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Conformational Ensembles Exhibit Extensive Molecular Recognition Features.

Robert I Cukier1

  • 1Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States.

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|August 29, 2019
PubMed
Summary

Intrinsically disordered proteins (IDPs) feature molecular recognition features (MoRFs) that become ordered upon binding. This study characterizes MoRFs using entropy and mutual information, revealing their presence in ubiquitin and other IDPs.

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Area of Science:

  • Protein structure and dynamics
  • Biophysics
  • Computational biology

Background:

  • Intrinsically disordered proteins (IDPs) are crucial for cellular signaling and regulation.
  • Unlike folded proteins, IDPs adopt diverse conformations.
  • IDPs contain specific regions called molecular recognition features (MoRFs) that gain structure upon binding.

Purpose of the Study:

  • To introduce a novel method for structurally characterizing MoRFs.
  • To analyze the conformational properties of MoRFs using entropy and mutual information (MI).
  • To investigate the presence and characteristics of MoRFs in ubiquitin, Sic1, and α-synuclein.

Main Methods:

  • Utilizing entropy and mutual information to define and identify MoRFs.
  • Applying the methodology to ubiquitin ensembles derived from nuclear magnetic resonance (NMR) experiments.
  • Analyzing additional IDP ensembles for cyclin-dependent kinase inhibitor Sic1 and amyloid protein α-synuclein.

Main Results:

  • A MoRF is defined as contiguous residues with high entropy and high MI, indicating coupled residue dynamics.
  • The denatured ubiquitin ensemble showed high entropy but negligible MI, suggesting independent residue sampling.
  • Ubiquitin ensembles exhibited MoRFs (residue sizes 2-10) in non-secondary structure regions, supporting a conformational selection mechanism.
  • Sic1 and α-synuclein ensembles also displayed MoRF-like characteristics.

Conclusions:

  • The proposed entropy and MI-based approach effectively characterizes MoRFs in IDPs.
  • The findings in ubiquitin suggest a conformational selection mechanism driven by MoRFs.
  • MoRFs appear to be a general feature of IDPs, including Sic1 and α-synuclein.