The effects of rigid motions on elastic network model force constants

Proteins. 2012 Apr;80(4):1133-42. doi: 10.1002/prot.24014. Epub 2012 Jan 7.


Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Anisotropy
  • Calcium Carbonate / chemistry
  • Citrates / chemistry
  • Crystallography, X-Ray
  • Drug Combinations
  • Elasticity*
  • Entropy
  • Magnesium Oxide / chemistry
  • Magnetic Resonance Spectroscopy
  • Models, Molecular*
  • Molecular Dynamics Simulation*
  • Molecular Structure
  • Protein Conformation
  • Proteins / chemistry*
  • Temperature


  • Citrates
  • Drug Combinations
  • Proteins
  • Suby's G solution
  • Magnesium Oxide
  • Calcium Carbonate