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Allosteric switch regulates protein-protein binding through collective motion.

Colin A Smith1, David Ban2, Supriya Pratihar3

  • 1Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany; Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany; colin.smith@mpibpc.mpg.de cigr@nmr.mpibpc.mpg.de donghan.lee@louisville.edu bgroot@gwdg.de.

Proceedings of the National Academy of Sciences of the United States of America
|March 11, 2016
PubMed
Summary

Internal protein motion facilitates allosteric communication, crucial for biological processes. A study on ubiquitin reveals a global motion enabling distant conformational switches and multispecific binding, particularly with deubiquitinases.

Keywords:
allosteryconcerted motionnuclear magnetic resonanceprotein dynamicsrelaxation dispersion

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Area of Science:

  • Biophysics
  • Structural Biology
  • Biochemistry

Background:

  • Allosteric communication is vital for protein function, but the role of internal protein dynamics in signal propagation is poorly understood.
  • Understanding how proteins transmit signals across their structure is key to deciphering complex biological processes.

Purpose of the Study:

  • To investigate the role of internal protein motion in allosteric communication using ubiquitin as a model system.
  • To identify specific dynamic motions linked to allosteric signaling and conformational changes.

Main Methods:

  • Combined experimental techniques and computational analysis to study the ground-state dynamics of ubiquitin.
  • Characterized collective global motions and their correlation with functional conformational switches.

Main Results:

  • Identified a specific collective global motion in ubiquitin associated with a distant conformational switch.
  • Demonstrated that this allosteric coupling is present in crystal structures and facilitates multispecificity, especially binding to ubiquitin-specific protease (USP) family deubiquitinases.
  • Found that the allosteric communication relies on domain-wide expansion and contraction, not localized changes.

Conclusions:

  • Collective protein motions are critical for allosteric communication and functional specificity.
  • Characterizing these dynamic networks offers new strategies for modulating protein interactions and function.
  • This work provides insights into the mechanisms underlying multispecificity in protein binding.