Electronic and vibrational circular dichroism of aromatic amino acids by density functional theory.
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.
Tanaka
Takeyuki
T
Department of Biosystems Science, Graduate School of Science and Technology, Kobe University, Kobe, Japan.
Kodama
Takashi S
TS
Morita
Hayato E
HE
Ohno
Takashi
T
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
D024322:Amino Acids, Aromatic