Direct Observation of the Folding Trajectory of a Slipknotted Protein

Abstract

Over the last two decades, as a surprising feature for proteins, knotted/slipknotted topology has been found in certain proteins. Such knotted/slipknotted proteins need to overcome the topological difficulty in order to reach their functional native states. It is challenging to understand the folding mechanism of such proteins. AFV3-109 is a small alpha/beta protein containing a slipknot. In our previous studies, we have shown that stretching AFV3-109 from its N-C termini can readily lead to the unfolding of AFV3-109 and untying the slipknotted structure. However, it has been challenging to monitor the folding process of AFV3-109 from its unfolded conformation enroute to its slipknotted native state. Here use single molecule optical tweezers to investigate the folding process of AFV3-109. Using constant velocity mode, we found that unfolded AFV3-109, which was prepared by mechanically stretching from its both termini, can readily refold at a force of ∼4 pN or lower to its native state with the slipknot conformation. The refolding of most AFV3-109 occurs in a sharp transition (with a time resolution of ∼50 us), indicative of a two-state like transition without the accumulation of intermediate states. The apparent ease of such a folding into the slipknotted conformation for most AFV3019 suggests the topological barrier is not high for forming a protein slipknot under the experimental setting. Moreover, we observed that a small fraction of unfolded AFV3-109 molecules refold into the native state via a continuous folding trajectory, suggesting a more complex refolding pathway. These results open the avenue towards understanding of the folding mechanism of slipknotted and knotted proteins.