Theoretical study on charge-transfer interaction between acyl-CoA dehydrogenase and 3-thiaacyl-CoA using density functional method

Journal of Biochemistry

Volumn 139, Issue 5, 2006, Pages 847-855

  Tanaka, Takeyuki ^a,c   Tamaoki, Haruhiko ^b   Nishina, Yasuzo ^b   Shiga, Kiyoshi ^b   Ohno, Takashi ^a   Miura, Retsu ^b  

^a KOBE UNIVERSITY   (Japan)

^b KUMAMOTO UNIVERSITY   (Japan)

^c EHIME UNIVERSITY   (Japan)

Author keywords

Acyl CoA dehydrogenase; Charge transfer; Density functional theory; Flavin; Hydrogen bond

Indexed keywords

3 THIAACYL COENZYME A ENZYME; 3 THIABUTANOATE ETHYLTHIOESTER; ACYL COENZYME A; ACYL COENZYME A DEHYDROGENASE ENZYME; CARBONYL DERIVATIVE; ESTER DERIVATIVE; HYDROXYL GROUP; LUMIFLAVINE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ELECTRICITY; ENZYME ACTIVITY; EXCITATION; HYDROGEN BOND; OSCILLATION; OXIDATION; PROTON TRANSPORT; SPECTRAL SENSITIVITY; STEREOSCOPIC VISION; THEORETICAL STUDY; X RAY ANALYSIS;

ACYL-COA DEHYDROGENASE; ELECTRON-TRANSFERRING FLAVOPROTEINS; FLAVIN-ADENINE DINUCLEOTIDE; FLAVINS; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 33745745675     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvj103     Document Type: Article

References (22)

1. Grane, F.L., Mii, S., Hauge, J.G., Green, D.E., and Beinert, H. (1956) On the mechanism of dehydrogenase of fatty acyl derivatives of coenzyme A. I. The general fatty acylcoenzyme A dehydrogenase. J. Biol. Chem. 218, 701-716
2. Ghisla, S. and Thorpe, C. (2004) Acyl-CoA dehydrogenases. A mechanistic overview. Eur. J. Biochem. 271, 494-508
3. Engel, P.C. (1992) Acyl-CoA dehydrogenases in Chemistry and Biochemistry of Flavoenzymes (Müller, F., eds.) Vol. III, pp. 597-655, CRC Press, Boca Raton, Ann Arbor, London
4. Kim, J.-J.P., Wang, M., and Paschke, R. (1993) Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc. Natl. Acad. Sci. USA 90, 7523-7527
5. Engst, S., Vock, P., Wang, M., Kim, J.-J.P., and Ghisla, S. (1999) Mechanism of activation of acyl-CoA substrates by medium chain acyl-CoA dehydrogenase. Interaction of the thioester carbonyl with the flavin adenine dinucleotide ribityl side chain. Biochemistry 38, 257-267
6. Thorpe, C. and Massey, V. (1983) Flavin analogue studies of pig kidney general acyl-CoA dehydrogenase. Biochemistry 22, 2972-2978
7. Lau, S.-M., Brantley, R.K., and Thorpe, C. (1988) The reductive half-reaction in acyl-CoA dehydrogenase from pig kidney. Studies with thiaoctanoyl-CoA and oxaoctanoyl-CoA analogs. Biochemistry 27, 5089-5095
8. Tamaoki, H., Nishina, Y., Shiga, K., and Miura, R. (1999) Mechanism for the recognition and activation of substrate in medium-chain acyl-CoA dehydrogenase. J. Biochem. 125, 285-296
9. Satoh, A., Nakajima, Y., Miyahara, I., Hirotsu, K., Tanaka, T., Nishina, Y., Shiga, K., Tamaoki, H., Setoyama, C., and Miura, R. (2003) 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. J. Biochem. 134, 297-304
10. Nishina, Y., Sato, K., Tamaoki, H., Tanaka, T., Setoyama, C., Miura, R., and Shiga, K. (2003) Molecular mechanism of the drop in the pKa of a substrate analog bound to medium-chain acyl-CoA dehydrogenase. Implications for substrate activation. J. Biochem. 134, 835-842
11. Edmondson, D.E. (1999) Electronic effects of 7 and 8 ring substituents as predictors of flavin oxidation-reduction potentials in Flavins and Flavoproteins 1999 (Ghisla, S. Kroneck, P., Macheroux, P., and Sund, H., eds.) pp. 71-76, Rudolf Weber, Berlin
12. Bach, R.D., Thorpe, C., and Dmitrenko, O. (2002) C-H⋯carboxylate oxygen hydrogen bonding in substrate activation by acyl-CoA dehydrogenases. Synergy between the H-bonds. J. Phys. Chem. B. 106, 4325-4335
13. Dmitrenko, O., Thorpe, C., and Bach, R.D. (2003) Effect of a charge-transfer interaction on the catalytic activity of acyl-CoA dehydrogenase. A theoretical study of the role of oxidized flavin. J. Phys. Chem. B. 107, 13229-13236
14. Bauernschmitt, R. and Ahlrichs, R. (1996) Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chem. Phys. Lett. 256, 454-464
15. Wiberg, K.B., Stratmann, R.E., and Frisch, M.J. (1998) A time-dependent density functional theory study of the electronically excited states of formaldehyde, acetaldehyde and acetone. Chem. Phys. Lett. 297, 60-64
16. Paddon-Row, M.N. and Shephard, M.J. (2002) A time-dependent density functional study of the singlet-triplet energy gap in charge-separated states of rigid bichromophoric molecules. J. Phys. Chem. A. 106, 2935-2944
17. Neiss, C., Saalfrank, P., Parac, M., and Grimme, S. (2003) Quantum chemical calculation of excited states of flavin-related molecules. J. Phys. Chem. A. 107, 140-147
18. Sikorska, E., Khmelinskii, I.V., Prukala, W., Williams, S.L., Patel, M., Worrall, D.R., Bourdelande, J.L., Koput, J., and Sikorski, M. (2004) Spectroscopy and photophysics of lumiflavins and lumichromes. J. Phys. Chem. A. 108, 1501-1508
19. Hirst, J.D., Colella, K., and Gilbert, A.T.B. (2003) Electronic circular dichroism of proteins from first-principles calculations. J. Phys. Chem. B. 107, 11813-11819
20. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robbins, D.J., Cheeseman, J.R., Montgomery, J.A., Jr., Vreven, I., Kudin, K., Burant, J.C., Millam, J.M., Iyenger, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.E., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann R.E., Yazyev, O., Salvador, A., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., Pople, J.A. (2003) Gaussian 03, Revision B.04, Gaussian, Inc., Pittsburgh, PA
21. Becke, A.D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652
22. Lee, C., Yang, W., Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B. 37, 785-789