Eur. Phys. J. E (2010) 33: 89-96
https://doi.org/10.1140/epje/i2010-10653-8

Regular Article

Vibrational entropy and the structural organization of proteins

¹ Departament de Fisica Fonamental, Facultat de Fisica, Universitat de Barcelona, Carrer Marti i Franquès, 1 E-08028, Barcelona, Spain
² Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Biophysique Statistique, ITP-SB, BSP-722, CH-1015, Lausanne, Switzerland
³ Dipartimento di Fisica e Astronomia and CSDC, Università di Firenze, and INFN, Sezione di Firenze, Via G. Sansone 1, 50019, Sesto Fiorentino (FI), Italy

^* e-mail: lbongini@ffn.ub.es

Received: 15 June 2010
Accepted: 16 August 2010
Published online: 18 September 2010

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.