Insight Into the Dipeptide Self-Assembly Process Using Density Functional Theory

Hydrophobic dipeptides like L-Ala-L-Val (AV), L-Val-L-Ala (VA), L-Ala-L-Ile (AI), L-Ile-L-Ala (IA), L-Val-L-Val (VV), L-Ile-L-Val (IV) and L-Val-L-Ile (VI), labeled class V-A dipeptides, self-assemble as crystals composed of elongated helical tubes with narrow hydrophobic channels, whereas other hydrophobic dipeptides like L-Phe-L-Phe (FF), L-Leu-L-Leu (LL), L-Leu-L-Phe (LF), L-Phe-L-Leu (FL), and L-Ile-L-Leu (IL), labeled class F-F dipeptides, crystallize as compact helical tubes with wide hydrophilic channels. To elucidate the molecular mechanism driving crystallization of these dipeptides, we use density functional theory for investigating the energetics and structural changes associated with the assembling process of isolated dipeptides into crystals and isolated helical tubes. It is shown that the position in which the side chain branches is the determining factor driving these dipeptides to form either hydrophobic or hydrophilic channels. Furthermore, the latter also favor the formation of class F-F isolated tubes while it disfavors the formation of the class V-A ones, indicating that the two sets of dipeptides follow different self-assembly paths.