Link Node: A Method to Characterize the Chain Topology of Intrinsically Disordered Proteins

Abstract

It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a challenge. Here, we analyze the chain topology of IDPs to characterize their conformations, in combination with molecular dynamics simulation (MD). We systematically compute the Gauss Linking Number ($GLN$) between segments in IDP, and show that the resulting GLN Map can effectively depict an unconventional structure -- physical link, i.e., the entanglement between two segments. The crossing points of physical links are further identified and denoted as Link Nodes. We show that the probability distribution of Link Nodes is highly heterogeneous and there are certain residues that largely affect the chain topology of IDP. Moreover, the structural fluctuations of the vicinity of these residues are largely suppressed, i.e., Link Node provides useful information about the topological constraint imposed on the residues during the conformation fluctuations of IDP. We further reveal that the evolution of the chain topology is considerably slow (with a timescale of hundreds of nanoseconds), which is distinct from the flipping of residue contact.