Stefano	Luccioli -	CNR-ISC Firenze	#	
Discrete 
breathers as energy-accumulating centres in a protein model.	
#

We report the results of molecular dynamics simulations of an 
off-lattice protein model featuring a physical force-field and 
amino-acid sequence. We show that localised modes of nonlinear 
origin, discrete breathers (DB), emerge naturally as 
continuations of a subset of high-frequency normal modes 
residing at specific sites dictated by the native fold. In the 
case of the small beta-barrel structure that we consider, 
DB-mediated localization occurs on the turns connecting the 
strands. At high energies, discrete breathers stabilise the 
structure by concentrating  energy on few sites, while their 
collapse marks the onset of large-amplitude fluctuations  of 
the protein. Furthermore, we show how breathers develop as 
energy-accumulating centres following perturbations even at 
distant locations, thus mediating efficient and irreversible 
energy transfers. Remarkably, due to the presence of angular 
potentials, the  breather induces a local static distortion of 
the native fold. Altogether, the combination of this two 
nonlinear effects may provide a ready means for remotely 
controlling local conformational changes in proteins.  Ref: S. 
Luccioli, A. Imparato, S. Lepri, F. Piazza and A. Torcini, 
"Discrete breathers in a realistic coarse-grained model of 
proteins", to appear in Physical Biology 2011.