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Thermodynamic Models for Assembly of Intrinsically Disordered Protein Hubs with Multiple Interaction Partners.

ByeongJin Cho1, Jaejun Choi1, RyeongHyeon Kim1

  • 1School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.

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Summary
This summary is machine-generated.

Intrinsically disordered protein (IDP) hubs regulate cellular processes by binding multiple targets. This study models IDP hub assembly, revealing complex binding dynamics in nucleocytoplasmic transport via Nup153 and karyopherin β1 interactions.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) and regions (IDRs) are crucial for forming macromolecular complexes and processing cellular signals.
  • The assembly and regulation mechanisms of IDP hubs are poorly understood due to complex protein-protein interaction networks.

Purpose of the Study:

  • To develop thermodynamic models for analyzing the assembly of IDP hubs with multiple target proteins.
  • To investigate the interaction between the Nup153 hub and multiple karyopherin β1 (Kap) molecules involved in nucleocytoplasmic transport.

Main Methods:

  • Construction of basic and advanced thermodynamic models using partition functions and fundamental binding parameters.
  • Quantitative analysis of the Nup153 C-terminal IDR binding to multiple Kaps, including assessment of cooperativity and competition.

Main Results:

  • A complex organization of Kap binding sites on Nup153 was revealed, featuring a high-affinity site and low-affinity sites exhibiting negative cooperativity.
  • Negative cooperativity arises from overlapping Kap binding sites within the Nup153 IDR.
  • Kap binding to Nup153 is modulated by Kap concentration and competing nuclear proteins, with fine-tuning possible through competition site localization.

Conclusions:

  • The study presents a quantitative model for Nup153 hub assembly, explaining how Kap binding is regulated.
  • The findings suggest a mechanism for manifold regulation of IDP functions by cellular signals, linking nuclear processes to transport activities.