Investigation on the individual contributions of NH···OC and CH···OC interactions to the binding energies of β-sheet models

✍ Scribed by Chang-Sheng Wang; Chang-Liang Sun

• Publisher: John Wiley and Sons
• Year: 2009
• Tongue: English
• Weight: 344 KB
• Volume: 31
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21390

✦ Synopsis

Abstract

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of NH···HN and CO···OC dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual NH···OC dipole–dipole attractive interaction is predicted to be −6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and −5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α^H···OC attractive interaction is −1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and −1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010