Precise side-chain conformation analysis of l-phenylalanine in alpha -helical polypeptide by quantum-chemical calculation and super(13)C CP-MAS NMR measurement

• Published in: Journal of molecular structure Vol. 969; no. 1-3; pp. 40 - 47
• Main Authors: Niimura, Subaru, Suzuki, Junya, Kurosu, Hiromichi, Yamanobe, Takeshi, Shoji, Akira
• Format: Journal Article
• Language: English
• Published: 22.04.2010
• Subjects: Density functional theory; Mathematical models; Molecular structure; Nuclear magnetic resonance; Optimization; Quantum chemistry; Residues; Stability
• ISSN: 0022-2860
• DOI: 10.1016/j.molstruc.2010.01.040

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 alpha -helical octadecapeptide composed of l-alanine (Ala) and l-phenylalanine (Phe) residues, H-(Ala) sub(8)-Phe-(Ala) sub(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 alpha -helix is affected dominantly by the side-chain conformation ([chi] sub(1)) of the Phe residue in this system: model A (T form: around 180 degree of [chi] sub(1)) is most stable in alpha -helix and model B (G super(+)form: around -60 degree of [chi] sub(1)) is next stable, but model C (G super(-)form: around 60 degree of [chi] sub(1)) is less stable. In addition, we demonstrate that the stable conformation of poly(l-phenylalanine) is an alpha -helix with the side-chain T form, by comparison of the carbonyl super(13)C chemical shift measured by super(13)C CP-MAS NMR and the calculated one.