Link node: A method to characterize the chain topology of intrinsically disordered proteins

Abstract

Intrinsically disordered proteins (IDP) are highly dynamic, and the effective characterization of IDP conformations is still a challenge. Here, we analyze the chain topology of IDPs and focus on the physical link of the IDP chain, that is, the entanglement between two segments along the IDP chain. The Gauss linking number of two segments throughout the IDP chain is systematically calculated to analyze the physical link. The crossing points of physical links are identified and denoted as link nodes. We notice that the residues involved in link nodes tend to have lower root mean square fluctuation (RMSF), that is, the entanglement of the IDP chain may affect its conformation fluctuation. Moreover, the evolution of the physical link is considerably slow with a timescale of hundreds of nanoseconds. The essential conformation evolution may be depicted on the basis of chain topology.

Keywords

chain topology / gauss linking number / intrinsically disordered protein / physical link

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The Author(s). Quantitative Biology published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.