Skip to main content

Long-Range Structural Regularities and Collectivity of Folded Proteins

  • Canan Atilgan (a1), Ibrahim Inanc (a2) and Ali Rana Atilgan (a3)

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.

Hide All
1Soyer A. Chomilier J. Mornon J. P. Jullien R. and Sadoc J. F. Phys. Rev. Lett. 85, 3532 (2000).
2Raghunathan G. and Jernigan R. L. Prot. Sci. 6, 2072 (1997).
3Atilgan A. R. Akan P. and Baysal C. Biophys. J. 86, 85 (2004).
4Liang J. and Dill K. A. Biophys. J. 81, 751 (2001).
5ben-Avraham D., Phys. Rev. B 47, 14559 (1993).
6Bahar I. Atilgan A. R. Demirel M. C. and Erman B. Phys. Rev. Lett. 80, 2733 (1998).
7Bahar I. and Rader A. J. Curr. Opin. Struct. Biol. 15, 586 (2005).
8Cui Q. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. (Chapman & Hall/CRC, FL, USA, 2006).
9Bahar I. Atilgan A. R. and Erman B. Folding & Design 2, 173 (1997).
10Tirion M. Phys. Rev. Lett. 77, 1905 (1996).
11Hinsen K. Proteins 33, 417 (1998).
12Yilmaz L. S. and Atilgan A. R. J. Chem. Phys. 113, 4454 (2000).
13Atilgan A. R. Durell S. R. Jernigan R. L. Demirel M. C. Keskin O. and Bahar I. Biophys. J. 80, 505 (2001).
14Doruker P. Atilgan A. R. and Bahar I. Proteins 40, 512 (2000).
15Yang L. Song G. and Jernigan R. L. Biophys. J. 93, 920 (2007).
16Petrone P. and Pande V. S. Biophys. J. 90, 1583 (2006).
17Fariselli P. and Casadio R. Prot. Eng. 12, 15 (1999).
18Berman H. M. et al., Nucl. Acids Res. 28, 235 (2000).
19Zhou Y. Q. Vitkup D. and Karplus M. J. Mol. Biol. 285, 1371 (1999).
20Kittel Charles, Introduction to Solid State Physics. (John Wiley & Sons, 2004), 8th ed.
21Svanidze A. V. et al., Ferroelectrics 348, 556 (2007).
22Reuveni S. Granek R. and Klafter J. Phys. Rev. Lett. 100, 4 (2008).
23Tama F. Wriggers W. and Brooks C. L. J. Mol. Biol. 321, 297 (2002).
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

MRS Online Proceedings Library (OPL)
  • ISSN: -
  • EISSN: 1946-4274
  • URL: /core/journals/mrs-online-proceedings-library-archive
Please enter your name
Please enter a valid email address
Who would you like to send this to? *



Full text views

Total number of HTML views: 0
Total number of PDF views: 2 *
Loading metrics...

Abstract views

Total abstract views: 123 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 19th January 2018. This data will be updated every 24 hours.