Discrete and Continuous Dynamical Systems - Series S (DCDS-S)

Breather-mediated energy transfer in proteins

Pages: 1247 - 1266, Volume 4, Issue 5, October 2011      doi:10.3934/dcdss.2011.4.1247

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Francesco Piazza - Centre de Biophysique Moleculaire (CBM-CNRS), University of Orleans, Rue Charles Sadron, 45071 Orleans, France (email)
Yves-Henri Sanejouand - Laboratoire Biotechnologie, Biocatalyse et Biorégulation, UMR 6204 du CNRS, Faculté des Sciences et des Techniques, 2, rue de la Houssinière, 44322 Nantes Cedex 3, France (email)

Abstract: In this paper we investigate how energy is redistributed across protein structures, following localized kicks, within the framework of a nonlinear network model. We show that energy is directed most of the times to a few specific sites, systematically within the stiffest regions. This effect is sharpened as the energy of the kicks is increased, with fractions of transferred energy as high as 70% already for kicks above $20$ kcal/mol. Remarkably, we show that such site-selective, high-yield transfers mark the spontaneous formation of spatially localized, time-periodic vibrations at the target sites, acting as efficient energy-collecting centers. A comparison of our simulations with a previously developed theory reveals that such energy-pinning modes are discrete breathers, able to carry energy across the structure in an quasi-coherent fashion by jumping from site to site.

Keywords:  Nonlinear dynamical systems, Proteins, Enzymes, Network models, Discrete Breathers, Energy transfer.
Mathematics Subject Classification:  Primary: 70-XX, 37-XX, 92-XX; Secondary: 70K75, 34C15, 37N25, 92C40.

Received: September 2009;      Revised: December 2009;      Available Online: December 2010.