Francesco Piazza - Centre de Biophysique Moleculaire (CBM-CNRS), University of Orleans, Rue Charles Sadron, 45071 Orleans, 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.
Received: September 2009; Revised: December 2009; Published: December 2010.