Searching for periodic structures in β-peptides

Hexamers of beta -amino acids with different substituent patterns at the C-alpha- and C-beta-backbone atoms (none, beta (2), beta (3), beta (2.2), beta (3,3), (RIS)beta (2,3), (S,S)beta (2,3)) were the subject of molecular dynamics simulations on the basis of the CHARMm23.1 force field to generate conformational free energy surfaces for concerted changes in (phi,psi) dihedrals employing a multidimensional conformational integration approach. Application of this technique provides insight into the intrinsic folding propensities of these homooligomers including cooperativity effects. The free energy surfaces give a complete overview of all possible periodic secondary structures. Most striking are the various helix types characterized by hydrogen-bonded pseudocycles of different size and direction of hydrogen bond formation, e.g. H-14, H-12, and H-10. There are also P-strand like periodic structures of considerable stability. It is shown that the formation of various helix types and sheetlike structures strongly depends on the substituent pattern. On the basis of this information, it might be possible to design definite secondary structures in P-peptides to mimic native peptide structures.