查看文章

Several protein structures have been reported to contain intricate knots of the polypeptide backbone but the mechanism of the (un)folding process of knotted proteins remains unknown. The members of the SPOUT superfamily of RNA methyltransferases are some of the most intensely studied systems for investigation of the knot formation and function. YibK (whose biochemical function remains unknown) is the representative protein of the SPOUT superfamily. This protein exhibits a deep trefoil knot at the C-terminus.

We conducted an extensive computational analysis of the unfolding process for the monomeric form of YibK. In order to predict the (un)folding pathway of YibK, we have calculated the order of secondary structure disassembly using UNFOLD, and performed thermal unfolding simulations using classical Molecular Dynamics (MD), as well as simulations employing reduced representation of the peptide …