Dodging the crisis of folding proteins with knots

DOI10.1073/PNAS.0811147106MaRDI QIDQ3066183zbMATH OpenOpenAlexWikidataFDO

Authors Joanna I. Sułkowska, Piotr Sulkowski, José Onuchic

Publication date 9 January 2011

Published in Proceedings of the National Academy of Sciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0912.5450

zbMATH Keywords

backtrackingmolecular dynamicsslipknotstopological barriers

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Abstract: Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in around 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

Recommendations

• Knotted proteins: Tie etiquette in structural biology
• Topological descriptions of protein folding
• Protein knots and fold complexity: some new twists
• scientific article; zbMATH DE number 841193
• A topological study of protein folding kinetics

Cites work

• Generalized Keller spaces
• Protein knots and fold complexity: some new twists

Cited in

(9)

• Protein folding: a good structure protector is also a good structure seeker
• Energy landscapes of protein self-assembly: lessons from native topology-based models
• Knotted proteins: Tie etiquette in structural biology
• Statics and dynamics of DNA knotting
• Entangled proteins: knots, slipknots, links, and lassos
• Unraveling the complexity of Exendin-4 folding through two distinct pathways
• Topology in soft and biological matter
• Knot theory in understanding proteins
• Protein folding invariants

This page was built for publication: Dodging the crisis of folding proteins with knots

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3066183)