Hostname: page-component-586b7cd67f-l7hp2 Total loading time: 0 Render date: 2024-11-25T16:56:33.153Z Has data issue: false hasContentIssue false
  • English
  • Français

Long-Range Structural Regularities and Collectivity of Folded Proteins

Published online by Cambridge University Press:  31 January 2011

Canan Atilgan ,
Ibrahim Inanc  and
Ali Rana Atilgan
Canan Atilgan
Affiliation:
[email protected], Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey
Ibrahim Inanc
Affiliation:
[email protected], Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey
Ali Rana Atilgan
Affiliation:
[email protected], Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey
Get access

Abstract

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.

Keywords

macromolecular structurestructuralbiological
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 1227: Symposium JJ – Multiscale Dynamics in Confining Systems , 2009 , 1227-JJ03-06
Copyright
Copyright © Materials Research Society 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

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