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Proper folding of deeply knotted proteins has a very low success rate even instructure-based models which favor formation of the native contacts but have notopological bias. By employing a structure-based model, we demonstrate thatcotranslational folding on a model ribosome may enhance the odds to formtrefoil knots for protein YibK without any need to introduce any non-nativecontacts. The ribosome is represented by a repulsive wall that keeps elongatingthe protein. On-ribosome folding proceeds through a a slipknot conformation. Weelucidate the mechanics and energetics of its formation. We show that theknotting probability in on-ribosome folding is a function of temperature andthat there is an optimal temperature for the process. Our model often leads tothe establishment of the native contacts without formation of the knot.

Cotranslational folding of deeply knotted proteins