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

Authors

  • Amit Srivastava,

    1. The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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    • Amit Srivastava and Roee Ben Halevi Contributed equally to this work.

  • Roee Ben Halevi,

    1. The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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    • Amit Srivastava and Roee Ben Halevi Contributed equally to this work.

  • Alexander Veksler,

    1. The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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  • Rony Granek

    Corresponding author
    1. The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
    2. The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
    • The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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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. Proteins 2012; © 2012 Wiley Periodicals, Inc.

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