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We report on atomistic simulation of the folding of a natively-knottedprotein, MJ0366, based on a realistic force field. To the best of our knowledgethis is the first reported effort where a realistic force field is used toinvestigate the folding pathways of a protein with complex native topology. Byusing the dominant-reaction pathway scheme we collected about 30 successfulfolding trajectories for the 82-amino acid long trefoil-knotted protein.Despite the dissimilarity of their initial unfolded configuration, thesetrajectories reach the natively-knotted state through a remarkably similarsuccession of steps. In particular it is found that knotting occurs essentiallythrough a threading mechanism, involving the passage of the C-terminal throughan open region created by the formation of the native beta-sheet at an earlierstage. The dominance of the knotting by threading mechanism is not observed inMJ0366 folding simulations using simplified, native-centric models. This pointsto a previously underappreciated role of concerted amino acid interactions,including non-native ones, in aiding the appropriate order of contact formationto achieve knotting.

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field