Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

TL;DR

This study uses molecular dynamics simulations to demonstrate that discrete breathers, localized nonlinear vibrational modes, naturally occur in a realistic protein model and influence energy transfer and structural stability.

Contribution

It reveals the emergence and role of discrete breathers in a coarse-grained protein model, linking nonlinear dynamics to protein stability and conformational control.

Findings

Discrete breathers emerge at specific sites in the protein model.

Breathers stabilize the structure by localizing energy.

Breathers facilitate energy transfer and induce local structural distortions.

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) 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, localization occurs on the turns connecting the strands. At high energies, discrete breathers 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.