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Anisotropy of fluctuation dynamics of proteins with an elastic network model

  1. Author:
    Atilgan, A. R.
    Durell, S. R.
    Jernigan, R. L.
    Demirel, M. C.
    Keskin, O.
    Bahar, I.

  2. Author Address

    NCI, MSS, LECB, DBS, NIH, Rm B-116, Bldg 12B, Bethesda, MD 20892 USA. Bogazici Univ, Sch Engn, TR-80815 Bebek, Istanbul, Turkey. Bogazici Univ, Ctr Polymer Res, TR-80815 Bebek, Istanbul, Turkey. TUBITAK, Adv Polymer Mat Res Ctr, TR-80815 Bebek, Istanbul, Turkey. NCI, MSS, LECB, DBS, NIH, Bethesda, MD 20892 USA. Sci Applicat Int Corp, NIH, Frederick, MD 20892 USA. Jernigan RL NCI, MSS, LECB, DBS, NIH, Rm B-116, Bldg 12B, Bethesda, MD 20892 USA.
    1. Year: 2001
  2. Journal: Biophysical Journal
    1. 80
    2. 1
    3. Pages: 505-515
  4. Type of Article: Article
  1. Abstract:

    Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein.

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  2. DOI: 10.1016/S0006-3495(01)76033-X
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