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Stochastic simulations of coarse-grained protein models are used toinvestigate the propensity to form knots in early stages of protein folding.The study is carried out comparatively for two homologouscarbamoyltransferases, a natively-knotted N-acetylornithinecarbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase(OTCase). In addition, two different sets of pairwise amino acid interactionsare considered: one promoting exclusively native interactions, and the otheradditionally including non-native quasi-chemical and electrostaticinteractions. With the former model neither protein show a propensity to formknots. With the additional non-native interactions, knotting propensity remainsnegligible for the natively-unknotted OTCase while for AOTCase it is muchenhanced. Analysis of the trajectories suggests that the different entanglementof the two transcarbamylases follows from the tendency of the C-terminal topoint away from (for OTCase) or approach and eventually thread (for AOTCase)other regions of partly-folded protein. The analysis of the OTCase/AOTCase pairclarifies that natively-knotted proteins can spontaneously knot during earlyfolding stages and that non-native sequence-dependent interactions areimportant for promoting and disfavoring early knotting events.

The Role of Non-native Interactions in the Folding of Knotted Proteins