title: 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.
authors.affiliation: CNR-Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy. stefano.luccioli@fi.isc.cnr.it
authors.forename: Stefano
authors.initials: S
authors.lastname: Luccioli
authors.forename: Alberto
authors.initials: A
authors.lastname: Imparato
authors.forename: Stefano
authors.initials: S
authors.lastname: Lepri
authors.forename: Francesco
authors.initials: F
authors.lastname: Piazza
authors.forename: Alessandro
authors.initials: A
authors.lastname: Torcini
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D010507:Periodicity; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014732:Vibration
chemical_list: D011506:Proteins