Site Specificity on OH α‑H Abstraction Reaction for a Zwitterionic β‑Hairpin Peptide in Aqueous Solution: A Theoretical Investigation

• Published in: The journal of physical chemistry. B 2013-01, Vol.117 (3), p.771-783
• Main Authors: Lin, Ren-Jie, Jang, Soonmin, Kim, Hyunsik, Wu, Chen-Chang, Li, Feng-Yin
• Format: Article
• Language: English
• Subjects: Aminoacids, peptides. Hormones. Neuropeptides; Analytical, structural and metabolic biochemistry; Aqueous solutions; Backbone; Biological and medical sciences; Free energy; Fundamental and applied biological sciences. Psychology; Hydrogen - chemistry; Hydrogen Bonding; Ions - chemistry; Mathematical models; Molecular Dynamics Simulation; Oligopeptides - chemistry; Oxidation; Peptides; Peptides - chemistry; Protein Structure, Secondary; Proteins; Simulation; Solvation; Thermodynamics; Water - chemistry
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp308879r

Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID ), with density functional theory calculation at B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation. To construct the reaction profile of these α-H abstraction reactions, the pre- and postreactive complexes along with their associated transition states were located and verified with the intrinsic reaction coordinate (IRC) method. The bond dissociation energy and reaction rates of these OH α-H abstraction reactions were calculated with transition state theory. The differences in this abstraction reaction between the neutral and zwitterionic forms of Chignolin were also compared. A molecular dynamics simulation was implemented to study the explicit solvation effect on the abstracted Chignolin structure. The range of the simulation time scale covers from femtoseconds to microseconds, i.e., from onset of the abstraction to the abstracted products reaching thermal equilibrium. Our results show that there are three kinds of site-specificity in this abstraction reaction. The reactivity and stability of the abstraction products and their abstraction modes are all dependent on the location where OH attacks. Furthermore, the free energy landscapes of these abstraction products are distinctively different. This may imply that the pathological disorders or diseases caused by this type of radicals are also dependent on the abstraction location.