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Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics.

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Intrinsically disordered proteins fold upon binding. This study reveals that specific leucine residues in c-Myb initiate binding and folding with the CREB-binding protein

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Area of Science:

  • Protein dynamics
  • Molecular recognition
  • Biophysics

Background:

  • Intrinsically disordered proteins (IDPs) are crucial for biological processes.
  • The mechanism of coupled folding and binding in IDPs remains unclear at the atomic level.
  • Key questions involve the temporal order of folding versus binding.

Purpose of the Study:

  • To investigate the atomistic details of binding and folding in intrinsically disordered proteins.
  • To elucidate the sequence of events in the coupled folding-binding process.
  • To understand the role of specific residues in initiating protein-protein interactions.

Main Methods:

  • Utilized a novel, unbiased, high-throughput adaptive sampling approach.
  • Reconstructed the long-term dynamical process of binding and folding.
  • Focused on the interaction between the c-Myb transactivation domain and the CREB-binding protein KIX domain.

Main Results:

  • Identified the binding of a specific α-helical segment of c-Myb.
  • Highlighted the critical role of leucine residues (Leu298-Leu302) in initiating native contacts.
  • Observed a combination of conformational selection and induced fit mechanisms during binding.

Conclusions:

  • The study provides atomistic insights into the coupled folding and binding of IDPs.
  • Specific amino acid sequences and residues can prime protein-protein interactions.
  • The findings contribute to understanding molecular recognition involving disordered proteins.