Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study.
We compare the structures and energies of beta-strands, alpha-helices, and 3(10)-helices for capped polyalanines, acetyl(ala)(N)()NH(2), for values of N from 2 to 18, using completely optimized mixed DFT/AM1 calculations. Non-pairwise additive cooperativity is manifest from the variation of the relative energies, helical strain, dipole moments, and H-bond lengths of both types of helices, but especially for the alpha-helices. While the gas-phase 3(10)-helices are more stable for small polyalanines, largely due to the additional H-bond, the alpha-helices become relatively more stable as the polyalanines increase in size.
Wieczorek
Robert
R
Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA.
Dannenberg
J J
JJ
D003198:Computer Simulation; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D009842:Oligopeptides; D010455:Peptides; C019529:polyalanine