Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence

Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of - and -amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by -amino acids are experimentally more stable than those formed by -amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo--alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo--alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12)-helical structures, possibly due to the sparse distribution of the 3(12)-helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the -alanine dodecamer had more stable and persistent <3.0 angstrom hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo--alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides. Proteins 2014; 82:3043-3061. (c) 2014 Wiley Periodicals, Inc.