Density functional theory study of β-hairpins in antiparallel β-sheets, a new classification based upon H-bond topology.
We present a new classification of β-turns specific to antiparallel β-sheets based upon the topology of H-bond formation. This classification results from ONIOM calculations using B3LYP/D95** density functional theory and AM1 semiempirical calculations as the high and low levels, respectively. We chose acetyl(Ala)(6)NH(2) as a model system as it is the simplest all-alanine system that can form all the H-bonds required for a β-turn in a sheet. Of the 10 different conformations we have found, the most stable structures have C(7) cyclic H-bonds in place of the C(10) interactions specified in the classic definition. Also, the chiralities specified for residues i + 1 and i + 2 in the classic definition disappear when the structures are optimized using our techniques, as the energetic differences among the four diastereomers of each structure are not substantial for 8 of the 10 conformations.
Department of Chemistry, Hunter College and Graduate School, City University of New York, New York 10065, United States.
Dipankar
D
Roy
Gabor
G
Pohl
Jorge
J
Ali-Torres
Mateusz
M
Marianski
J J
JJ
Dannenberg
D006860:Hydrogen Bonding; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011789:Quantum Theory; D013816:Thermodynamics
D009842:Oligopeptides