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A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.

Haleh Abdizadeh1, Farzaneh Jalalypour2, Ali Rana Atilgan2

  • 1Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.

Frontiers in Molecular Biosciences
|November 16, 2020
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Summary

Predicting protein complex dissociation is now possible using perturbation response scanning (PRS). This method identifies key residues that trigger protein complex disassembly through remote electromechanical control, offering insights into protein interactions.

Keywords:
allosterycooperative conformational changeelastic network modelelectrostatic potential distributionperturbation response scanningprotein complexesprotein–protein dissociationstructural motifs

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein complexes are crucial for cellular functions.
  • Understanding protein complex dissociation is vital for drug discovery and molecular mechanism elucidation.
  • Predicting dissociation triggers remains a challenge in structural biology.

Purpose of the Study:

  • To develop and validate a computational method for predicting residues that trigger protein complex dissociation.
  • To investigate the mechanisms underlying protein complex dissociation.
  • To identify distinct modes of dissociation control in protein complexes.

Main Methods:

  • Utilized a dataset of 25 protein complexes with high-resolution structures in bound and unbound states.
  • Integrated elastic network models with perturbation response scanning (PRS) methodology.
  • Employed an electromechanical coupling model to analyze dissociation mechanisms.

Main Results:

  • Identified specific residues that trigger protein complex dissociation using PRS.
  • Discovered two primary dissociation control modes: remote electromechanical control and remote mechanical control.
  • Found that dissociation is often mediated by remote residues, not solely interface residues.
  • Demonstrated that identified residues are functionally important or highly conserved.

Conclusions:

  • Perturbation response scanning (PRS) is an effective method for predicting dissociation-triggering residues in protein complexes.
  • Protein complex dissociation can be controlled remotely through electromechanical or mechanical pathways.
  • The findings provide a deeper understanding of protein complex dynamics and regulation.