Site specificity of the αCH bond dissociation energy for a naturally occurring β-hairpin peptide—An ab initio study
✍ Scribed by Wan-Chun Cheng; Soonmin Jang; Chen-Chang Wu; Ren-Jie Lin; Hsiu-Feng Lu; Feng-Yin Li
- Publisher
- John Wiley and Sons
- Year
- 2009
- Tongue
- English
- Weight
- 255 KB
- Volume
- 30
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
A naturally occurring β‐hairpin peptide (PDB ID 1UAO) was used as a model to study the backbone oxidation of a protein with ab initio calculation at the B3LYB/6‐31G(d) without any constraints. The ^α^CH bond dissociation energy of three different glycyl radicals located at different sites on the β‐hairpin peptide was calculated to evaluate the site specificity of backbone oxidation. The molecular and electronic structures of these glycyl radicals were analyzed to rationalize this site specificity. The overall molecular structure of the α‐H abstracted β‐hairpin peptide remained almost unchanged with the exception of the local conformation of the attacked residue. However, the ^α^CH bond strength varied dramatically among these different sites. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009