Multiple folding pathways of proteins with shallow knots and co-translational folding

Abstract

We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

12 pages, 7 figures

References in corpus (5)

• Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
• Tightening of knots in proteins
• Tightening the knot in phytochrome by single molecule atomic force microscopy
• Cotranslational folding of deeply knotted proteins
• Sequence-specific size, structure, and stability of tight protein knots

Cited by in corpus (4)

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