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Why are large conformational changes well described by harmonic normal modes?

Yves Dehouck1, Ugo Bastolla1

  • 1Centro de Biologia Molecular "Severo Ochoa," CSIC-UAM Cantoblanco, Madrid, Spain.

Biophysical Journal
|October 28, 2021
PubMed
Summary
This summary is machine-generated.

Elastic network models predict protein motion, but harmonic approximations limit accuracy. This study shows that collective motion and reduced degrees of freedom improve normal mode analysis for large conformational changes.

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Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Elastic network models (ENMs) are widely used to study protein dynamics.
  • Low-frequency normal modes often correlate with large conformational changes.
  • The harmonic approximation in ENMs is typically valid only near the native structure.

Purpose of the Study:

  • To investigate how deviations from the harmonic approximation affect the ability of ENMs to capture large protein conformational changes.
  • To evaluate different variants of the torsional network model (TNM) and their relationship with anharmonicity.
  • To identify strategies for improving the accuracy of normal mode analysis for protein dynamics.

Main Methods:

  • Utilized 12 variants of the torsional network model (TNM), an ENM in torsion angle space.
  • Assessed deviations from the harmonic approximation using an anharmonic energy function.
  • Correlated mode anharmonicity with mode collectivity (number of displaced atoms) and amplitude.
  • Evaluated strategies to minimize anharmonicity, including reducing degrees of freedom and applying torsional harmonic potentials.

Main Results:

  • TNM variants showed significant differences in predicting conformational changes, linked to anharmonicity.
  • Mode anharmonicity was more strongly related to mode collectivity than amplitude.
  • Sufficiently collective low-frequency modes can remain harmonic even at large amplitudes.
  • Reducing degrees of freedom or regularizing torsional potentials improved normal mode accuracy.

Conclusions:

  • Anharmonicity significantly impacts the prediction of large conformational changes by ENMs.
  • Mode collectivity is a key factor in maintaining harmonicity.
  • Strategies like reducing degrees of freedom and torsional regularization enhance the predictive power of normal mode analysis for protein dynamics.