Work

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

Year: 2025

Type: article

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.

Source: Quantitative Biology

DOI: 10.1002/qub2.96

Authors: Danqi Lang, Le Chen, Moxin Zhang, Haoyu Song, Jingyuan Li

Institutions: École Normale Supérieure - PSL, Zhejiang University

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: diamond

Funder: National Natural Science Foundation of China

Awards: G1036606367, G1530063796