Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins

J Chem Inf Model. 2023 Apr 24;63(8):2586-2602. doi: 10.1021/acs.jcim.3c00391. Epub 2023 Apr 7.

Abstract

Intrinsically disordered proteins (IDPs) lack a stable native conformation, making it challenging to characterize their structure and dynamics. Key topological motifs with fundamental biological relevance are often hidden in the conformational noise, eluding detection. Here, we develop a circuit topology toolbox to extract conformational patterns, critical contacts, and timescales from simulated dynamics of intrinsically disordered proteins. We follow the dynamics of IDPs by providing a smart low-dimensionality representation of their three-dimensional (3D) configuration in the topology space. Such an approach allows us to quantify topological similarity in dynamic systems, therefore providing a pipeline for structural comparison of IDPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Intrinsically Disordered Proteins* / chemistry
  • Protein Conformation

Substances

  • Intrinsically Disordered Proteins