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Proteins must fold quickly to acquire their biologically functionalthree-dimensional native structures. Hence, these are mainly stabilized bylocal contacts, while intricate topologies such as knots are rare. Here, wereveal the existence of specific patterns adopted by protein sequences andstructures to deal with backbone self-entanglement. A large scale analysis ofthe Protein Data Bank shows that loops significantly intertwined with anotherchain portion are typically closed by weakly bound amino acids. Why is thisenergetic frustration maintained? A possible picture is that entangled loopsare formed only toward the end of the folding process to avoid kinetic traps.Consistently, these loops are more frequently found to be wrapped around aportion of the chain on their N-terminal side, the one translated earlier atthe ribosome. Finally, these motifs are less abundant in natural native statesthan in simulated protein-like structures, yet they appear in 32% of proteins,which in some cases display an amazingly complex intertwining.

Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding