Discrete breathers in a realistic coarse-grained model of proteins

Stefano Luccioli, Alberto Imparato, Stefano Lepri, Francesco Piazza, Alessandro Torcini
2011 Physical Biology  
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 localized modes of nonlinear origin (discrete breathers) 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 β-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete
more » ... hers stabilize 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.
doi:10.1088/1478-3975/8/4/046008 pmid:21670494 fatcat:moblbkakgvcltcqrpimqacitja