  The aim of this work was to find a minimal set of structurally stable
pentapeptides, which allows forming a polypeptide chain of a required 3D
structure. To search for factors that ensure structural stability of the
pentapeptide, we generated peptide sequences with no more than three functional
groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures
of peptides by the molecular dynamics method and found that 1,225 pentapeptides
over 80% of the simulation time were in a stable conformation. Clustering of
these conformations revealed 54 topological types of conformationally stable
pentapeptides. These conformations relate to different combined elements of the
protein secondary structure. So, we obtained a minimal set of amino acid
structures of conformationally stable pentapeptides, creating a complete set of
different topologies that ensure the formation of pre-folded conformation of
protein structures.
