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The European Physical Journal E

, Volume 33, Issue 1, pp 89–96 | Cite as

Vibrational entropy and the structural organization of proteins

  • L. BonginiEmail author
  • F. Piazza
  • L. Casetti
  • P. De Los Rios
Regular Article

Abstract.

In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force constants displayed by protein arrangements and also incorporates side chain degrees of freedom. Our analysis shows that vibrational entropy per unit residue correlates with the content of secondary structure. Furthermore, we assess the individual contribution to vibrational entropy of the novel features of our scheme as compared with the predictions of state-of-the-art network models. This analysis highlights the importance of properly accounting for the intrinsic hierarchy in force strengths typical of the different atomic bonds that build up and stabilize protein scaffolds. Finally, we discuss possible implications of our findings in the context of protein aggregation phenomena.

Keywords

Vibrational Spectrum Vibrational Entropy Gaussian Network Model Anisotropic Network Model Secondary Structure Level 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    B. Ma, C.-J. Tsai, R. Nussinov, Biophys. J. 79, 2577 (2000)CrossRefGoogle Scholar
  2. 2.
    F. Tama, Y.H. Sanejouand, Protein Engin. Design Select. 14, 1 (2001)CrossRefGoogle Scholar
  3. 3.
    W. Kabsch, C. Sander, Biopolymers 22, 2577 (1983)CrossRefGoogle Scholar
  4. 4.
    S. Ventura, Microbial Cell Factories 4, 11 (2005)CrossRefGoogle Scholar
  5. 5.
    U. Hobohm, C. Sander, Protein Sci. 3, 522 (1994)CrossRefGoogle Scholar
  6. 6.
    M. Tirion, D. ben Avraham, M. Lorenz, K. Holmes, Biophys. J. 68, 5 (1995)CrossRefADSGoogle Scholar
  7. 7.
    M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996)CrossRefADSGoogle Scholar
  8. 8.
    P. Doruker, A.R. Atilgan, I. Bahar, Proteins 40, 512 (2000)CrossRefGoogle Scholar
  9. 9.
    I. Bahar, A.R. Atilgan, B. Erman, Folding Design 2, 173 (1997)CrossRefGoogle Scholar
  10. 10.
    E. Eyal, L.-W. Yang, I. Bahar, Bioinformatics 22, 2619 (2006)CrossRefGoogle Scholar
  11. 11.
    W. Zheng, B.R. Brooks, Biophys. J. 88, 3109 (2005)CrossRefADSGoogle Scholar
  12. 12.
    F. Tama, W. Wriggers, C.L. Brooks, J. Mol. Biol. 321, 297 (2002)CrossRefGoogle Scholar
  13. 13.
    M. Delarue, Y.-H. Sanejouand, J. Mol. Biol. 320, 1011 (2002)CrossRefGoogle Scholar
  14. 14.
    P. De Los Rios, F. Cecconi, A. Pretre, G. Dietler, O. Michielin, F. Piazza, B. Juanico, Biophys. J. 89, 14 (2005)CrossRefGoogle Scholar
  15. 15.
    K. Hinsen, N. Reuter, J. Navaza, D.L. Stokes, J.J. Lacapere, Biophys. J. 88, 818 (2005)CrossRefGoogle Scholar
  16. 16.
    K. Hinsen, Proteins 33, 417 (1998)CrossRefGoogle Scholar
  17. 17.
    D. Sciretti, P. Bruscolini, A. Pelizzola, M. Pretti, A. Jaramillo, Proteins 74, 176 (2009)CrossRefGoogle Scholar
  18. 18.
    M. Zacharias, Protein Sci. 12, 1271 (2003)CrossRefGoogle Scholar
  19. 19.
    D. Eisenberg, R. Nelson, M.R. Sawaya, M. Balbirnie, S. Sambashivan, M.I. Ivanova, A.O. Madsen, C. Riekel, Acc. Chem. Res. 39, 568 (2006)CrossRefGoogle Scholar
  20. 20.
    J.R. Banavar, A. Flammini, D. Marenduzzo, A. Maritan, A. Trovato, Complexus 1, 4 (2003)CrossRefGoogle Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • L. Bongini
    • 1
    Email author
  • F. Piazza
    • 2
  • L. Casetti
    • 3
  • P. De Los Rios
    • 2
  1. 1.Departament de Fisica Fonamental, Facultat de FisicaUniversitat de BarcelonaBarcelonaSpain
  2. 2.Ecole Polytechnique Fédérale de LausanneLaboratoire de Biophysique StatistiqueLausanneSwitzerland
  3. 3.Dipartimento di Fisica e Astronomia and CSDCUniversità di Firenze, and INFN, Sezione di FirenzeSesto Fiorentino (FI)Italy

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