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Structural compliance: A new metric for protein flexibility.

Domenico Scaramozzino1, Pranav M Khade2, Robert L Jernigan2

  • 1Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy.

Proteins
|June 18, 2020
PubMed
Summary

We introduce structural compliance, a new metric for protein flexibility. This measure better correlates with experimental B-factors than traditional methods, reflecting protein deformability under various forces.

Keywords:
B-factorelastic network modelprotein flexibilityprotein stiffnessstructural compliance

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Protein dynamics are crucial for molecular functions and are often studied using intrinsic fluctuations.
  • Protein motions are influenced by solvent interactions, which traditional methods may not fully capture.

Purpose of the Study:

  • Introduce structural compliance as a novel metric for evaluating protein deformability.
  • Assess the correlation of structural compliance and stiffness with experimental B-factors.
  • Explore the applicability of this approach to other biomolecular structures.

Main Methods:

  • Developed a new concept: structural compliance, to assess global and local protein deformability.
  • Applied pairwise pulling forces to a protein elastic network model.
  • Computed structural compliance and its inverse, structural stiffness.

Main Results:

  • Structural compliance shows improved correlation with experimental B-factors compared to mean square fluctuations.
  • Structural stiffness exhibits a clear anticorrelation with experimental B-factors.
  • The approach is applicable to proteins and potentially other biomolecular structures like RNA.

Conclusions:

  • Structural compliance offers a potentially superior metric for protein flexibility, especially for local perturbations.
  • The concept of structural compliance and stiffness can be extended to molecular dynamics simulations.
  • This work provides a new tool for analyzing protein dynamics and flexibility.