations.

Abstract

Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead to a straightforward interpretation of the mechanism. For the case of the Fip35 WW-domain where multiple long trajectories of 100 {\mu}s are available from D. E. Shaw Research, different interpretations emerged. Some of those are in clear contradiction with each other while others are in qualitative agreement. Here, we present a network-based analysis of the same data by looking at the local fluctuations of conventional order parameters for folding. We found that folding occurs through two major pathways, one almost four times more populated than the other. Each pathway involves the formation of an intermediate with one of the two hairpins in a native configuration. The quantitative agreement of our results with a state-of-the-art reaction coordinate optimization procedure as well as qualitative agreement with other Markov-state-models and different simulation schemes provides strong evidence for a multiple folding pathways scenario with the presence of intermediates.