Folding interpenetration in a gliadin model: the role of the characteristic octapeptide motif Original Research Article

A model of a rheologically relevant protein, ω-gliadin, is proposed and studied in this work by means of molecular dynamics techniques. The model is based on an octapeptide repeat motif that is experimentally described as characteristic of that protein and as constituting it almost entirely. The initial molecular structure consisted of 20 such repeats. It was optimized and the dynamics developed along 980 ps, at dielectric constant ε=80. Remarkable structural features were observed for the model built, such as an elongated, twisted tubular overall structure with a peculiar interpenetrating folding pattern, of a very regular character, organized strand formation, topologically segregated sites on the outer surface with an alternate hydrophilic/hydrophobic character and a hydrophilic inner cavity. Dynamics produced significantly more relaxed structures, but was not able to change the main geometric features presented by the original structure. Preliminary attempts of correlating some structural/dynamic aspects observed for the model with features of gliadin rheological behavior are presented.