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Dodging The Crisis Of Folding Proteins With Knots

2009; Elsevier BV; Volume: 96; Issue: 3 Linguagem: Inglês

10.1016/j.bpj.2008.12.319

1542-0086

Joanna I. Sułkowska, Piotr Sułkowski, José N. Onuchic,

Connective tissue disorders research

We prove that proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. Our studies are based on a simple coarse-grained model with interactions modeled only by the native contacts. We demonstrate that folding of knotted proteins YibK and YbeA proceeds through an intermediate configuration with a slipknot. Analysis of topological barriers and backtracking associated to these trajectories reveals to which extent various native contacts are responsible for a folding process. From this we conclude how to modify their strength to get more realistic model, with a higher ratio of properly folded structures. We also discuss how folding properties of knotted proteins are affected when additional chains are attached to one or both termini, and when protein does not have knot topology.