Tightening of knots in proteins

Abstract

We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Larger knots do not return to their native locations when a protein is released after stretching.

arXiv comment4 pages, 5 figures

References in corpus (5)

• What is the length of a knot in a polymer?
• Universality classes in folding times of proteins
• Topologically Driven Swelling of a Polymer Loop
• Diffusion mechanisms of localised knots along a polymer
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Cited by in corpus (17)

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• Cotranslational folding of deeply knotted proteins
• Sequence-specific size, structure, and stability of tight protein knots
• Jamming proteins with slipknots and their free energy landscape
• Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
• The Egg of Columbus for making the world toughest fibres
• Multiple folding pathways of proteins with shallow knots and co-translational folding
• Structural entanglements in protein complexes
• Stretching and twisting of the DNA duplexes in coarse grained dynamical models
• Universality in the diffusion of knots
• Topological effects in the thermal properties of knotted polymer rings
• A study of polymer knots using a simple knot invariant written consisting of multiple contour integrals
• A Stochastic Model of Translocation of Knotted Proteins