title: Electronic and vibrational circular dichroism of aromatic amino acids by density functional theory.
abstract: Structures of model compounds mimicking aromatic amino acid residues in proteins are optimized by density functional theory (DFT), assuming that the main-chain conformation was a random coil. Excitation energies and dipole and rotational strengths for the optimized structures were calculated based on time-dependent DFT (TD-DFT). The electronic circular dichroism (ECD) bands of the models were significantly affected by side-chain conformations. Hydration models of the aromatic residues were also subjected to TD-DFT calculations, and the ECD bands of these models were found to be highly perturbed by the hydration of the main-chain amide groups. In addition to calculating the random-coil conformation, we also performed TD-DFT calculations of the aromatic residue models, assuming that the main-chain conformation was an alpha-helix or beta-strand. As expected, the overall feature of the ECD bands was also perturbed by the main-chain conformations. Moreover, vibrational circular dichroism (VCD) spectra of the hydration models in a random-coil structure were simulated by DFT, which showed that the VCD spectra are more sensitive to the side-chain conformations than the ECD spectra. The present results show that analyses combining ECD and VCD spectroscopy and using DFT calculations can elucidate the main- and side-chain conformations of aromatic residues in proteins.
authors.affiliation: Department of Biosystems Science, Graduate School of Science and Technology, Kobe University, Kobe, Japan.
authors.forename: Takeyuki
authors.initials: T
authors.lastname: Tanaka
authors.forename: Takashi S
authors.initials: TS
authors.lastname: Kodama
authors.forename: Hayato E
authors.initials: HE
authors.lastname: Morita
authors.forename: Takashi
authors.initials: T
authors.lastname: Ohno
mesh_terms: D024322:Amino Acids, Aromatic / Q000032:analysis* / Q000737:chemistry; D002942:Circular Dichroism / Q000379:methods*; D004581:Electronics; D008956:Models, Chemical; D015394:Molecular Structure; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012680:Sensitivity and Specificity; D013237:Stereoisomerism
chemical_list: D024322:Amino Acids, Aromatic