In an attempt to determine intrinsically stable hairpin geometries, a number of triamide conformations of For-Ala-Ala-NH2 were investigated using ab initio calculations (HF/3-21G). Previous ab initio calculations of selected diamides of single amino acid residues (e.g., For-Ala-NH2) suggested that the αL-type backbone conformation (ɸ ≈ −54°, ψ ≈ −45°) is not a minimal energy structure, although in globular proteins the (αL)n units (referred to as α-helices) are the most frequently found conformations. The lack of the αL conformation made the application of ab initio calculations in peptide geometry analyses questionable. In contrast, for triamides (e.g., For-Ala-Ala-NH2) the appearance of the αL backbone subconformation is confirmed in the αLδL conformation (usually referred to as type I β-turn). This intrinsically stable conformation is the most frequently found hairpin structure in proteins. The existence of the ϵL conformation (ɸ ≈ −60°, ψ ≈ 120°) in chiral diamides (such as For-Ala-NH2, For-Ser-NH2, or For-Val-NH2) has never been confirmed by ab initio studies, although X-ray analyses of proteins revealed the existence of the polyproline II conformation [(ϵL)n] a long time ago. The herein presented stable γDϵL and δDϵL hairpin conformations, calculated by ab initio methods, legitimize the “missing” ϵL backbone geometry. The fact that some legitimate backbone conformations (αL and ϵL) appear only in triamides and not in diamide systems assigns a specific role to triamide models in understanding protein conformations. The importance of some triamide conformations, especially type I and type II β-turns, is emphasized. This study summarizes all the possible [18 (30) conformations depending on the d or τ “selection rule”] hairpin geometries determined for For-Ala-Ala-NH2 using ab initio computations. We were able to identify all 30 ab initio yielded conformations as backbone substructures of globular proteins, determined by X-ray crystallography. The 30 optimized triamide structures present a unique opportunity to understand the conformational behavior of β-turns (β-bends or hairpins). This may have far-reaching consequences in understanding the β-turn-mediated protein folding.
ASJC Scopus subject areas
- Colloid and Surface Chemistry