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Resolving Conformational Heterogeneity in Intrinsically Disordered Proteins via Experimentally Guided Multi-Replica

Wangfei Yang1, Sichun Yang2, Wenwei Zheng1,3

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We developed a new method to map protein shapes, revealing hidden states in disordered proteins. This approach integrates multiple experimental data types to accurately model protein dynamics.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Intrinsically disordered proteins (IDPs) possess dynamic conformational landscapes that are challenging to characterize due to ensemble averaging in experimental data.
  • Understanding IDP conformational ensembles is crucial for elucidating their diverse biological functions.

Purpose of the Study:

  • To present Multi-replica Averaged Restraint Simulation (MARS), a novel data-driven framework for reconstructing IDP conformational landscapes.
  • To validate MARS using the estrogen receptor alpha N-terminal domain (ERα-NTD) and integrate diverse biophysical data.

Main Methods:

  • MARS enforces ensemble-averaged restraints across multiple simulation replicas without prior structural assumptions.
  • Simultaneously integrated small-angle X-ray scattering (SAXS) and six paramagnetic relaxation enhancement (PRE) profiles, providing over 600 pairwise restraints.
  • Generated conformational ensembles quantitatively fitting all experimental input data.

Main Results:

  • The MARS-derived ensemble for ERα-NTD accurately reproduced experimental data, including backbone relaxation measurements.
  • Identified two distinct conformational states: a predominant extended state and a functionally relevant, low-populated compact state.
  • Demonstrated that SAXS and PRE data provide orthogonal global and local structural constraints, respectively.

Conclusions:

  • MARS successfully reconstructs complex conformational landscapes of IDPs by integrating orthogonal experimental data.
  • The framework resolves both dominant and rare functional states, offering insights into IDP mechanisms.
  • MARS provides a scalable and powerful approach for structural characterization of dynamic biological molecules.