Application of Density Functional Theory Calculations to Favoenzymes

• Project/Area Number: 15607015
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: 計算科学
• Research Institution: Kumamoto University
• Principal Investigator: TAMAOKI Haruhiko Kumamoto University, Graduate School of Medical Sciences, Research Associate, 大学院・医学薬学研究部, 助手 (80264290)
• Co-Investigator(Kenkyū-buntansha): TANAKA Takeyuki Kobe University, Graduate School of Science and Technology, Research Associate, 大学院・自然科学研究科, 助手 (50332763)
• Project Period (FY): 2003 – 2004
• Project Status: Completed (Fiscal Year 2004)
• Budget Amount: ¥3,000,000 (Direct Cost: ¥3,000,000); Fiscal Year 2004: ¥1,400,000 (Direct Cost: ¥1,400,000); Fiscal Year 2003: ¥1,600,000 (Direct Cost: ¥1,600,000)
• Keywords: Molecular Orbital Calculation / Charge-Transfer Interaction / Aryl-CoA Dehydrogenase / Flavoproteins / NMR Chemical Shift / Infrared Absorption Spectroscopy / Electronic Absorption / Molecular Vibration / X線結晶構造解析 / アシルCoA酸化酵素 / D-アミノ酸酸化酵素

Research Abstract

Density functional theory was applied to acyl-CoA dehydrogenase(ACD) and the calculated results were discussed with reference to the experimental ones. Especially, we focused on the CT interaction observed in the complex between ACD and substrate analog. 3-Thiaacyl-CoA is known to be a transition-state analog, which is transferred to an anionic form through an α-proton abstraction process by a catalytic base glutamate and interacts with oxidized flavin in the active site. The common α-proton abstraction process is caused in the dehydrogenation of substrate, thus the CT interaction with 3-thiaacyl-CoA is expected to reflect the initial stage of dehydrogenation reaction.
The calculation model was simplified as the complex of lumiflavin and ethylthioester of 3-thiabutanoic acid, and the model was energetically optimized using the density functional of B3LYP/6-311G(d). The geometry and orientation of the two molecules was optimized to reach a structure that was quite similar to the X-ray structure reported. This represents that the spatial arrangement of the CT complex is determinant due to electrostatic interaction between an oxidized flavin and an anionic 3-thiaacyl chain. Electronic absorption spectrum was also simulated in this molecular geometry on the same basis set. The calculations reproduced a CT band at long-wavelength region.
In this project, we also have developed the methodology on difference infrared absorption(IR) spectra to selectively observe a vibrational mode in the enzyme complex. This method utilizes the synthetic compounds(flavins or ligands) labeled with stable isotopes, e.g.13C,15N or 18O. Calculated vibrational frequencies and infrared intensities showed to reproduce the experimental ones. This method is highly expected to be applicable to the other enzyme systems to investigate the molecular interactions in the active sites.

Research Products

• [Journal Article] Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination : Applied for Bioactive Peptide Endothelin-1 to Determine C-Terminal Folding (2004)
  • Author(s): Takashimaら
  • Journal Title: J.Am.Chem.Soc. 126 Pages: 4504-4505
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination : Applied for Bioactive Peptide Endothelin-1 to Determine C-Terminal Folding (2004)
  • Author(s): Takashima, H., Mimura, N., Ohkubo, T., Yoshida, T., Tamaoki, H., Kobayashi, Y.
  • Journal Title: Journal of American Chemical Society 126 Pages: 4504-4505
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination (2004)
  • Author(s): Takashimaら
  • Journal Title: J.Am.Chem.Soc. 126 Pages: 4504-4505
• [Journal Article] Structure of the Transition State Analog of Medium-Chain Acyl-CoA Dehydrogenase Crystallographic and Molecular Orbital Studies on Dehydrogenase with 3-Thiaoctanoyl-CoA (2003)
  • Author(s): Satohら
  • Journal Title: J.Biochemistry 134 Pages: 297-304
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Molecular Mechanism of the Drop in the pKa of a Substrate Analog Bound to Medium-Chain Acyl-CoA Dehydrogenase : Implication for Substrate Activation (2003)
  • Author(s): Nishinaら
  • Journal Title: J.Biochemistry 134 Pages: 835-842
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structure of the Transition State Analog of Medium-Chain Acyl-CoA Dehydrogenase. Crystallographic and Molecular Orbital Studies on Dehydrogenase with 3-Thiaoctanoyl-CoA (2003)
  • Author(s): Satoh, A., Nakajima, Y., Miyahara, I., Hirotsu, K., Tanaka, T., Nishina, Y., Shiga, K., Tamaoki, H., Setoyama, C., Miura, R.
  • Journal Title: Journal of Biochemistry 134 Pages: 297-304
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Molecular Mechanism of the Drop in the pKa of a Substrate Analog Bound to Medium-Chain Acyl-CoA Dehydrogenase : Implication for Substrate Activation (2003)
  • Author(s): Nishina, Y., Sato, K., Tamaoki, H., Tanaka, T., Setoyama, C., Miura, R., Shiga, K.
  • Journal Title: Journal of Biochemistry 134 Pages: 835-842
  • NAID: 130003534635
  • Description: 「研究成果報告書概要(欧文)」より
• [Publications] Satoh, A.et al.: "Structure of the Transition State Analog of Medium-Chain Acyl-CoA Dehydrogenase. Crystallographic and Molecular Orbital Studies on the Charge-Transfer Complex of Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA"Journal of Biochemistry. 134. 297-304 (2003)
• [Publications] Nishina, Y.et al.: "Molecular Mechanism of the Drop in the pKa of a Substrate Analog Bound to Medium-Chain Acyl-CoA Dehydrogenase : Implications for Substrate Activation"Journal of Biochemistry. 134. 835-842 (2003)