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  • MRS Proceedings, Volume 1227
  • January 2009, 1227-JJ03-06

Long-Range Structural Regularities and Collectivity of Folded Proteins

  • Canan Atilgan (a1), Ibrahim Inanc (a2) and Ali Rana Atilgan (a3)
  • DOI:
  • Published online: 01 January 2011

Coarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematic application to proteins are used to explain the role of network models in defining the collective properties of the system. The analysis is based on the radial distribution function, a newly defined angular distribution function and the spectral dimensions of a large set of globular proteins. Our analysis shows that after reaching a certain threshold for cut-off distance, network construction has negligible effect on the collective motions and the fluctuation patterns of the residues.

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1A. Soyer J. Chomilier J. P. Mornon R. Jullien and J. F. Sadoc Phys. Rev. Lett. 85, 3532 (2000).

2G. Raghunathan and R. L. Jernigan Prot. Sci. 6, 2072 (1997).

3A. R. Atilgan P. Akan and C. Baysal Biophys. J. 86, 85 (2004).

4J. Liang and K. A. Dill Biophys. J. 81, 751 (2001).

5D. ben-Avraham , Phys. Rev. B 47, 14559 (1993).

6I. Bahar A. R. Atilgan M. C. Demirel and B. Erman Phys. Rev. Lett. 80, 2733 (1998).

7I. Bahar and A. J. Rader Curr. Opin. Struct. Biol. 15, 586 (2005).

9I. Bahar A. R. Atilgan and B. Erman Folding & Design 2, 173 (1997).

10M. Tirion Phys. Rev. Lett. 77, 1905 (1996).

11K. Hinsen Proteins 33, 417 (1998).

12L. S. Yilmaz and A. R. Atilgan J. Chem. Phys. 113, 4454 (2000).

13A. R. Atilgan S. R. Durell R. L. Jernigan M. C. Demirel O. Keskin and I. Bahar Biophys. J. 80, 505 (2001).

14P. Doruker A. R. Atilgan and I. Bahar Proteins 40, 512 (2000).

15L. Yang G. Song and R. L. Jernigan Biophys. J. 93, 920 (2007).

16P. Petrone and V. S. Pande Biophys. J. 90, 1583 (2006).

17P. Fariselli and R. Casadio Prot. Eng. 12, 15 (1999).

18H. M. Berman et al., Nucl. Acids Res. 28, 235 (2000).

19Y. Q. Zhou D. Vitkup and M. Karplus J. Mol. Biol. 285, 1371 (1999).

21A. V. Svanidze et al., Ferroelectrics 348, 556 (2007).

22S. Reuveni R. Granek and J. Klafter Phys. Rev. Lett. 100, 4 (2008).

23F. Tama W. Wriggers and C. L. Brooks J. Mol. Biol. 321, 297 (2002).

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