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Discrete breathers in nonlinear network models of proteins

par Webmaster - 19 décembre 2007

Orateur :

Francesco Piazza, Laboratoire de Biophysique Statistique, ITP/SB, Ecole Politechnique Fédérale de Lausanne, Suisse

Salle :

C023 (RDC LR6 côté CECAM)

Sujet :

Discrete breathers (DB) are spatially-localized, time-periodic vibrations that arise under general conditions in discrete nonlinear systems. While much is known concerning their existence and stability in spatially periodic media, much less is known about the interplay of nonlinearity and spatal heterogeneity in disordered systems, where localization is also fostered as a result of breaking of translational invariance.

We introduce a coarse-grained topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity in biological molecules. DB solutions, characterized both numerically with the surface cooling technique and analytically, show that localization of energy occurs generically also in the presence of disorder, but is a site-dependent and, on a larger scale, fold-dependent process. In particular, contrary to what happens in ordered systems, we find that a non-zero energy gap for exciting a DB may or may not exist depending on the site, and in the latter case it appears to vanish as a result of the impossibility of exciting small-amplitude DBs at all. Interestingly, our cooling simulations show that localized modes of nonlinear origin form spontaneously in the stiffest parts of the structure. Such results provide a straightforward way for understanding the recently discovered link between local stiffness of proteins and enzymatic activity. They strongly suggest that nonlinear phenomena may play an important role in enzyme function, allowing for a ready energy storage channel during the catalytic process.

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