Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities

Amit Srivastava, Roee Ben Halevi, Alexander Veksler, Rony Granek

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

We present a tensorial elastic network model (TNM) to describe the equilibrium fluctuations of proteins near their native fold structure. The model combines the anisotropic network model (ANM), bond bending elasticity, and backbone twist elasticity, and can predict both the isotropic fluctuations, similar to the Gaussian network model (GNM), and anisotropic fluctuations, similar to the ANM. TNM performs equally well for B-factor predictions as GNM and predicts the anisotropy of B-factors better than ANM. The model also outperforms the ANM in its predictability of the complete anisotropic displacement parameters.

Original languageEnglish
Pages (from-to)2692-2700
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume80
Issue number12
DOIs
StatePublished - 1 Dec 2012

Keywords

  • Anisotropic displacement parameters
  • Anisotropic network model
  • Bond bending
  • Elastic network models
  • Gaussian network model
  • Normal mode analysis
  • Protein data bank
  • Twist elasticity

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