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.

arXiv comment15 pages, 9 figures

References in corpus (7)

• Folding Kinetics of Protein Like Heteropolymers
• Dodging the crisis of folding proteins with knots
• Universality classes in folding times of proteins
• Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
• Tightening of knots in proteins
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Cited by in corpus (8)

• How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
• Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding
• Multiple folding pathways of proteins with shallow knots and co-translational folding
• Structural entanglements in protein complexes
• 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