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Biochemical Reconstitution of Steroid Receptor•Hsp90 Protein Complexes and Reactivation of Ligand Binding
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Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling.

Batuhan Kav1,2, Murat Öztürk2,3, Alkan Kabakçιoğlu2

  • 1Department of Theory & Biosystems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, Potsdam, 14476, Germany.

Proteins
|February 14, 2016
PubMed
Summary

Nonlinear protein dynamics reveal crucial amino acids involved in function. This method predicts functional sites by analyzing protein configurational distributions, aiding in understanding evolutionary changes.

Keywords:
: mode couplingallosteryanharmonicityglucocorticoid receptorsmolecular dynamicsprotein evolution

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Area of Science:

  • Protein dynamics
  • Computational biophysics
  • Molecular evolution

Background:

  • Nonlinear effects in protein dynamics are crucial for function, especially allosteric regulation.
  • These effects facilitate energy transfer between vibrational modes.
  • A novel method analyzes non-Gaussian protein configurational populations to identify functional amino acids.

Purpose of the Study:

  • To apply a recently developed method for analyzing nonlinear protein dynamics.
  • To identify amino acids relevant to function in ancestral glucocorticoid receptor (GR) proteins.
  • To correlate identified sites with evolutionary functional restrictions.

Main Methods:

  • Application of a method analyzing the non-Gaussian shape of configurational populations near equilibrium.
  • Projection of dynamic information onto real space to pinpoint functional amino acids.
  • Analysis of three ancestral proteins within the GR family.

Main Results:

  • Significant correlation found between mutations restricting functional activity during GR evolution and sites highlighted by nonlinear dynamics.
  • The method successfully identified key amino acids relevant to protein function.
  • Nonlinear contributions to near-native configurational distribution were significant indicators.

Conclusions:

  • Analysis of nonlinear effects in protein dynamics is a viable predictive tool for functional site determination.
  • This approach can elucidate the role of protein dynamics in molecular evolution.
  • The findings support the importance of nonlinear dynamics in protein allosteric function.