Abstract
To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a well-defined α-helical octadecapeptide composed of l-alanine (Ala) and l-phenylalanine (Phe) residues, H–(Ala) 8–Phe–(Ala) 9–OH, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy and the precise secondary structural parameters such as main-chain dihedral angles and hydrogen-bond parameters of the optimized structure, we confirmed that the conformational stability of an α-helix is affected dominantly by the side-chain conformation ( χ 1) of the Phe residue in this system: model A ( T form: around 180° of χ 1) is most stable in α-helix and model B ( G + form: around −60° of χ 1) is next stable, but model C ( G − form: around 60° of χ 1) is less stable. In addition, we demonstrate that the stable conformation of poly( l-phenylalanine) is an α-helix with the side-chain T form, by comparison of the carbonyl 13C chemical shift measured by 13C CP-MAS NMR and the calculated one.
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