Nonlinear dynamics of secondary protein folding

We propose a simple phenomenological model that describes the conformational dynamics of proteins from the primary to the secondary structure. The folding pathway is determined by the local potential energy of individual amino acids in a protein chain, by the spring tension of the protein representing the internal hydrogen bonds that hold the helices and sheets together, and by the strength of nonlinear excitations that propagate through the protein backbone. Two opposite cases are considered with the length scale of an excitation being much larger or much smaller than the characteristic scale on which the conformational energy field varies.