Cotranslational folding of deeply knotted proteins

Abstract

Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

15 pages, 9 figures

References in corpus (4)

• Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
• Tightening of knots in proteins
• Sequence-specific size, structure, and stability of tight protein knots
• Thermal unfolding of proteins

Cited by in corpus (8)

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• Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length and macromolecular crowding
• Chain stiffness bridges conventional polymer and bio-molecular phases}
• Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures
• Topological transformations in proteins: effects of heating and proximity of an interface