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 ch...

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Bibliographic Details
Published in:Biochemistry (Easton) 2012-07, Vol.51 (27), p.5387-5393
Main Authors: Roy, Dipankar, Pohl, Gabor, Ali-Torres, Jorge, Marianski, Mateusz, Dannenberg, J. J
Format: Article
Language:English
Subjects:
Hydrogen Bonding
Models, Molecular
Oligopeptides - chemistry
Protein Structure, Secondary
Quantum Theory
Thermodynamics
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Summary: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)6NH2 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 C7 cyclic H-bonds in place of the C10 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.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi3006785