Discrete breathers in a realistic coarse-grained model of proteins.

Abstract : 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 (DBs), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. DBs are time-periodic, space-localized vibrational modes that exist generically in nonlinear discrete systems and are known for their resilience and ability to concentrate energy for long times. In the case of the small β-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, DBs stabilize the structure by concentrating energy on a 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 these two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.
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Submitted on : Wednesday, July 25, 2012 - 11:57:21 AM
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Stefano Luccioli, Alberto Imparato, Stefano Lepri, Francesco Piazza, Alessandro Torcini. Discrete breathers in a realistic coarse-grained model of proteins.. Physical Biology, Institute of Physics: Hybrid Open Access, 2011, 8 (4), pp.046008. ⟨10.1088/1478-3975/8/4/046008⟩. ⟨hal-00720642⟩



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