Discrete Nonlinear Schrödinger Equation and Polygonal Solitons with Applications to Collapsed Proteins

We introduce a novel generalization of the discrete nonlinear Schrödinger equation. It supports solitons that we utilize to model chiral polymers in the collapsed phase and, in particular, proteins in their native state. As an example we consider the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approaches to protein folding. We use its backbone as a template to explicitly construct a two-soliton configuration. Each of the two solitons describe well over 7.000 supersecondary structures of folded proteins in the Protein Data Bank with sub-angstrom accuracy suggesting that these solitons are common in nature.