Misfolded protein structures with non-native topological entanglements

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Native contact; Misfolded protein; Closed loop formed by the native contact; Threading segment;
Native protein; Native structure of the region; Native structure of the region;
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Watch this video to see how we identify the entanglement as deep or shallow.

Details of the definition of parameter G that is used to detect the topological entanglement for a given protein structure can be found here.

Please note: If you consider a consecutive backbone between the threading segment and the closed loop, the shallow entanglement of DHFR state P2 will have 0 linking number, i.e., gC = 0. However, we excluded 4 residues before and after the closed loop when we calculated the G metric, which yields gC = 1. The topology graph of DHFR state P2 with consecutive backbone is shown on the right.

N-ter C-ter 7 112 gN = 0; gC = 0

Cited by: Jiang, Y., et al. How synonymous mutations alter enzyme structure and function over long timescales. Nature Chemistry, 2023, 15, 308–318. (link to the paper)

Created by Yang Jiang at July 2020. Last updated at May 2022.